Merge branch 'add-craft' into 'master'

Add craft

See merge request !7

Dockerfile

@@ -84,6 +84,7 @@ RUN chown -R www-data:www-data /var/www
 # ajustement pour version web : pas de print sur sdtout mais envoie d'une réponse CGI de type content-type/html
 COPY ./pampa /var/www/cgi-bin/pampa/pampa
 COPY ./main_taxonomy_filtering.py /var/www/cgi-bin/pampa/pampa/
+COPY ./table_maker.py /var/www/cgi-bin/pampa/pampa
 
 # Ajustage des droits
 RUN chmod +x /var/www/cgi-bin/pampa/*

docker-compose.yml

+version: '3.8'
+
+services:
+  pampa:
+    build:
+      context: .
+      args:
+        - DEBIAN_FRONTEND=noninteractive
+        - SERVER_NAME=localhost
+    ports:
+      - "80:80"
+    volumes:
+      - postgres_data:/var/lib/postgresql/12/main
+    environment:
+      - SERVER_NAME=localhost
+    restart: unless-stopped
+
+volumes:
+  postgres_data:
\ No newline at end of file

main_taxonomy_filtering.py

@@ -43,11 +43,11 @@ def main():
     # parsing models for peptide tables, sequences or limits
     set_of_taxid=set()
     if args.peptide_table :
-        set_of_markers = pt.parse_peptide_tables(args.peptide_table, args.limit, primary_taxonomy)
-        set_of_taxid.update({m.taxid for m in set_of_markers})
+        set_of_markers, _ = pt.parse_peptide_tables(args.peptide_table, args.limit, primary_taxonomy)
+        set_of_taxid.update({m.taxid() for m in set_of_markers})
     if args.fasta or args.directory:
         set_of_sequences = fa.build_set_of_sequences(args.fasta, args.directory, None, primary_taxonomy)
-        set_of_taxid.update({s.taxid for s in set_of_sequences})
+        set_of_taxid.update({s.taxid() for s in set_of_sequences})
     if args.limit:
         list_of_constraints=limit.parse_limits(args.limit)
         set_of_taxid.update({t for dict in list_of_constraints for t in dict["OX"]}) 

table_maker.py

+import argparse
+import json
+import csv
+
+
+from src import markers
+from src import peptide_table as pt
+from src import config
+from src import utils
+from functools import cmp_to_key, partial
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("-g", dest="or_data")
+    parser.add_argument("-r", dest="out_data")
+    parser.add_argument("-o", dest="output")
+    parser.add_argument("-m", dest="method")
+    args = parser.parse_args()
+
+    table_maker(args.out_data, args.or_data, args.output, args.method)
+
+def compare_file(or_markers, out_markers):
+    group = {}
+
+    for or_marker in or_markers:
+        group[or_marker] = []
+        or_data = or_marker.field
+        keys = or_data.keys()
+        for out_marker in out_markers:
+            out_data = out_marker.field
+
+            results = {}
+            for key in keys:
+
+                if or_data[key] == out_data[key]:
+                    results[key] = True
+                elif key == "Mass":
+                    if round(float(or_data[key]),1) == round(float(out_data[key]),1):
+                        results[key] = True
+                    else:
+                        results[key] = False
+                else:
+                    results[key] = False
+            if all(results.values()):
+                group[or_marker].append(out_marker)
+
+    return group
+
+
+def generate_json_result(original_path, output_path, outfile_name):
+    JSON_file = open(outfile_name, "w")
+    or_markers, _ = pt.parse_peptide_tables(original_path, None, None, False)
+    out_markers, list_of_headers = pt.parse_peptide_tables(output_path, None, None, False)
+
+    #pt.build_peptide_table_from_set_of_markers(out_markers, "test.tsv")
+
+    group = compare_file(or_markers, out_markers)
+
+    if not list_of_headers:
+        headers={pt.restitute_field(key) for m in out_markers for key in m.field}
+        list_of_headers=(config.sort_headers(headers))
+    else:
+        list_of_headers=list(map(pt.restitute_field, list_of_headers))
+
+    list_of_headers.append('__modifiedCells')
+
+    reverse_map = {}
+    for orig_marker, out_list in group.items():
+        for out_m in out_list:
+            reverse_map[out_m] = orig_marker
+
+    dicts = []
+    for out_m in out_markers:
+        orig_m = reverse_map.get(out_m, None)
+        status = {}
+        for field, value in out_m.field.items():
+            if orig_m is None:
+                status[field] = 'new'
+            else:
+                if field in orig_m.field:
+                    orig_val = orig_m.field[field]
+                    if field == "Mass":
+                        if orig_val != value:
+                            status[field] = 'modified'
+                        else:
+                            status[field] = 'original'
+                    else:
+                        status[field] = 'modified' if value != orig_val else 'original'
+                else:
+                    status[field] = 'added'
+        out_m.field['__modifiedCells'] = dict(zip(list_of_headers, status.values()))
+        dicts.append(out_m)
+
+    set_of_codes=[m.code() for m in dicts]
+    list_of_codes=config.sort_headers(set_of_codes)
+    dicts.sort(key=cmp_to_key(partial(pt.marker_order, list_of_codes=list_of_codes)))
+
+    result = []
+    for m in dicts:
+        result.append(dict(zip(list_of_headers, m.field.values())))
+    json.dump(result, JSON_file)
+    JSON_file.close()
+
+    return result, list_of_headers
+
+
+
+def read_tsv(file_path):
+    data = []
+    with open(file_path, "r", newline="") as file:
+        reader = csv.DictReader(file, delimiter="\t")
+        headers = reader.fieldnames
+        for row in reader:
+            data.append(row)
+    return data, headers
+
+
+def table_maker(peptide_out, peptide_or, output_file, method):
+    if method == "fillin":
+        dicts, header = generate_json_result([peptide_or], [peptide_out], "test.json")
+        header.pop()
+    else :
+        dicts, header = read_tsv(peptide_out)
+    html = '''
+        <div id="results" style="height: 500px; margin-bottom: 20px;" class="ag-theme-alpine"></div>
+        <div style="margin-top: 10px;">
+            <button onclick="exportData()">Download Results (.TSV)</button>
+            <button onclick="deleteSelectedRows()" style="margin-left: 10px;">Delete Selected Rows</button>
+        </div>
+
+        <script src="https://cdn.jsdelivr.net/npm/ag-grid-community/dist/ag-grid-community.min.js"></script>
+        <script type="text/javascript">
+            function initGrid() {
+                let gridApi;
+                const outData = ''' + json.dumps(dicts) + ''';
+                const columnDefs = ''' + json.dumps([{"field": h, "headerName": h, "editable": True} for h in header]) + ''';
+
+                const gridOptions = {
+                    theme: agGrid.themeBalham,
+                    rowData: outData,
+                    columnDefs: columnDefs.map(col => ({
+                        ...col,
+                        cellStyle: params => {
+                            const status = params.data.__modifiedCells?.[col.field];
+                            if (status === 'modified') return { backgroundColor: '#ffff00'};
+                            if (status === 'added') return { backgroundColor: '#00ff00'};
+                            if (status === 'new') return { backgroundColor: '#0000ff'};
+                            return null;
+                        }
+                    })),
+                    pagination: true,
+                    paginationPageSize: 20,
+                    defaultColDef: {
+                        sortable: true,
+                        filter: true,
+                        resizable: true,
+                        editable: true
+                    },
+                    autoSizeStrategy: {
+                        type: "fitCellContents",
+                    },
+                    rowSelection: 'multiple',
+                    onCellValueChanged: function(event) {
+                        console.log('Cell modified:', event);
+                    },
+                };
+
+                function autoSizeAll(skipHeader) {
+                    const allColumnIds = [];
+                    gridApi.getColumns().forEach((column) => {
+                        allColumnIds.push(column.getId());
+                    });
+                    gridApi.autoSizeColumns(allColumnIds, skipHeader);
+                    gridApi.sizeColumnsToFit();
+                }
+
+                gridApi = agGrid.createGrid(document.querySelector("#results"), gridOptions);
+                window.gridApi = gridApi;
+
+                autoSizeAll(true);
+
+                window.exportData = function() {
+                    gridApi.exportDataAsCsv({
+                        fileName: "result.tsv",
+                        columnSeparator: '\\t',
+                        suppressQuotes: true,
+                        skipBOM: true
+                    });
+                };
+
+                window.deleteSelectedRows = function() {
+                    const selectedNodes = gridApi.getSelectedNodes();
+                    const selectedData = selectedNodes.map(node => node.data);
+                    gridApi.applyTransaction({ remove: selectedData });
+                };
+            }
+
+            if(document.readyState === 'loading') {
+                document.addEventListener('DOMContentLoaded', initGrid);
+            } else {
+                initGrid();
+            }
+        </script>
+        <div id="status" style="margin-top: 10px; color: #666;"></div>
+    '''
+
+    with open(output_file, 'w') as f:
+        f.write(html)
+
+
+if __name__ == '__main__':
+    main()
\ No newline at end of file

www/cgi-bin/pampa/common.py

@@ -24,6 +24,16 @@ TAXONOMY_REDUCED_FILE = DATA_PAMPA_DIR + "taxonomy_reduced.tsv"
 
 SPECTRA_EXAMPLE_1 = DATA_PAMPA_DIR + "example_1.zip"
 
+# ---- CRAFT ----
+HOMOLOGY_PEPTIDE = DATA_PAMPA_DIR + "homology_peptides.tsv"
+HOMOLOGY_SEQUENCES = DATA_PAMPA_DIR + "homology_sequences.fasta"
+
+FILLIN_PEPTIDE = DATA_PAMPA_DIR + "fillin_peptides.tsv"
+FILLIN_SEQUENCES = DATA_PAMPA_DIR + "fillin_sequences.fasta"
+
+ALLPEPTIDES_SEQUENCES = DATA_PAMPA_DIR + "allpeptides_sequences.fasta"
+
+
 
 #Renvoie le pwd pour le dossier tmp/
 def tmp_dir(run_id):    

www/cgi-bin/pampa/craft_render_result.py

+import cgitb; cgitb.enable()
+import json
+import os, sys
+from html_utils import *
+import common
+import zipfile
+import operator
+#import table_maker
+from tools import *
+
+"""
+NOTES
+
+- en ajoutant de nouvelles tables de peptides par défaut autres que mammals dans nos données, il faut adapter dans la partie de génération de l'arbre taxonomique section 'reduction by taxonomic groups' la vérification que toutes les tables (groupes taxonomiques) ont été inclues.
+
+"""
+
+def results_output(run_id, job_name=None):
+    """
+    Produit la liste des fichiers téléchargeables par l'utilisateur.
+    """
+ 
+    output_files_title = {
+        "out_"+run_id+".tsv": "Assignments: ",
+        "detail_out_"+run_id+".tsv": "More details: ",
+        "report_out_"+run_id+".txt": "Report on the run: ",
+        "table_out_"+run_id+".tsv": "Peptides table built: ",
+        "data_result_"+run_id+".zip": "Downloads all results and data: "
+    }
+    head_out = "All results are available in the following files."
+    html = head_out
+    
+    html += "<ul>"
+    listdir = os.listdir(path=common.RESULT_DIR+run_id)
+    for fn in output_files_title:
+        if fn in listdir:
+            if job_name is not None:
+                parts = os.path.splitext(fn)
+                dwl_name = parts[0] + "_" + job_name + parts[1]
+            else: 
+                dwl_name = fn
+            html += li(output_files_title[fn] + href_dl(fn, dwl_name))
+    html += "</ul>"
+
+    return  html
+
+def write_main_page(run_id, taxo_used, or_data, method, job_name=None):
+    """Write a- HTML page. The result page shown first when the PAMPA analysis is done."""
+    html = ""
+
+    # Insert HTML header and page head
+    html += open(f"{common.HTML_PATH}/header.php", "r").read()
+    html += '''
+    <div class="frametitle"><h1 id="title">Pampa-Craft</h1></div>
+    <div id="center_sup">
+        <div class="theme-border" style="display:none"></div>
+        <div id="link_home" style="display:inline-block">
+            <a href="/" class="text_onglet">
+                <img src="/Style/icon/home_w.png" alt="home_general"/>
+            </a>
+        </div>
+        <div class="tabs" id="menu_central" style="display:inline-block">'''
+    html += open(f"{common.HTML_PATH}/menu_central.txt", "r").read()
+    html += '''</div></div><div id="main"><div id="center">'''
+
+    table_dir = common.RESULT_DIR + run_id + "/table.php"
+
+    command = f"/usr/bin/python {common.PAMPA_DIR}table_maker.py -g {or_data} -r {taxo_used} -o {table_dir} -m {method}"
+    os.chdir(format(os.getcwd()) + "/pampa/")
+    os.system(command)
+
+    if os.path.exists(table_dir):
+        html += f'<h2>Results for job {run_id}{f" ({job_name})" if job_name else ""}</h2>'
+
+        # Show warnings if they exist
+        warning_file = common.RESULT_DIR + run_id + "/warning.log"
+        if os.path.exists(warning_file):
+            with open(warning_file) as fileOut:
+                content = fileOut.read().strip()
+                if content:
+                    html += '''
+                    <div id="warnings_hidden" style="display: block;">
+                        <p>Warning(s) were raised during the execution. <a id="show_warnings">View report</a></p>
+                    </div>
+                    <div id="warnings_shown" style="display: none;">
+                        <p>Warning(s) were raised during the execution. <a id="hide_warnings">Hide</a></p>
+                        <table class="vide">'''
+                    for line in content.split('\n'):
+                        if line:
+                            html += f'<tr><td>{line}</td></tr>'
+                    html += '''</table></div><br>'''
+
+        html+= '''        
+        <h3>Peptide Table</h3>
+        <p>editable preview of the results file. <b>Use the bouton bellow to download edited result.</b></p>'''
+
+        html += '<iframe id="results" src="table.php" style="border: none; width: 100%; height: 575px;"></iframe>'
+        # Download section
+        html += '''
+        <h3>Download</h3>''' + results_output(run_id, job_name=job_name) + '<br>'
+
+        # Retrieve results
+        html += f'''
+        <h3>Retrieve results with an ID</h3>
+        <p>Your result remains available for at least one month.</p>
+        <p>To access it, you can either save the URL or <a id="copy" data-copy="{run_id}">copy the ID</a> {run_id}.</p>
+        <br>'''
+
+    else:
+        html += f'''<div id="error">
+        <h2>something went wrong in job ({run_id}).</h2>
+        <p>The problem might be related to one of the input files.</p>
+        <p>For more details, Please contact <a href="mailto:areski.flissi@univ-lille.fr?Subject=[Pampa ERROR - JOB: {run_id}]">PAMPA</a>.</p>
+        </div>'''
+
+    # Insert page footer
+    html += '</div></div>'
+    html += open(f"{common.HTML_PATH}/footer.php", "r").read()
+    html += '</body></html>'
+
+    # Save the HTML file
+    open(common.RESULT_DIR + run_id + "/results.php", "w").write(html)
+
+
+
+def write_no_results_page(run_id, job_name=None):
+    """Write a HTML page. The result page shown first when the PAMPA analysis is done."""
+    html = ""
+
+    # Insert HTML header and page head
+    html += (open(f"{common.HTML_PATH}/header.php", "r").read())
+    html += '<div class="frametitle"><h1 id="title">Pampa</h1></div><div id="center_sup"><div class="theme-border" style="display:none"></div><div id="link_home" style="display:inline-block"><a href="/" class="text_onglet"><img src="/Style/icon/home_w.png" alt="home_general"/></a></div><div class="tabs" id="menu_central" style="display:inline-block">'
+    html += open(f"{common.HTML_PATH}/menu_central.txt", 'r').read()
+    html += '</div></div><div id="main"><div id="center">'
+
+    html += (f'<h2>Results for job {run_id}{f" ({job_name})" if job_name else ""}</h2>')
+
+    html += '<h4><font color="red">No results</font></h4>'
+    open(common.RESULT_DIR + run_id + "/results.php", "w").write(html)
+
+
+# Main program
+def main():
+    # Ce script est lancé avec un paramètre : le nom d'un fichier json
+    # ce fichier contient diverses informations qui vont guider la construction de la page de résultats.
+    json_params_file = sys.argv[1]
+    params = json.load(open(json_params_file, "r"))
+    run_id = params["run_id"]
+
+    if "job_name" in params:
+        job_name = params['job_name']
+    else:
+        job_name = None
+    if "peptides_path" in params:
+        table_files = params["peptides_path"]
+    else:
+        table_files = None
+    if "sequences_files" in params:
+        fasta_file = params["sequences_files"]
+    method = params["method"]
+
+    zip_results(["out_"+run_id+".tsv", "report_out_"+run_id+".txt", ], run_id, job_name=job_name)
+
+    write_main_page(run_id, common.RESULT_DIR+ run_id + "/out_"+run_id+".tsv", table_files, method, job_name=job_name)
+
+
+main()
+

www/cgi-bin/pampa/pampa-craft.py

+#!/usr/bin/python
+# -*- coding: utf-8 -*-
+import cgitb;cgitb.enable()
+import os
+import cgi
+import json
+import re
+import sys
+import common
+import shutil
+import zipfile
+from tools import *
+
+# Fonction permettant de vérifier les données soumises dans le formulaire, retour dans un dictionnaire (req)
+# Fonction qui sera modifiée pour le traitement de vos données
+def extract_request(form):
+    """ check the validity of the different fields of form
+
+    Cette section vérifie la validité des argument soumis et les conditionne afin de lancer PAMPA comme souhaité.
+    """
+    error_found = False
+    error_messages = []
+    req = {}
+
+    # fichier de log où les points importants du traitement de la requête seront incris
+    log = open('log.txt', 'w')
+    log.write(f'Starting log file\n')  # log
+
+    resdir = common.RESULT_DIR + form['run_id'].value
+    log.write(f"Result directory : {resdir}\n")
+
+    req['files_uploaded'] = []
+
+    extract_job(form, log, req, error_messages)
+
+    if 'method' in form:
+        req["method"] = form['method'].value
+        method = form['method'].value
+    else:
+        method = None
+        error_messages.append(f"Method is required")
+
+    if 'craft-example' in form:
+        if method == "homology":
+            extract_files_from_list([common.HOMOLOGY_PEPTIDE], resdir)
+            req["peptides_path"] = resdir + '/' + "homology_peptides.tsv"
+        elif method == "fillin":
+            extract_files_from_list([common.FILLIN_PEPTIDE], resdir)
+            req["peptides_path"] = resdir + '/' + "fillin_peptides.tsv"
+    elif 'peptides_file' in form and form['peptides_file'].filename != "":
+        f = form['peptides_file'].filename
+        fn = os.path.basename(f)
+        uploaded, not_uploaded = extract_files_from_fileitems([form['peptides_file']], resdir, extensions_list=[".tsv", ".csv"],
+                                                              unzip=False)
+        req["peptides_path"] = resdir + '/' + fn
+        req['files_uploaded'].extend(uploaded)
+        for fn in uploaded:
+            log.write(f"file {fn}\n")
+        for fn in not_uploaded:
+            error_messages.append(f"{fn} : The peptide table file must be in TSV format.")
+
+    rel_sequences_dir = "sequences"
+    rel_spectra_dir = "spectra"
+    abs_sequences_dir = os.path.join(resdir, rel_sequences_dir)
+    abs_spectra_dir = os.path.join(resdir, rel_spectra_dir)
+
+    if 'craft-example' in form:
+        req['sequences_dir'] = abs_sequences_dir
+        if method == "homology":
+            extract_files_from_list([common.HOMOLOGY_SEQUENCES], abs_sequences_dir)
+        elif method == "fillin":
+            extract_files_from_list([common.FILLIN_SEQUENCES], abs_sequences_dir)
+        elif method == "allpeptides":
+            extract_files_from_list([common.ALLPEPTIDES_SEQUENCES], abs_sequences_dir)
+    elif 'sequences_files' in form:
+        req['sequences_dir'] = abs_sequences_dir
+        fileitems = form['sequences_files']
+        if not isinstance(fileitems, list):
+            fileitems = [fileitems]
+        if fileitems[0].filename == "":
+            if method != "fillin" and method != "deamidation" and method != "selection":
+                error_messages.append("At least one FASTA file is required.")
+        else:
+            uploaded, not_uploaded = extract_files_from_fileitems(fileitems, abs_sequences_dir,
+                                                                  extensions_list=[".txt", ".fasta"], unzip=True)
+            req['files_uploaded'].extend(uploaded)
+            for fn in uploaded:
+                log.write(f"file {fn}\n")
+                req['sequences_file'] = fn
+            for fn in not_uploaded:
+                if fn in uploaded:
+                    error_messages.append(
+                        f'The File {fn} appears to be present several times in the data supplied.')
+                else:
+                    error_messages.append(f"{fn} : Sequences must be in FASTA or in a ZIP archive.")
+    else:
+        if method != "fillin" and method != "deamidation" and method != "selection":
+            error_messages.append("At least one sequence is required.")
+
+    if 'limit_file' in form and form['limit_file'].filename != "":
+        f = form['limit_file'].filename
+        fn = os.path.basename(f)
+        uploaded, not_uploaded = extract_files_from_fileitems([form['limit_file']], resdir, extensions_list=[".txt"],
+                                                              unzip=False)
+        req["limit_path"] = resdir + '/' + fn
+        req['files_uploaded'].extend(uploaded)
+        for fn in uploaded:
+            log.write(f"file {fn}\n")
+        for fn in not_uploaded:
+            error_messages.append(f"{fn} : The taxonomy file must be in TSV format.")
+
+    if method == "fillin":
+        if 'error' in form:
+            error_value = form['error'].value.strip()
+            if error_value:
+                req['error_margin'] = error_value
+            else:
+                req['error_margin'] = "0.1"
+    if method == "allpeptides" or method == "selection":
+        extract_error_margin(form, log, req, error_messages)
+
+    if method == "selection" or method == "allpeptides":
+        if 'spectra_files' in form:
+            # spectres utilisateurs
+            fileitems = form['spectra_files']
+            if not isinstance(fileitems, list):
+                fileitems = [fileitems]
+            if fileitems[0].filename == "":
+                if method != "allpeptides":
+                    error_messages.append("At least one spectrum is required.")
+            else:
+                req['spectra_dir'] = abs_spectra_dir
+                uploaded, not_uploaded = extract_files_from_fileitems(fileitems, abs_spectra_dir, extensions_list=[".csv", ".mgd", ".mzml"], unzip=True)
+                req['files_uploaded'].extend(uploaded)
+                for fn in uploaded:
+                    log.write(f"file {fn}\n")
+                for fn in not_uploaded:
+                    if fn in uploaded :
+                        error_messages.append(f'The mass spectrum {fn} appears to be present several times in the data supplied.')
+                    else:
+                        error_messages.append(f"{fn} : Spectra must be in CSV, MGD or mzML format or in a ZIP archive.")
+        else:
+            if method != "allpeptides":
+                error_messages.append("At least one spectrum is required.")
+
+    if method == "fillin" or method == "homology":
+        extract_taxonomy_selection(form, log, req, error_messages, resdir)
+
+
+    log.write("Recap downloads :\n")
+    for fn in req['files_uploaded']:
+        log.write(f"dwl {fn}\n")
+
+    req["error_messages"] = error_messages
+    log.write("Error messages :\n")
+    for e in error_messages:
+        log.write(f"error: {e}\n")
+    log.close()
+    return req
+
+
+# Lance le programme en fonction des données contenant dans req
+# Fonction à modifier pour l'adapter à votre programme
+def launch_software(run_id, req):
+    # Build the command line for PAMPA
+    output_arg = "out_" + run_id + ".tsv"
+    method = req['method']
+
+    command = "python pampa_craft.py --" + method + " -o " + common.RESULT_DIR + run_id + "/" + output_arg
+    if 'peptides_path' in req:
+        peptides_arg = req['peptides_path']
+        command += " -p " + peptides_arg
+    if 'sequences_dir' in req:
+        sequences_arg = req['sequences_dir']
+        command += " -d " + sequences_arg
+    if 'spectra_dir' in req:
+        spectra_arg = req['spectra_dir']
+        command += " -s " + spectra_arg
+    if 'limit_path' in req:
+        limit_arg = req["limit_path"]
+        command += " -l " + limit_arg
+    if 'error_margin' in req:
+        error_arg = req["error_margin"]
+        command += " -e " + str(error_arg)
+    if 'taxo_file' in req:
+        taxo_file_arg = req["taxo_file"]
+        command += " -t " + taxo_file_arg
+    command += " --web"
+    open("acommand.txt", "w").write(f"{command}")  # log
+
+    # Launch the analysis
+    cwd = format(os.getcwd())
+    os.chdir(format(os.getcwd()) + "/pampa/")
+    os.system(command)
+    os.chdir(cwd)
+
+    # Écrit un fichier de résultats d'erreurs si PAMPA a planté, sinon affiche les résultats
+    if open(common.RESULT_DIR + run_id + "/error.log", "r").read() != "":
+        # Manage PAMPA errors (error.log)
+        json_file = common.RESULT_DIR + run_id + "/render_error_pampa.json"
+        os.system(f"python render_error_pampa.py {run_id}")
+
+    else:
+        # Params in json for render_result.py -> le json est écrit dans le dossier result/{run_id}
+        json_file = common.RESULT_DIR + run_id + "/render_result_params.json"
+        render_result_dict = {"run_id": run_id}
+        if "job_name" in req:
+            render_result_dict["job_name"] = req['job_name']  # nom du job
+        if "peptides_path" in req:
+            render_result_dict["peptides_path"] = req['peptides_path']
+        if "sequences_dir" in req:
+            render_result_dict["sequences_files"] = req['sequences_dir']  # tables de peptides utilisées
+        if "method" in req:
+            render_result_dict["method"] = req['method']
+
+        json.dump(render_result_dict, open(json_file, "w"))
+        os.system(f"python craft_render_result.py {json_file}")
+
+
+# Vérifie si il n'y a pas d'erreur au retour des données soumises par le formulaire
+def process_request(form):
+    run_id = form['run_id'].value
+    error = 0
+    error_page = []
+
+    req = extract_request(form)
+
+    if len(req['error_messages']) > 0:
+        error_page = req['error_messages']
+        error = 1
+        json_file = common.RESULT_DIR + run_id + "/render_error_params.json"
+        render_error_dict = {"result_path": common.RESULT_DIR, "run_id": run_id, "error_list": req['error_messages']}
+        json.dump(render_error_dict, open(json_file, "w"))
+        os.system(f"python render_error.py {json_file}")
+    else:
+        launch_software(run_id, req)
+
+    return (error, error_page)
+
+
+def main():
+    fs = cgi.FieldStorage()
+
+    error, error_page = process_request(fs)
+
+    sys.stdout.write("Content-Type: application/json")
+
+    sys.stdout.write("\n")
+    sys.stdout.write("\n")
+
+    result = {}
+    if error == 0 or error == 1:
+        result['success'] = True
+        result['run_id'] = fs['run_id'].value
+        result['path_result'] = common.RESULT_DIR + fs['run_id'].value + "/results.php"
+    else:
+        result['success'] = False
+
+    sys.stdout.write(json.dumps(result, indent=1))
+    sys.stdout.write("\n")
+
+
+main()
+

www/cgi-bin/pampa/pampa.py

@@ -7,102 +7,7 @@ import json
 import re
 import sys
 import common
-import shutil
-import zipfile
-
-
-#Vérification du mail
-def verif_mail(mail):
-    """ check the validity of email address """
-
-    res = mail.strip()
-    if res.find(' ') > 0:
-        return False
-    a = res.find('@')
-    if a <= 0:
-        return False
-    if res.find('@', a+1) > 0:
-        return False
-    return True
-
-def extract_files_from_fileitems(fileitems, final_dir, extensions_list=None, unzip=False):
-    """
-    Gère les fichiers uploadés (dont ZIP) et les copie dans le dossier cible.
-
-    Args:
-        fileitems (list): Liste de fichiers type Werkzeug FileStorage
-        final_dir (str): Dossier de destination
-        extensions_list (list): Extensions autorisées (ex: ['.txt', '.csv'])
-        unzip (bool): Auto-extraction des ZIP si True
-
-    Returns:
-        tuple: (fichiers transférés, fichiers rejetés)
-    """
-    files_moved = []
-    files_not_moved = []
-
-    final_dir = final_dir.rstrip('/')
-    if not os.path.exists(final_dir):
-        os.makedirs(final_dir, exist_ok=True)
-
-    if extensions_list:
-        extensions = "|".join(extensions_list)
-
-    for f in fileitems:
-        fn = os.path.basename(f.filename)
-        re_extension = re.compile(os.path.splitext(fn)[1], re.IGNORECASE)
-
-        if unzip and re_extension.search(".zip"):
-            with zipfile.ZipFile(f.file, "r") as myzip:
-                for element in myzip.infolist():
-                    fname = os.path.basename(element.filename)
-
-                    if element.is_dir():
-                        continue
-
-                    re_extension = re.compile(os.path.splitext(fname)[1], re.IGNORECASE)
-                    if (extensions_list is None or re_extension.search(extensions)) and not os.path.exists(
-                            os.path.join(final_dir, fname)):
-                        with myzip.open(element.filename, "r") as src, open(os.path.join(final_dir, fname),
-                                                                            'wb') as dst:
-                            dst.write(src.read())
-                        files_moved.append(fname)
-                    else:
-                        files_not_moved.append(fname)
-        elif (extensions_list is None or re_extension.search(extensions)) and not os.path.exists(
-                os.path.join(final_dir, fn)):
-            with open(os.path.join(final_dir, fn), 'wb') as dst:
-                dst.write(f.file.read())
-            files_moved.append(fn)
-        else:
-            files_not_moved.append(fn)
-
-    return files_moved, files_not_moved
-
-
-def extract_files_from_list(filename_list, final_dir):
-    """
-    Déplacement de fichiers internes.
-    l'unzip est systématique
-    """
-    final_dir = final_dir.rstrip('/')
-    if not os.path.exists(final_dir):
-        os.mkdir(final_dir)
-
-    for fn in filename_list:
-        if os.path.exists(fn):
-            re_extension = re.compile(os.path.splitext(fn)[1], re.IGNORECASE)  # to detect ZIP archive
-            if re_extension.search(".zip"):
-                with zipfile.ZipFile(fn, "r") as myzip:
-                    for element in myzip.filelist:
-                        fname = element.filename 
-                        if fname[-1] != "/":  # not a directory
-                            open(final_dir + '/' + fname, 'wb').write(myzip.open(fname, "r").read())  # cp file
-            else:
-                open(final_dir + '/' + os.path.basename(fn), 'w').write(open(fn, "r").read())  # cp file
-    return None
-
-
+from tools import *
 
 #Fonction permettant de vérifier les données soumises dans le formulaire, retour dans un dictionnaire (req)
 #Fonction qui sera modifiée pour le traitement de vos données
@@ -142,17 +47,7 @@ def extract_request(form):
     #req['pampa_version'] = form['pampa_version']
 
     # Job name parsing (optionnal)
-    if "job_name" in form:
-        job_name = form["job_name"].value.strip().replace(' ', '_')
-        if job_name == "":
-            log.write("Job name: None\n")  # log
-        elif len(job_name) <= 30:
-            req['job_name'] = job_name
-            log.write(f"Job name: {job_name}\n")  # log
-        else:
-            error_messages.append(f"The job name cannot exceed 30 characters. Current size: {len(job_name)}.")
-    else:
-        log.write("Job name: None\n")
+    extract_job(form, log, req, error_messages)
     
     # Spectra files parsing
     rel_spectra_dir = "spectra"
@@ -184,35 +79,7 @@ def extract_request(form):
         error_messages.append("At least one spectrum is required.")
     
     # Mass error parsing
-    if "error_margin_selection" in form:
-        error_margin_selection = form['error_margin_selection'].value
-        error_margin = 0
-        if error_margin_selection == "MALDI_TOF":
-            # valeur par défaut
-            error_margin = 50
-        elif error_margin_selection == "MALDI_FTICR":
-            # valeur par défaut
-            error_margin = 5
-        elif error_margin_selection == "ppm":
-            if "error_margin_ppm" in form:
-                error_margin = int(form['error_margin_ppm'].value)
-                if error_margin < 1 or error_margin > 1000:
-                    error_messages.append(f"The mass error in ppm must be within the range 1-1000. Input value: {error_margin}.")
-            else:
-                error_messages.append(f"With the custom value in ppm option, a mass error value is required.")
-        elif error_margin_selection == "daltons":
-            if "error_margin_daltons" in form:
-                error_margin = float(form['error_margin_daltons'].value)
-                if not (error_margin > 0 and error_margin < 1):
-                    error_messages.append(f"The mass error in daltons must be within the range 0.002-0.998. Input value: {error_margin}.")
-            else:
-                error_messages.append(f"With the custom value in Daltons option, a mass error value is required.")
-        else:
-            error_messages.append(f"Internal error. An unknow value have been entered in the 'error_margin_selection' input: {error_margin_selection}")
-        log.write(f"Error margin: {error_margin}\n")
-        req['error_margin'] = error_margin
-    else:
-        error_messages.append("A mass error selection is necessary for the analysis.")
+    extract_error_margin(form, log, req, error_messages)
     
     # 'Choice of the markers and organisms' parsing (default data or upload custom data)
     if "reference_source" not in form :
@@ -329,38 +196,7 @@ def extract_request(form):
             error_messages.append("Internal error. Issue in the formular structure ('peptides_files' or 'sequences_files' input).")
         
         # Taxonomy parsing
-        if "taxonomy_selection" in form:
-            taxonomy_selection = form["taxonomy_selection"].value
-            if taxonomy_selection == "default":
-                # sur les données (table/sequences) utilisateurs, on utilise la taxonomy_all.tsv qui est plus générale.
-                f = common.TAXONOMY_ALL_FILE
-                fn = os.path.basename(f)
-                extract_files_from_list([f], resdir)
-                req["taxo_file"] = resdir + '/' + fn  # for the command
-                req["taxo_source"] = "default_all"
-                log.write(f"file {fn}\n")  # log
-            elif taxonomy_selection == "no":
-                # pas d'information taxonomique -> pas de fichier taxo.tsv
-                log.write("No taxonomy\n")
-            elif taxonomy_selection == "custom":
-                # upload de la taxonomie utilisateur si possible, sinon erreur
-                if 'taxo_file' in form and not isinstance(form['taxo_file'], list) and form['taxo_file'].filename != "":
-                    f = form['taxo_file'].filename
-                    fn = os.path.basename(f)
-                    uploaded, not_uploaded = extract_files_from_fileitems([form['taxo_file']], resdir, extensions_list=[".tsv"], unzip=False)
-                    req["taxo_file"] = resdir + '/' + fn  # for the command
-                    req["taxo_source"] = "user"
-                    req['files_uploaded'].extend(uploaded)  # for the render_result
-                    for fn in uploaded:
-                        log.write(f"file {fn}\n")
-                    for fn in not_uploaded:
-                        error_messages.append(f"{fn} : The taxonomy file must be in TSV format.")
-                else:
-                    error_messages.append("If you choose to upload your own taxonomy, a taxonomy file is required.")
-            else:
-                error_messages.append(f"Internal error. An unexpected value has been submitted in the 'taxonomy_selection' input : {taxonomy_selection}")
-        else:
-            error_messages.append("A choice is required in the 'Taxonomy' section.")
+        extract_taxonomy_selection(form, log, req, error_messages, resdir)
 
     # option -n nombre et/ou -a (solution suboptimales)
     if 'nearoptimal_selection' in form:

www/cgi-bin/pampa/render_result.py

@@ -6,6 +6,7 @@ import common
 import zipfile
 import operator
 from render_sub_assignment import *
+from tools import *
 
 """
 NOTES
@@ -14,15 +15,6 @@ NOTES
 
 """
 
-
-
-def href_dl(link, name):
-    """
-    Construit une balise <a> ouvrant la page sur un nouvel onglet.
-    """
-    result = f'<a href="{link}" download="{name}" target="_blank">{name}</a>'
-    return result
-
 def command_builder_taxoreducer(taxonomy, output, reroot=False, peptides_tables=None, sequence_dir=None, limit_file=None):
     """
     Construit la ligne de commande adaptée à l'utilisation du script 'main_taxonomy_reduced'. Ce script produit une taxonomie réduite sur la base de l'ensemble des espèces sur lesquelles des données sont renseignées (sous la forme de tables de peptides ou d'un dossier de fichiers fasta de séquences de collagène) ou d'un limit_file (au format employé par PAMPA).
@@ -41,25 +33,6 @@ def command_builder_taxoreducer(taxonomy, output, reroot=False, peptides_tables=
         command += " -r"
     return command
 
-def zip_results(file_names, run_id, job_name=None):
-    """
-    Produit un fichier ZIP contenant tous les fichiers de résultat : 
-    - out.tsv
-    - detail_out.tsv
-    - report_out.txt
-    Ce fichier ZIP pourra être téléchargé par l'utilisateur.
-    """
-    with zipfile.ZipFile(f"{common.RESULT_DIR}{run_id}/data_result_{run_id}.zip", "a", compression=zipfile.ZIP_DEFLATED) as dwl_zip:
-        for fn in file_names:
-            abs_path = common.RESULT_DIR + run_id + '/' + fn
-            if os.path.exists(abs_path):
-                if job_name is not None:
-                    parts = os.path.splitext(fn)
-                    dwl_name = parts[0] + "_" + job_name + parts[1]
-                else: 
-                    dwl_name = fn
-                dwl_zip.write(abs_path, arcname=dwl_name)
-
 def results_output(run_id, job_name=None):
     """
     Produit la liste des fichiers téléchargeables par l'utilisateur.

www/cgi-bin/pampa/tools.py

+import os
+import zipfile
+import cgi
+import re
+import common
+
+# -------------------------------------
+# Form
+
+def verif_mail(mail):
+    """
+    Vérification d'une adresse email.
+
+    Args:
+        mail (str): Email à valider
+
+    Returns:
+        bool: True/False
+    """
+    res = mail.strip()
+    if res.find(' ') > 0:
+        return False
+    a = res.find('@')
+    if a <= 0:
+        return False
+    if res.find('@', a + 1) > 0:
+        return False
+    return True
+
+
+def extract_files_from_fileitems(fileitems, final_dir, extensions_list=None, unzip=False):
+    """
+    Gère les fichiers uploadés (dont ZIP) et les copie dans le dossier cible.
+
+    Args:
+        fileitems (list): Liste de fichiers type Werkzeug FileStorage
+        final_dir (str): Dossier de destination
+        extensions_list (list): Extensions autorisées (ex: ['.txt', '.csv'])
+        unzip (bool): Auto-extraction des ZIP si True
+
+    Returns:
+        tuple: (fichiers transférés, fichiers rejetés)
+    """
+    files_moved = []
+    files_not_moved = []
+
+    final_dir = final_dir.rstrip('/')
+    if not os.path.exists(final_dir):
+        os.makedirs(final_dir, exist_ok=True)
+
+    if extensions_list:
+        extensions = "|".join(extensions_list)
+
+    for f in fileitems:
+        fn = os.path.basename(f.filename)
+        re_extension = re.compile(os.path.splitext(fn)[1], re.IGNORECASE)
+
+        if unzip and re_extension.search(".zip"):
+            with zipfile.ZipFile(f.file, "r") as myzip:
+                for element in myzip.infolist():
+                    fname = os.path.basename(element.filename)
+
+                    if element.is_dir():
+                        continue
+
+                    re_extension = re.compile(os.path.splitext(fname)[1], re.IGNORECASE)
+                    if (extensions_list is None or re_extension.search(extensions)) and not os.path.exists(os.path.join(final_dir, fname)):
+                        with myzip.open(element.filename, "r") as src, open(os.path.join(final_dir, fname), 'wb') as dst:
+                            dst.write(src.read())
+                        files_moved.append(fname)
+                    else:
+                        files_not_moved.append(fname)
+        elif (extensions_list is None or re_extension.search(extensions)) and not os.path.exists(
+                os.path.join(final_dir, fn)):
+            with open(os.path.join(final_dir, fn), 'wb') as dst:
+                dst.write(f.file.read())
+            files_moved.append(fn)
+        else:
+            files_not_moved.append(fn)
+
+    return files_moved, files_not_moved
+
+def extract_files_from_list(filename_list, final_dir):
+    """
+    Copie des fichiers locaux vers un dossier cible avec extraction automatique des ZIP.
+
+    Args:
+        filename_list (list): Liste de chemins de fichiers locaux
+        final_dir (str): Dossier de destination
+    """
+    final_dir = final_dir.rstrip('/')
+    if not os.path.exists(final_dir):
+        os.mkdir(final_dir)
+
+    for fn in filename_list:
+        if os.path.exists(fn):
+            re_extension = re.compile(os.path.splitext(fn)[1], re.IGNORECASE)  # to detect ZIP archive
+            if re_extension.search(".zip"):
+                with zipfile.ZipFile(fn, "r") as myzip:
+                    for element in myzip.filelist:
+                        fname = element.filename
+                        if fname[-1] != "/":  # not a directory
+                            open(final_dir + '/' + fname, 'wb').write(myzip.open(fname, "r").read())  # cp file
+            else:
+                open(final_dir + '/' + os.path.basename(fn), 'w').write(open(fn, "r").read())  # cp file
+    return None
+
+# -------------------------------------
+# Extract form data
+
+def extract_job(form, log, req, error_messages):
+    if "job_name" in form:
+        job_name = form["job_name"].value.strip().replace(' ', '_')
+        if job_name == "":
+            log.write("Job name: None\n")
+        elif len(job_name) <= 30:
+            req['job_name'] = job_name
+            log.write(f"Job name: {job_name}\n")
+        else:
+            error_messages.append(f"The job name cannot exceed 30 characters. Current size: {len(job_name)}.")
+    else:
+        log.write("Job name: None\n")
+
+def extract_error_margin(form, log, req, error_messages):
+    if "error_margin_selection" in form:
+        error_margin_selection = form['error_margin_selection'].value
+        error_margin = 0
+        if error_margin_selection == "MALDI_TOF":
+            # valeur par défaut
+            error_margin = 50
+        elif error_margin_selection == "MALDI_FTICR":
+            # valeur par défaut
+            error_margin = 5
+        elif error_margin_selection == "ppm":
+            if "error_margin_ppm" in form and form["error_margin_ppm"].value != '':
+                error_margin = int(form['error_margin_ppm'].value)
+                if error_margin < 1 or error_margin > 1000:
+                    error_messages.append(
+                        f"The mass error in ppm must be within the range 1-1000. Input value: {error_margin}.")
+            else:
+                error_messages.append(f"With the custom value in ppm option, a mass error value is required.")
+        elif error_margin_selection == "daltons":
+            if "error_margin_daltons" in form and form["error_margin_daltons"].value != '':
+                error_margin = float(form['error_margin_daltons'].value)
+                if not (error_margin > 0 and error_margin < 1):
+                    error_messages.append(
+                        f"The mass error in daltons must be within the range 0.002-0.998. Input value: {error_margin}.")
+            else:
+                error_messages.append(f"With the custom value in Daltons option, a mass error value is required.")
+        else:
+            error_messages.append(
+                f"Internal error. An unknow value have been entered in the 'error_margin_selection' input: {error_margin_selection}")
+        log.write(f"Error margin: {error_margin}\n")
+        req['error_margin'] = error_margin
+    else:
+        error_messages.append("A mass error selection is necessary for the analysis.")
+
+def extract_taxonomy_selection(form, log, req, error_messages, resdir):
+    if "taxonomy_selection" in form:
+        taxonomy_selection = form["taxonomy_selection"].value
+        if taxonomy_selection == "default":
+            # sur les données (table/sequences) utilisateurs, on utilise la taxonomy_all.tsv qui est plus générale.
+            f = common.TAXONOMY_ALL_FILE
+            fn = os.path.basename(f)
+            extract_files_from_list([f], resdir)
+            req["taxo_file"] = resdir + '/' + fn  # for the command
+            req["taxo_source"] = "default_all"
+            log.write(f"file {fn}\n")  # log
+        elif taxonomy_selection == "no":
+            # pas d'information taxonomique -> pas de fichier taxo.tsv
+            log.write("No taxonomy\n")
+        elif taxonomy_selection == "custom":
+            # upload de la taxonomie utilisateur si possible, sinon erreur
+            if 'taxo_file' in form and not isinstance(form['taxo_file'], list) and form['taxo_file'].filename != "":
+                f = form['taxo_file'].filename
+                fn = os.path.basename(f)
+                uploaded, not_uploaded = extract_files_from_fileitems([form['taxo_file']], resdir,
+                                                                      extensions_list=[".tsv"], unzip=False)
+                req["taxo_file"] = resdir + '/' + fn  # for the command
+                req["taxo_source"] = "user"
+                req['files_uploaded'].extend(uploaded)  # for the render_result
+                for fn in uploaded:
+                    log.write(f"file {fn}\n")
+                for fn in not_uploaded:
+                    error_messages.append(f"{fn} : The taxonomy file must be in TSV format.")
+            else:
+                error_messages.append("If you choose to upload your own taxonomy, a taxonomy file is required.")
+        else:
+            error_messages.append(
+                f"Internal error. An unexpected value has been submitted in the 'taxonomy_selection' input : {taxonomy_selection}")
+    else:
+        error_messages.append("A choice is required in the 'Taxonomy' section.")
+
+# -------------------------------------
+# Result
+
+def href_dl(link, name):
+    """
+    Génère un lien HTML de téléchargement.
+
+    Args:
+        link (str): URL du fichier
+        name (str): Nom affiché du fichier
+
+    Returns:
+        str: Balise HTML <a> formatée
+    """
+    result = f'<a href="{link}" download="{name}" target="_blank">{name}</a>'
+    return result
+
+def zip_results(file_names, run_id, job_name=None):
+    """
+    Crée une archive ZIP des résultats d'analyse.
+
+    Args:
+        file_names (list): Noms des fichiers à archiver
+        run_id (str): Identifiant unique de l'analyse
+        job_name (str): Optionnel - suffixe pour les noms de fichiers
+    """
+    with zipfile.ZipFile(f"{common.RESULT_DIR}{run_id}/data_result_{run_id}.zip", "a",
+                            compression=zipfile.ZIP_DEFLATED) as dwl_zip:
+        for fn in file_names:
+            abs_path = common.RESULT_DIR + run_id + '/' + fn
+            if os.path.exists(abs_path):
+                if job_name is not None:
+                    parts = os.path.splitext(fn)
+                    dwl_name = parts[0] + "_" + job_name + parts[1]
+                else:
+                    dwl_name = fn
+                dwl_zip.write(abs_path, arcname=dwl_name)
\ No newline at end of file

www/html/pampa/craft-allpeptides.php

+<?php include('header.php') ?>
+
+
+<body>
+  <div class="frametitle">
+   <h1 id="title">Pampa-Craft</h1>
+  </div>
+
+  <div id="center_sup">
+     <div class="theme-border" style="display:none"></div>
+     <div id="link_home" style="display:inline-block"><a href="/" class="text_onglet"><img src="/Style/icon/home_w.png" alt="home_general"/></a></div>
+   <div class="tabs" id="menu_central" style="display:inline-block"><?php include("menu_central.txt")?></div>
+  </div>
+<div id="main">
+  <div id="center">
+
+    <form id="formulaire-craft-f" method="post" enctype="multipart/form-data">
+
+    <input type="hidden" name="pampa_version" value="assign"/>
+    <input type="hidden" name="method" value="allpeptides"/>
+
+    <div class="formulaire">
+      <table class="vide pampa_choice">
+        <tr>
+          <td class="label">
+            <h2>Name of the job <span style="font-weight: normal">(optional) :</span></h2>
+          </td>
+          <td>
+            <input type="text" name="job_name" maxlength="30"/>
+          </td>
+        </tr>
+      </table>
+    </div>
+
+    <div class="formulaire">
+      <h2>Target sequences</h2>
+        <table class="vide">
+          <tr>
+            <td class="label">
+              <B>Upload</B> The fasta files that you will use to complete your table.
+            </td>
+          </tr>
+          <tr id="sequences_input">
+            <td>
+              <input type="file" name="sequences_files" value="file" accept=".fasta,.zip" multiple required/>
+            </td>
+          </tr>
+          <tr id="sequences_example" style="display: none;">
+            <td>
+              <input class="file_input" id="back_to_normal" type="button" value="Parcourir..."/>
+              craft-example.zip
+              <input type="checkbox" style="display: none;" name="craft-example"/>
+            </td>
+          </tr>
+        </table>
+        <br>
+
+        <table class="vide">
+          <tr>
+            <td class="label">
+              <B>Upload</B> The limit file (optional, doc : https://github.com/touzet/pampa/wiki/Limiting-searches).
+            </td>
+          </tr>
+          <tr id="limit_input">
+            <td>
+              <input type="file" name="limit_file" value="file" accept=".txt"/>
+            </td>
+          </tr>
+        </table>
+    </div>
+
+        <div class="formulaire">
+      <h2>Mass spectra</h2>
+      <table class="vide">
+        <tr>
+          <td class="label">
+          <B>Upload</B> your MS spectra files in CSV, MGF or mzML format (or in a .ZIP archive)
+          </td>
+        </tr>
+        <tr id="spectra_input">
+          <td>
+            <input type="file" name="spectra_files" value="file" accept=".csv,.mgf,.mzml,.zip" multiple/>
+          </td>
+        </tr>
+        <tr id="spectra_example" style="display: none;">
+          <td>
+            <input class="file_input" id="back_to_normal" type="button" value="Parcourir..."/>
+            craft_example.zip
+            <input type="checkbox" style="display: none;" name="spectra_example_1"/>
+          </td>
+        </tr>
+      </table>
+      <br>
+
+      <b>Mass error</b>
+      <table class="vide pampa_choice">
+        <tr>
+          <td>
+            <input type="radio" name="error_margin_selection" value="MALDI_TOF" checked/>
+            Optimize for MALDI-TOF spectra
+          </td>
+        </tr>
+        <tr>
+          <td>
+            <input type="radio" name="error_margin_selection" value="MALDI_FTICR"/>
+            Optimize for MALDI-FTICR spectra
+          </td>
+        </tr>
+        <tr>
+          <td>
+            <input type="radio" name="error_margin_selection" value="ppm"/>
+            Custom value in ppm
+          </td>
+          <td>
+            <input type="number" name="error_margin_ppm" step="1" min="1" max="1000" placeholder="between 1 and 1000"/>
+          </td>
+        </tr>
+        <tr>
+          <td>
+            <input type="radio" name="error_margin_selection" value="daltons">
+            Custom value in Daltons
+          </td>
+          <td>
+            <input type="number" name="error_margin_daltons" step="0.002" min="0.002" max="0.998" placeholder="between 0.002 and 0.998"/>
+          </td>
+        </tr>
+      </table>
+    </div>
+
+    <div class="center">
+      <input type="button" id="example-allpeptides" name="example-allpeptides" value="Example">
+    </div>
+
+    <div class="center">
+      <input type="submit" id="reset-craft-a" name="reset" value="Reset" />
+      <input type="submit" id="run" name="button" value="Run" />
+      <input type="hidden" name="command" value="request" />
+    </div>
+
+  </form>
+
+</div><!--bloc -->
+</div><!-- main-->
+
+<!-- chargement de la librairie php lib.inc -->
+   <?php require("../lib.inc")?>
+<!-- appel de la fonction footer qui permet d'afficher au bas de la page (nom du logiciel, un lien vers le mail, la date de modif -->
+<!-- A modifier en fonction de votre logiciel -->
+   <?php footer("Pampa","Pampa", "areski.flissi@univ-lille.fr","2025"); ?>
+
+
+
+</body>
+</html>
+

www/html/pampa/craft-deamidation.php

+<?php include('header.php') ?>
+
+
+<body>
+  <div class="frametitle">
+   <h1 id="title">Pampa-Craft</h1>
+  </div>
+
+  <div id="center_sup">
+     <div class="theme-border" style="display:none"></div>
+     <div id="link_home" style="display:inline-block"><a href="/" class="text_onglet"><img src="/Style/icon/home_w.png" alt="home_general"/></a></div>
+   <div class="tabs" id="menu_central" style="display:inline-block"><?php include("menu_central.txt")?></div>
+  </div>
+<div id="main">
+  <div id="center">
+
+    <form id="formulaire-craft-f" method="post" enctype="multipart/form-data">
+
+    <input type="hidden" name="pampa_version" value="assign"/>
+    <input type="hidden" name="method" value="deamidation"/>
+
+    <div class="formulaire">
+      <table class="vide pampa_choice">
+        <tr>
+          <td class="label">
+            <h2>Name of the job <span style="font-weight: normal">(optional) :</span></h2>
+          </td>
+          <td>
+            <input type="text" name="job_name" maxlength="30"/>
+          </td>
+        </tr>
+      </table>
+    </div>
+
+    <div class="formulaire">
+      <h2>Peptides Table</h2>
+      <table class="vide">
+        <tr>
+          <td class="label">
+            <B>Upload</B> the peptides table that you want to complete in (.csv or .tsv)
+          </td>
+        </tr>
+        <tr id="peptide_input">
+          <td>
+            <input type="file" name="peptides_file" value="file" accept=".tsv,.csv" required/>
+          </td>
+        </tr>
+        <tr id="peptide_example" style="display: none;">
+          <td>
+            <input class="file_input" id="back_to_normal" type="button" value="Parcourir..."/>
+            craft-example.tsv
+            <input type="checkbox" style="display: none;" name="craft-example"/>
+          </td>
+        </tr>
+      </table>
+      <br>
+    </div>
+
+    <div class="formulaire">
+      <h2>Limit File</h2>
+        <table class="vide">
+          <tr>
+            <td class="label">
+              <B>Upload</B> The limit file (optional, doc : https://github.com/touzet/pampa/wiki/Limiting-searches).
+            </td>
+          </tr>
+          <tr id="limit_input">
+            <td>
+              <input type="file" name="limit_file" value="file" accept=".txt"/>
+            </td>
+          </tr>
+        </table>
+    </div>
+
+    <div class="center">
+      <input type="submit" id="run" name="button" value="Run" />
+      <input type="hidden" name="command" value="request" />
+    </div>
+
+  </form>
+
+</div><!--bloc -->
+</div><!-- main-->
+
+<!-- chargement de la librairie php lib.inc -->
+   <?php require("../lib.inc")?>
+<!-- appel de la fonction footer qui permet d'afficher au bas de la page (nom du logiciel, un lien vers le mail, la date de modif -->
+<!-- A modifier en fonction de votre logiciel -->
+   <?php footer("Pampa","Pampa", "areski.flissi@univ-lille.fr","2025"); ?>
+
+
+
+</body>
+</html>
+

www/html/pampa/craft-fillin.php

+<?php include('header.php') ?>
+
+
+<body>
+  <div class="frametitle">
+   <h1 id="title">Pampa-Craft</h1>
+  </div>
+
+  <div id="center_sup">
+     <div class="theme-border" style="display:none"></div>
+     <div id="link_home" style="display:inline-block"><a href="/" class="text_onglet"><img src="/Style/icon/home_w.png" alt="home_general"/></a></div>
+   <div class="tabs" id="menu_central" style="display:inline-block"><?php include("menu_central.txt")?></div>
+  </div>
+<div id="main">
+  <div id="center">
+
+    <form id="formulaire-craft-f" method="post" enctype="multipart/form-data">
+
+    <input type="hidden" name="pampa_version" value="assign"/>
+    <input type="hidden" name="method" value="fillin"/>
+
+    <div class="formulaire">
+      <table class="vide pampa_choice">
+        <tr>
+          <td class="label">
+            <h2>Name of the job <span style="font-weight: normal">(optional) :</span></h2>
+          </td>
+          <td>
+            <input type="text" name="job_name" maxlength="30"/>
+          </td>
+        </tr>
+      </table>
+    </div>
+
+    <div class="formulaire">
+      <h2>Peptide table</h2>
+      <table class="vide">
+        <tr>
+          <td class="label">
+            <B>Upload</B> the peptide table that you want to complete in (.csv or .tsv)
+          </td>
+        </tr>
+        <tr id="peptide_input">
+          <td>
+            <input type="file" name="peptides_file" value="file" accept=".tsv,.csv" required/>
+          </td>
+        </tr>
+        <tr id="peptide_example" style="display: none;">
+          <td>
+            <input class="file_input" id="back_to_normal" type="button" value="Parcourir..."/>
+            craft-example.tsv
+            <input type="checkbox" style="display: none;" name="craft-example"/>
+          </td>
+        </tr>
+      </table>
+      <br>
+    </div>
+
+    <div class="formulaire">
+      <h2>Target sequences</h2>
+        <table class="vide">
+          <tr>
+            <td class="label">
+              <B>Upload</B> The fasta files that you will use to complete your table.
+            </td>
+          </tr>
+          <tr id="sequences_input">
+            <td>
+              <input type="file" name="sequences_files" value="file" accept=".fasta,.zip" multiple/>
+            </td>
+          </tr>
+          <tr id="sequences_example" style="display: none;">
+            <td>
+              <input class="file_input" id="back_to_normal" type="button" value="Parcourir..."/>
+              craft-example.zip
+              <input type="checkbox" style="display: none;" name="craft-example"/>
+            </td>
+          </tr>
+        </table>
+        <br>
+
+        <table class="vide">
+          <tr>
+            <td class="label">
+              <B>Upload</B> The limit file (optional, doc : https://github.com/touzet/pampa/wiki/Limiting-searches).
+            </td>
+          </tr>
+          <tr id="limit_input">
+            <td>
+              <input type="file" name="limit_file" value="file" accept=".txt"/>
+            </td>
+          </tr>
+        </table>
+        <br>
+        <table>
+          <tr>
+            <td class="label">
+              <B>Enter</B> The margin error
+            </td>
+          </tr>
+          <tr id="error_input">
+            <td>
+              <input type="number" name="error" step="0.0001" min="0.0001" max="1" placeholder="between 0.0001 and 1"/>
+            </td>
+          </tr>
+        </table>
+    </div>
+
+    <div class="formulaire">
+        <h2>Taxonomy</h2>
+        <table class="vide">
+          <tr>
+            <td colspan="2">
+              <input type="radio" name="taxonomy_selection" value="default"/>
+              Use NCBI taxonomy
+            </td>
+          </tr>
+          <tr>
+            <td colspan="2">
+              <input type="radio" name="taxonomy_selection" value="no" checked/>
+              Provide no taxonomy
+            </td>
+          </tr>
+          <tr>
+            <td>
+              <input type="radio" name="taxonomy_selection" value="custom"/>
+              Upload your own taxonomy
+            </td>
+            <td>
+              <input type="file" name="taxo_file" value="file" accept=".tsv"/>
+            </td>
+          </tr>
+        </table>
+      </div>
+
+    <div class="center">
+      <input type="button" id="example-fillin" name="example-fillin" value="Example">
+    </div>
+
+    <div class="center">
+      <input type="submit" id="reset-craft-f" name="reset" value="Reset" />
+      <input type="submit" id="run" name="button" value="Run" />
+      <input type="hidden" name="command" value="request" />
+    </div>
+
+  </form>
+
+</div><!--bloc -->
+</div><!-- main-->
+
+<!-- chargement de la librairie php lib.inc -->
+   <?php require("../lib.inc")?>
+<!-- appel de la fonction footer qui permet d'afficher au bas de la page (nom du logiciel, un lien vers le mail, la date de modif -->
+<!-- A modifier en fonction de votre logiciel -->
+   <?php footer("Pampa","Pampa", "areski.flissi@univ-lille.fr","2025"); ?>
+
+
+
+</body>
+</html>
+

www/html/pampa/craft-homology.php

+<?php include('header.php') ?>
+
+
+<body>
+  <div class="frametitle">
+   <h1 id="title">Pampa-Craft</h1>
+  </div>
+
+  <div id="center_sup">
+     <div class="theme-border" style="display:none"></div>
+     <div id="link_home" style="display:inline-block"><a href="/" class="text_onglet"><img src="/Style/icon/home_w.png" alt="home_general"/></a></div>
+   <div class="tabs" id="menu_central" style="display:inline-block"><?php include("menu_central.txt")?></div>
+  </div>
+<div id="main">
+  <div id="center">
+
+    <form id="formulaire-craft-h" method="post" enctype="multipart/form-data">
+
+    <input type="hidden" name="pampa_version" value="assign"/>
+    <input type="hidden" name="method" value="homology"/>
+
+    <div class="formulaire">
+      <table class="vide pampa_choice">
+        <tr>
+          <td class="label">
+            <h2>Name of the job <span style="font-weight: normal">(optional) :</span></h2>
+          </td>
+          <td>
+            <input type="text" name="job_name" maxlength="30"/>
+          </td>
+        </tr>
+      </table>
+    </div>
+
+    <div class="formulaire">
+      <h2>Peptide Table</h2>
+      <table class="vide">
+        <tr>
+          <td class="label">
+            <B>Upload</B> the peptide table that you want to complete in (.csv or .tsv)
+          </td>
+        </tr>
+        <tr id="peptide_input">
+          <td>
+            <input type="file" name="peptides_file" value="file" accept=".tsv,.csv" required/>
+          </td>
+        </tr>
+        <tr id="peptide_example" style="display: none;">
+          <td>
+            <input class="file_input" id="back_to_normal" type="button" value="Parcourir..."/>
+            craft-example.tsv
+            <input type="checkbox" style="display: none;" name="craft-example"/>
+          </td>
+        </tr>
+      </table>
+      <br>
+    </div>
+
+    <div class="formulaire">
+      <h2>Target sequences</h2>
+        <table class="vide">
+          <tr>
+            <td class="label">
+              <B>Upload</B> The fasta files that you will use to complete your table.
+            </td>
+          </tr>
+          <tr id="sequences_input">
+            <td>
+              <input type="file" name="sequences_files" value="file" accept=".fasta,.zip" multiple required/>
+            </td>
+          </tr>
+          <tr id="sequences_example" style="display: none;">
+            <td>
+              <input class="file_input" id="back_to_normal" type="button" value="Parcourir..."/>
+              craft-example.zip
+              <input type="checkbox" style="display: none;" name="craft-example"/>
+            </td>
+          </tr>
+        </table>
+        <br>
+
+        <table class="vide">
+          <tr>
+            <td class="label">
+              <B>Upload</B> The limit file (optional, doc : https://github.com/touzet/pampa/wiki/Limiting-searches).
+            </td>
+          </tr>
+          <tr id="limit_input">
+            <td>
+              <input type="file" name="limit_file" value="file" accept=".txt"/>
+            </td>
+          </tr>
+        </table>
+    </div>
+
+    <div class="formulaire">
+      <h2>Taxonomy</h2>
+      <table class="vide">
+        <tr>
+          <td colspan="2">
+            <input type="radio" name="taxonomy_selection" value="default"/>
+            Use NCBI taxonomy
+          </td>
+        </tr>
+        <tr>
+          <td colspan="2">
+            <input type="radio" name="taxonomy_selection" value="no" checked/>
+            Provide no taxonomy
+          </td>
+        </tr>
+        <tr>
+          <td>
+            <input type="radio" name="taxonomy_selection" value="custom"/>
+            Upload your own taxonomy
+          </td>
+          <td>
+            <input type="file" name="taxo_file" value="file" accept=".tsv"/>
+          </td>
+        </tr>
+      </table>
+    </div>
+
+    <div class="center">
+      <input type="button" id="example-homology" name="example-homology" value="Example">
+    </div>
+
+    <div class="center">
+      <input type="submit" id="reset-craft-h" name="reset" value="Reset" />
+      <input type="submit" id="run" name="button" value="Run" />
+      <input type="hidden" name="command" value="request" />
+    </div>
+
+  </form>
+
+</div><!--bloc -->
+</div><!-- main-->
+
+<!-- chargement de la librairie php lib.inc -->
+   <?php require("../lib.inc")?>
+<!-- appel de la fonction footer qui permet d'afficher au bas de la page (nom du logiciel, un lien vers le mail, la date de modif -->
+<!-- A modifier en fonction de votre logiciel -->
+   <?php footer("Pampa","Pampa", "areski.flissi@univ-lille.fr","2025"); ?>
+
+
+
+</body>
+</html>
+

www/html/pampa/craft-selection.php

+<?php include('header.php') ?>
+
+
+<body>
+  <div class="frametitle">
+   <h1 id="title">Pampa-Craft</h1>
+  </div>
+
+  <div id="center_sup">
+     <div class="theme-border" style="display:none"></div>
+     <div id="link_home" style="display:inline-block"><a href="/" class="text_onglet"><img src="/Style/icon/home_w.png" alt="home_general"/></a></div>
+   <div class="tabs" id="menu_central" style="display:inline-block"><?php include("menu_central.txt")?></div>
+  </div>
+<div id="main">
+  <div id="center">
+
+    <form id="formulaire-craft-f" method="post" enctype="multipart/form-data">
+
+    <input type="hidden" name="pampa_version" value="assign"/>
+    <input type="hidden" name="method" value="selection"/>
+
+    <div class="formulaire">
+      <table class="vide pampa_choice">
+        <tr>
+          <td class="label">
+            <h2>Name of the job <span style="font-weight: normal">(optional) :</span></h2>
+          </td>
+          <td>
+            <input type="text" name="job_name" maxlength="30"/>
+          </td>
+        </tr>
+      </table>
+    </div>
+
+    <div class="formulaire">
+      <h2>Peptide Table</h2>
+      <table class="vide">
+        <tr>
+          <td class="label">
+            <B>Upload</B> the peptide table that you want to complete in (.csv or .tsv)
+          </td>
+        </tr>
+        <tr id="peptide_input">
+          <td>
+            <input type="file" name="peptides_file" value="file" accept=".tsv,.csv" required/>
+          </td>
+        </tr>
+        <tr id="peptide_example" style="display: none;">
+          <td>
+            <input class="file_input" id="back_to_normal" type="button" value="Parcourir..."/>
+            craft-example.tsv
+            <input type="checkbox" style="display: none;" name="craft-example"/>
+          </td>
+        </tr>
+      </table>
+      <br>
+    </div>
+
+        <div class="formulaire">
+      <h2>Mass spectra</h2>
+      <table class="vide">
+        <tr>
+          <td class="label">
+          <B>Upload</B> your MS spectra files in CSV, MGF or mzML format (or in a .ZIP archive)
+          </td>
+        </tr>
+        <tr id="spectra_input">
+          <td>
+            <input type="file" name="spectra_files" value="file" accept=".csv,.mgf,.mzml,.zip" multiple required/>
+          </td>
+        </tr>
+        <tr id="spectra_example" style="display: none;">
+          <td>
+            <input class="file_input" id="back_to_normal" type="button" value="Parcourir..."/>
+            pampa_example_1.zip
+            <input type="checkbox" style="display: none;" name="spectra_example_1"/>
+          </td>
+        </tr>
+      </table>
+      <br>
+
+      <b>Mass error</b>
+      <table class="vide pampa_choice">
+        <tr>
+          <td>
+            <input type="radio" name="error_margin_selection" value="MALDI_TOF" checked/>
+            Optimize for MALDI-TOF spectra
+          </td>
+        </tr>
+        <tr>
+          <td>
+            <input type="radio" name="error_margin_selection" value="MALDI_FTICR"/>
+            Optimize for MALDI-FTICR spectra
+          </td>
+        </tr>
+        <tr>
+          <td>
+            <input type="radio" name="error_margin_selection" value="ppm"/>
+            Custom value in ppm
+          </td>
+          <td>
+            <input type="number" name="error_margin_ppm" step="1" min="1" max="1000" placeholder="between 1 and 1000"/>
+          </td>
+        </tr>
+        <tr>
+          <td>
+            <input type="radio" name="error_margin_selection" value="daltons">
+            Custom value in Daltons
+          </td>
+          <td>
+            <input type="number" name="error_margin_daltons" step="0.002" min="0.002" max="0.998" placeholder="between 0.002 and 0.998"/>
+          </td>
+        </tr>
+      </table>
+    </div>
+
+    <div class="center">
+      <input type="submit" id="run" name="button" value="Run" />
+      <input type="hidden" name="command" value="request" />
+    </div>
+
+  </form>
+
+</div><!--bloc -->
+</div><!-- main-->
+
+<!-- chargement de la librairie php lib.inc -->
+   <?php require("../lib.inc")?>
+<!-- appel de la fonction footer qui permet d'afficher au bas de la page (nom du logiciel, un lien vers le mail, la date de modif -->
+<!-- A modifier en fonction de votre logiciel -->
+   <?php footer("Pampa","Pampa", "areski.flissi@univ-lille.fr","2025"); ?>
+
+
+
+</body>
+</html>
+

www/html/pampa/css/pampa.css

@@ -11,7 +11,7 @@ blockquote {
   padding-left: 8px;
 }
 
-.formulaire {
+.formulaire, .formulaire-craft-h, .formulaire-craft-f {
     border: 1px solid #CCCCCC;
     color: #000000;
     margin: auto auto 10pt;

www/html/pampa/data_pampa/allpeptides_sequences.fasta

+>XP_027830506.1 OS=Ovis aries OX=9940 GN=COL1A1 A 
+MFSFVDLRLLLLLAATALLTHGQEEGQEEGQEEDIPPVTCVQNGLRYHDRDVWKPVPCQICVCDNGNVLCDDVICDELKDCPNAKVPTDECCPVCPEGQESTTDQETTGVEGPKGDTGPRGPRGPAGPPGRDGIPGQPGLPGPPGPPGPPGPPGLGGNFAPQLSYGYDEKSTGISVPGPMGPSGPRGLPGPPGAPGPQGFQGPPGEPGEPGASGPMGPRGPPGPPGKNGDDGEAGKPGRPGERGPPGPQGARGLPGTAGLPGMKGHRGFSGLDGAKGDAGPAGPKGEPGSPGENGAPGQMGPRGLPGERGRPGAPGPAGARGNDGATGAAGPPGPTGPAGPPGFPGAVGAKGEAGPQGPRGSEGPQGVRGEPGPPGPAGAAGPAGNPGADGQPGAKGANGAPGIAGAPGFPGARGPSGPQGPSGPPGPKGNSGEPGAPGSKGDTGAKGEPGPTGIQGPPGPAGEEGKRGARGEPGPAGLPGPPGERGGPGSRGFPGSDGVAGPKGPAGERGAPGPAGPKGSPGEAGRPGEAGLPGAKGLTGSPGSPGPDGKTGPPGPAGQDGRPGPPGPPGARGQAGVMGFPGPKGAAGEPGKAGERGVPGPPGAVGPAGKDGEAGAQGPPGPAGPAGERGEQGPAGSPGFQGLPGPAGPPGEAGKPGEQGVPGDLGAPGPSGARGERGFPGERGVQGPPGPAGPRGANGAPGNDGAKGDAGAPGAPGSQGAPGLQGMPGERGAAGLPGPKGDRGDAGPKGADGAPGKDGVRGLTGPIGPPGPAGAPGDKGETGPSGPAGPTGARGAPGDRGEPGPPGPAGFAGPPGADGQPGAKGEPGDAGAKGDAGPPGPAGPAGPPGPIGNVGAPGPKGARGSAGPPGATGFPGAAGRVGPPGPSGNAGPPGPPGPAGKEGSKGPRGETGPAGRAGEVGPPGPPGPAGEKGAPGADGPAGAPGTPGPQGIAGQRGVVGLPGQRGERGFPGLPGPSGEPGKQGPSGASGERGPPGPMGPPGLAGPPGESGREGAPGAEGSPGRDGAPGAKGDRGETGPAGPPGAPGAPGAPGPVGPAGKSGDRGETGPAGPAGPIGPVGARGPAGPQGPRGDKGETGEQGDRGIKGHRGFSGLQGPPGPPGSPGEQGPSGASGPAGPRGPPGSAGTPGKDGLNGLPGPIGPPGPRGRTGDAGPAGPPGPPGPPGPPGPPSGGYDLSFLPQPPQEKAHDGGRYYRADDANVVRDRDLEVDTTLKSLSQQIENIRSPEGSRKNPARTCRDLKMCHPDWKSGEYWIDPNQGCNLDAIKVFCNMETGETCVYPTQPSVPQKNWYISKNPKDKRHVWYGESMTGGFQFEYGGQGSDPADVAIQLTFLRLMSTEASQNITYHCKNSVAYMDQQTGSLKKALLLQGSNEIEIRAEGNSRFTYSVTYDGCTSHTGAWGKTVIEYKTTKTSRLPIIDVAPLDVGAPDQEFGFDIGSVCFL
+>XP_004007775.1 OS=Ovis aries OX=9940 GN=COL1A2 A 
+MLSFVDTRTLLLLAVTSCLATCQSLQEATARKGPSGDRGPRGERGPPGPPGRDGDDGIPGPPGPPGPPGPPGLGGNFAAQFDGKGGGPGPMGLMGPRGPPGASGAPGPQGFQGPPGEPGEPGQTGPAGARGPPGPPGKAGEDGHPGKPGRPGERGVVGPQGARGFPGTPGLPGFKGIRGHNGLDGLKGQPGAPGVKGEPGAPGENGTPGQTGARGLPGERGRVGAPGPAGARGSDGSVGPVGPAGPIGSAGPPGFPGAPGPKGELGPVGNPGPAGPAGPRGEVGLPGLSGPVGPPGNPGANGLPGAKGAAGLPGVAGAPGLPGPRGIPGPVGAAGATGARGLVGEPGPAGSKGESGNKGEPGAVGQPGPPGPSGEEGKRGSTGEIGPAGPPGPPGLRGNPGSRGLPGADGRAGVMGPAGSRGATGPAGVRGPNGDSGRPGEPGLMGPRGFPGSPGNIGPAGKEGPAGLPGIDGRPGPIGPAGARGEPGNIGFPGPKGPTGDPGKAGEKGHAGLAGPRGAPGPDGNNGAQGPPGLQGVQGGKGEQGPAGPPGFQGLPGPAGTAGEAGKPGERGIPGEFGLPGPAGARGERGPPGESGAAGPTGPIGSRGPSGPPGPDGNKGEPGVVGAPGTAGPSGPSGLPGERGAAGIPGGKGEKGETGLRGDVGSPGRDGARGAPGAVGAPGPAGANGDRGEAGPAGPAGPAGPRGSPGERGEVGPAGPNGFAGPAGAAGQPGAKGERGTKGPKGENGPVGPTGPVGAAGPSGPNGPPGPAGSRGDGGPPGATGFPGAAGRTGPPGPAGISGPPGPPGPAGKEGLRGPRGDQGPVGRTGEPGAAGPPGFVGEKGPSGEPGTAGPPGTPGPQGLLGAPGFLGLPGSRGERGLPGVAGSVGEPGPLGIAGPPGARGPPGNVGNPGVNGAPGEAGRDGNPGNDGPPGRDGQPGHKGERGYPGNAGPVGAAGAPGPQGPVGPTGKHGSRGEPGPVGAVGPAGAVGPRGPSGPQGIRGDKGEPGDKGPRGLPGLKGHNGLQGLPGLAGHHGDQGAPGAVGPAGPRGPAGPTGPAGKDGRTGQPGAVGPAGIRGSQGSQGPAGPPGPPGPPGPPGPSGGGYDFGFDGDFYRADQPRSPASLRPKDYEVDATLKSLNNQIETLLTPEGSRKNPARTCRDLRLSHPEWSSGYYWIDPNQGCTMDAIKVYCDFSTGETCIRAQPEDIPVKNWYRNSKAKKHVWVGETINGGTQFEYNVEGVTTKEMATQLAFMRLLANHASQNITYHCKNSIAYMDEETGNLKKAVILQGSNDVELVAEGNSRFTYTVLVDGCSKKTNEWKKTIIEYKTNKPSRLPILDIAPLDIGGADQEIRLNIGPVCFK

www/html/pampa/data_pampa/fillin_peptides.tsv

+Taxon	Marker	Sequence	Mass	PTM	Hel	Gene	SeqID	Begin	End
+Mus musculus	A		1178.6			COL1A2
+Mus musculus	A		1194.6			COL1A2
+Mus musculus	B		1453.7			COL1A2
+Mus musculus	C		1592.8			COL1A2

www/html/pampa/data_pampa/fillin_sequences.fasta

+>NP_031768.2 OS=Mus musculus OX=10090 GN=COL1A1 
+MFSFVDLRLLLLLGATALLTHGQEDIPEVSCIHNGLRVPNGETWKPEVCLICICHNGTAVCDDVQCNEELDCPNPQRREGECCAFCPEEYVSPNSEDVGVEGPKGDPGPQGPRGPVGPPGRDGIPGQPGLPGPPGPPGPPGPPGLGGNFASQMSYGYDEKSAGVSVPGPMGPSGPRGLPGPPGAPGPQGFQGPPGEPGEPGGSGPMGPRGPPGPPGKNGDDGEAGKPGRPGERGPPGPQGARGLPGTAGLPGMKGHRGFSGLDGAKGDAGPAGPKGEPGSPGENGAPGQMGPRGLPGERGRPGPPGTAGARGNDGAVGAAGPPGPTGPTGPPGFPGAVGAKGEAGPQGARGSEGPQGVRGEPGPPGPAGAAGPAGNPGADGQPGAKGANGAPGIAGAPGFPGARGPSGPQGPSGPPGPKGNSGEPGAPGNKGDTGAKGEPGATGVQGPPGPAGEEGKRGARGEPGPSGLPGPPGERGGPGSRGFPGADGVAGPKGPSGERGAPGPAGPKGSPGEAGRPGEAGLPGAKGLTGSPGSPGPDGKTGPPGPAGQDGRPGPAGPPGARGQAGVMGFPGPKGTAGEPGKAGERGLPGPPGAVGPAGKDGEAGAQGAPGPAGPAGERGEQGPAGSPGFQGLPGPAGPPGEAGKPGEQGVPGDLGAPGPSGARGERGFPGERGVQGPPGPAGPRGNNGAPGNDGAKGDTGAPGAPGSQGAPGLQGMPGERGAAGLPGPKGDRGDAGPKGADGSPGKDGARGLTGPIGPPGPAGAPGDKGEAGPSGPPGPTGARGAPGDRGEAGPPGPAGFAGPPGADGQPGAKGEPGDTGVKGDAGPPGPAGPAGPPGPIGNVGAPGPKGPRGAAGPPGATGFPGAAGRVGPPGPSGNAGPPGPPGPVGKEGGKGPRGETGPAGRPGEVGPPGPPGPAGEKGSPGADGPAGSPGTPGPQGIAGQRGVVGLPGQRGERGFPGLPGPSGEPGKQGPSGSSGERGPPGPMGPPGLAGPPGESGREGSPGAEGSPGRDGAPGAKGDRGETGPAGPPGAPGAPGAPGPVGPAGKNGDRGETGPAGPAGPIGPAGARGPAGPQGPRGDKGETGEQGDRGIKGHRGFSGLQGPPGSPGSPGEQGPSGASGPAGPRGPPGSAGSPGKDGLNGLPGPIGPPGPRGRTGDSGPAGPPGPPGPPGPPGPPSGGYDFSFLPQPPQEKSQDGGRYYRADDANVVRDRDLEVDTTLKSLSQQIENIRSPEGSRKNPARTCRDLKMCHSDWKSGEYWIDPNQGCNLDAIKVYCNMETGQTCVFPTQPSVPQKNWYISPNPKEKKHVWFGESMTDGFPFEYGSEGSDPADVAIQLTFLRLMSTEASQNITYHCKNSVAYMDQQTGNLKKALLLQGSNEIELRGEGNSRFTYSTLVDGCTSHTGTWGKTVIEYKTTKTSRLPIIDVAPLDIGAPDQEFGLDIGPACFV
+>NP_031769.2 OS=Mus musculus OX=10090 GN=COL1A2
+MLSFVDTRTLLLLAVTSCLATCQYLQSGSVRKGPTGDRGPRGQRGPAGPRGRDGVDGPMGPPGPPGSPGPPGSPAPPGLTGNFAAQYSDKGVSSGPGPMGLMGPRGPPGAVGAPGPQGFQGPAGEPGEPGQTGPAGPRGPAGSPGKAGEDGHPGKPGRPGERGVVGPQGARGFPGTPGLPGFKGVKGHSGMDGLKGQPGAQGVKGEPGAPGENGTPGQAGARGLPGERGRVGAPGPAGARGSDGSVGPVGPAGPIGSAGPPGFPGAPGPKGELGPVGNPGPAGPAGPRGEVGLPGLSGPVGPPGNPGTNGLTGAKGATGLPGVAGAPGLPGPRGIPGPAGAAGATGARGLVGEPGPAGSKGESGNKGEPGSVGAQGPPGPSGEEGKRGSPGEAGSAGPAGPPGLRGSPGSRGLPGADGRAGVMGPPGNRGSTGPAGIRGPNGDAGRPGEPGLMGPRGLPGSPGNVGPSGKEGPVGLPGIDGRPGPIGPAGPRGEAGNIGFPGPKGPSGDPGKPGERGHPGLAGARGAPGPDGNNGAQGPPGPQGVQGGKGEQGPAGPPGFQGLPGPSGTTGEVGKPGERGLPGEFGLPGPAGPRGERGTPGESGAAGPSGPIGSRGPSGAPGPDGNKGEAGAVGAPGSAGASGPGGLPGERGAAGIPGGKGEKGETGLRGDTGNTGRDGARGIPGAVGAPGPAGASGDRGEAGAAGPSGPAGPRGSPGERGEVGPAGPNGFAGPAGAAGQPGAKGEKGTKGPKGENGIVGPTGSVGAAGPSGPNGPPGPVGSRGDGGPPGMTGFPGAAGRTGPPGPSGIAGPPGPPGAAGKEGIRGPRGDQGPVGRTGETGASGPPGFVGEKGPSGEPGTAGAPGTAGPQGLLGAPGILGLPGSRGERGLPGIAGALGEPGPLGISGPPGARGPPGAVGSPGVNGAPGEAGRDGNPGSDGPPGRDGQPGHKGERGYPGSIGPTGAAGAPGPHGSVGPAGKHGNRGEPGPAGSVGPVGAVGPRGPSGPQGIRGDKGEPGDKGHRGLPGLKGYSGLQGLPGLAGLHGDQGAPGPVGPAGPRGPAGPSGPVGKDGRSGQPGPVGPAGVRGSQGSQGPAGPPGPPGPPGPPGVSGGGYDFGFEGDFYRADQPRSQPSLRPKDYEVDATLKSLNNQIETLLTPEGSRKNPARTCRDLRLSHPEWNSDYYWIDPNQGCTMDAIKVYCDFSTGETCIQAQPVNTPAKNSYSRAQANKHVWLGETINGGSQFEYNVEGVSSKEMATQLAFMRLLANRASQNITYHCKNSIAYLDEETGSLNKAVLLQGSNDVELVAEGNSRFTYSVLVDGCSKKTNEWGKTIIEYKTNKPSRLPFLDIAPLDIGGADQEFRVEVGPVCFK
+>XP_032768589.1 OS=Rattus rattus OX=10117 GN=COL1A1
+MFSFVDLRLLLLLGATALLTHGQEDIPEVSCIHNGLRVPNGETWKPDVCLICICHNGTAVCDGVLCKEDLDCPNPQRREGECCPFCPEEYVSPDAEVIGVEGPKGDPGPQGPRGPVGPPGQDGIPGQPGLPGPPGPPGPPGPPGLGGNFASQMSYGYDEKSAGVSVPGPMGPSGPRGLPGPPGAPGPQGFQGPPGEPGEPGASGPMGPRGPPGPPGKNGDDGEAGKPGRPGERGPPGPQGARGLPGTAGLPGMKGHRGFSGLDGAKGDTGPAGPKGEPGSPGENGAPGQMGPRGLPGERGRPGPPGSAGARGNDGAVGAAGPPGPTGPTGPPGFPGAAGAKGEAGPQGARGSEGPQGVRGEPGPPGPAGAAGPAGNPGADGQPGAKGANGAPGIAGAPGFPGARGPSGPQGPSGAPGPKGNSGEPGAPGNKGDTGAKGEPGPAGVQGPPGPAGEEGKRGARGEPGPSGLPGPPGERGGPGSRGFPGADGVAGPKGPAGERGSPGPAGPKGSPGEAGRPGEAGLPGAKGLTGSPGSPGPDGKTGPPGPAGQDGRPGPAGPPGARGQAGVMGFPGPKGTAGEPGKAGERGVPGPPGAVGPAGKDGEAGAQGAPGPAGPAGERGEQGPAGSPGFQGLPGPAGPPGEAGKPGEQGVPGDLGAPGPSGARGERGFPGERGVQGPPGPAGPRGNNGAPGNDGAKGDTGAPGAPGSQGAPGLQGMPGERGAAGLPGPKGDRGDAGPKGADGSPGKDGVRGLTGPIGPPGPAGAPGDKGETGPSGPAGPTGARGAPGDRGEPGPPGPAGFAGPPGADGQPGAKGEPGDTGVKGDAGPPGPAGPAGPPGPIGNVGAPGPKGTRGAAGPPGATGFPGAAGRVGPPGPSGNAGPPGPPGPVGKEGGKGPRGETGPAGRPGEVGPPGPPGPAGEKGSPGADGPAGSPGTPGPQGIAGQRGVVGLPGQRGERGFPGLPGPSGEPGKQGPSGASGERGPPGPMGPPGLAGPPGESGREGSPGAEGSPGRDGAPGAKGDRGETGPAGPPGAPGAPGAPGPVGPAGKNGDRGETGPAGPAGPIGPAGARGPAGPQGPRGDKGETGEQGDRGIKGHRGFSGLQGPPGSPGSPGEQGPSGASGPAGPRGPPGSAGSPGKDGLNGLPGPIGPPGPRGRTGDSGPAGPPGPPGPPGPPGPPSGGYDFSFLPQPPQEKSQDGGRYYRADDANVVRDRDLEVDTTLKSLSQQIENIRSPEGSRKNPARTCRDLKMCHSDWKSGEYWIDPNQGCNLDAIKVYCNMETGQTCVFPTQPSVPQKNWYISPNPKEKTHIWFGESMSGGFQFEYGSEGSDPADVAIQLTFLRLMSTEASQNITYHCKNSVAYMDQQTGNLKKSLLLQGSNEIELRGEGNSRFTYSTLVDGCTSHTGTWGKTVIEYKTTKTSRLPIIDVAPLDIGAPDQEFGMDVGPACFV
+>XP_032762867.1 OS=Rattus rattus OX=10117 GN=COL1A2
+MLSFVDTRTLLLLAVTSCLATCQSLQMGSVRKGPTGDRGPRGQRGPAGPRGRDGVDGPVGPPGPAGAPGPPGPPGPPGLTGNFAAQYSDKGVSAGPGPMGLMGPRGPPGAVGAPGPQGFQGPAGEPGEPGQTGPAGSRGPAGPPGKAGEDGHPGKPGRPGERGVVGPQGARGFPGTPGLPGFKGIRGHNGLDGLKGQPGAQGVKGEPGAPGENGTPGQAGARGLPGERGRVGAPGPAGARGSDGSVGPVGPAGPIGSAGPPGFPGAPGPKGELGPVGNPGPAGPAGPRGEAGLPGLSGPVGPPGNPGANGLTGAKGATGLPGVAGAPGLPGPRGIPGPVGAAGATGPRGLVGEPGPAGSKGETGNKGEPGSAGAQGPPGPSGEEGKRGSPGEPGSAGPAGPPGLRGSPGSRGLPGADGRAGVMGPPGNRGSTGPAGVRGPNGDAGRPGEPGLMGPRGLPGSPGNVGPAGKEGPVGLPGIDGRPGPIGPAGPRGEAGNIGFPGPKGPSGDPGKPGEKGHPGLAGARGAPGPDGNNGAQGPPGPQGVQGGKGEQGPAGPPGFQGLPGPSGTAGEVGKPGERGLPGEFGLPGPAGPRGERGPPGESGAAGPSGPIGSRGPSGAAGPDGNKGEAGAVGAPGSAGASGPGGLPGERGAAGIPGGKGEKGETGLRGEIGNPGRDGARGAPGAIGAPGPAGASGDRGEAGAAGPSGPAGPRGSPGERGEVGPAGPNGFAGPAGSAGQPGAKGEKGTKGPKGENGIVGPTGPVGAAGPSGPNGPPGPAGTRGDGGPPGMTGFPGAAGRTGPPGPSGITGPPGPPGAAGKEGIRGPRGDQGPVGRTGEIGASGPPGFAGEKGPSGEPGTAGPPGTAGPQGLLGAPGILGLPGSRGERGLPGIAGALGEPGPLGIAGPPGARGPPGAVGSPGVNGAPGEAGRDGNPGSDGPPGRDGQPGHKGERGYPGNIGPTGAAGAPGPHGSVGPAGKHGNRGEPGPAGSVGPVGAVGPRGPSGPQGIRGDKGEPGDKGARGLPGLKGHNGLQGLPGLAGLHGDQGAPGPVGPAGPRGPAGPSGPVGKDGRSGHPGPVGPAGVRGSQGSQGPAGPPGPPGPPGPPGVSGGGYDFGFEGDFYRADQPRSQPSLRPKDYEVDATLKSLNNQIETLLTPEGSKKNPARTCRDLRLSHPEWKSDYYWIDPNQGCTMDAIKVYCDFSTGETCIQAQPVNTPAKNAYSRAQANKHVWLGETINGGSQFEYNAEGVSSKEMATQLAFMRLLANRASQNITYHCKNSIAYLDEETGRLNKAVILQGSNDVELVAEGNSRFTYTVLVDGCSKKTNEWDKTIIEYKTNKPSRLPFLDIAPLDIGGANQEFRVEVGPVCFK
+>NP_445756.1 OS=Rattus norvegicus OX=10116 GN=COL1A1 
+MFSFVDLRLLLLLGATALLTHGQEDIPEVSCIHNGLRVPNGETWKPDVCLICICHNGTAVCDGVLCKEDLDCPNPQKREGECCPFCPEEYVSPDAEVIGVEGPKGDPGPQGPRGPVGPPGQDGIPGQPGLPGPPGPPGPPGPPGLGGNFASQMSYGYDEKSAGVSVPGPMGPSGPRGLPGPPGAPGPQGFQGPPGEPGEPGASGPMGPRGPPGPPGKNGDDGEAGKPGRPGERGPPGPQGARGLPGTAGLPGMKGHRGFSGLDGAKGDTGPAGPKGEPGSPGENGAPGQMGPRGLPGERGRPGPPGSAGARGNDGAVGAAGPPGPTGPTGPPGFPGAAGAKGEAGPQGARGSEGPQGVRGEPGPPGPAGAAGPAGNPGADGQPGAKGANGAPGIAGAPGFPGARGPSGPQGPSGAPGPKGNSGEPGAPGNKGDTGAKGEPGPAGVQGPPGPAGEEGKRGARGEPGPSGLPGPPGERGGPGSRGFPGADGVAGPKGPAGERGSPGPAGPKGSPGEAGRPGEAGLPGAKGLTGSPGSPGPDGKTGPPGPAGQDGRPGPAGPPGARGQAGVMGFPGPKGTAGEPGKAGERGVPGPPGAVGPAGKDGEAGAQGAPGPAGPAGERGEQGPAGSPGFQGLPGPAGPPGEAGKPGEQGVPGDLGAPGPSGARGERGFPGERGVQGPPGPAGPRGNNGAPGNDGAKGDTGAPGAPGSQGAPGLQGMPGERGAAGLPGPKGDRGDAGPKGADGSPGKDGVRGLTGPIGPPGPAGAPGDKGETGPSGPAGPTGARGAPGDRGEPGPPGPAGFAGPPGADGQPGAKGEPGDTGVKGDAGPPGPAGPAGPPGPIGNVGAPGPKGSRGAAGPPGATGFPGAAGRVGPPGPSGNAGPPGPPGPVGKEGGKGPRGETGPAGRPGEVGPPGPPGPAGEKGSPGADGPAGSPGTPGPQGIAGQRGVVGLPGQRGERGFPGLPGPSGEPGKQGPSGASGERGPPGPMGPPGLAGPPGESGREGSPGAEGSPGRDGAPGAKGDRGETGPAGPPGAPGAPGAPGPVGPAGKNGDRGETGPAGPAGPIGPAGARGPAGPQGPRGDKGETGEQGDRGIKGHRGFSGLQGPPGSPGSPGEQGPSGASGPAGPRGPPGSAGSPGKDGLNGLPGPIGPPGPRGRTGDSGPAGPPGPPGPPGPPGPPSGGYDFSFLPQPPQEKSQDGGRYYRADDANVVRDRDLEVDTTLKSLSQQIENIRSPEGSRKNPARTCRDLKMCHSDWKSGEYWIDPNQGCNLDAIKVYCNMETGQTCVFPTQPSVPQKNWYISPNPKEKKHVWFGESMTDGFQFEYGSEGSDPADVAIQLTFLRLMSTEASQNITYHCKNSVAYMDQQTGNLKKSLLLQGSNEIELRGEGNSRFTYSTLVDGCTSHTGTWGKTVIEYKTTKTSRLPIIDVAPLDIGAPDQEFGMDIGPACFV
+>NP_445808.2 OS=Rattus norvegicus OX=10116 GN=COL1A2  
+MLSFVDTRTLLLLAVTSCLATCQSLQMGSVRKGPTGDRGPRGQRGPAGPRGRDGVDGPVGPPGPPGAPGPPGPPGPPGLTGNFAAQYSDKGVSAGPGPMGLMGPRGPPGAVGAPGPQGFQGPAGEPGEPGQTGPAGSRGPAGPPGKAGEDGHPGKPGRPGERGVVGPQGARGFPGTPGLPGFKGIRGHNGLDGLKGQPGAQGVKGEPGAPGENGTPGQAGARGLPGERGRVGAPGPAGARGSDGSVGPVGPAGPIGSAGPPGFPGAPGPKGELGPVGNPGPAGPAGPRGEAGLPGLSGPVGPPGNPGANGLTGAKGATGLPGVAGAPGLPGPRGIPGPVGAAGATGPRGLVGEPGPAGSKGETGNKGEPGSAGAQGPPGPSGEEGKRGSPGEPGSAGPAGPPGLRGSPGSRGLPGADGRAGVMGPPGNRGSTGPAGVRGPNGDAGRPGEPGLMGPRGLPGSPGNVGPAGKEGPVGLPGIDGRPGPIGPAGPRGEAGNIGFPGPKGPSGDPGKPGEKGHPGLAGARGAPGPDGNNGAQGPPGPQGVQGGKGEQGPAGPPGFQGLPGPSGTAGEVGKPGERGLPGEFGLPGPAGPRGERGPPGESGAAGPSGPIGSRGPSGAPGPDGNKGEAGAVGAPGSAGASGPGGLPGERGAAGIPGGKGEKGETGLRGEIGNPGRDGARGAPGAIGAPGPAGASGDRGEAGAAGPSGPAGPRGSPGERGEVGPAGPNGFAGPAGSAGQPGAKGEKGTKGPKGENGIVGPTGPVGAAGPSGPNGPPGPAGSRGDGGPPGMTGFPGAAGRTGPPGPSGITGPPGPPGAAGKEGIRGPRGDQGPVGRTGEIGASGPPGFAGEKGPSGEPGTTGPPGTAGPQGLLGAPGILGLPGSRGERGLPGIAGALGEPGPLGIAGPPGARGPPGAVGSPGVNGAPGEAGRDGNPGSDGPPGRDGQPGHKGERGYPGNIGPTGAAGAPGPHGSVGPAGKHGNRGEPGPAGSVGPVGAVGPRGPSGPQGIRGDKGEPGDKGARGLPGLKGHNGLQGLPGLAGLHGDQGAPGPVGPAGPRGPAGPSGPIGKDGRSGHPGPVGPAGVRGSQGSQGPAGPPGPPGPPGPPGVSGGGYDFGFEGDFYRADQPRSQPSLRPKDYEVDATLKSLNNQIETLLTPEGSRKNPARTCRDLRLSHPEWKSDYYWIDPNQGCTMDAIKVYCDFSTGETCIQAQPVNTPAKNAYSRAQANKHVWLGETINGGSQFEYNAEGVSSKEMATQLAFMRLLANRASQNITYHCKNSIAYLDEETGRLNKAVILQGSNDVELVAEGNSRFTYTVLVDGCSKKTNEWDKTIIEYKTNKPSRLPFLDIAPLDIGGTNQEFRVEVGPVCFK
+
+

www/html/pampa/data_pampa/homology_peptides.tsv

+Taxon name	Sequence	PTM	Marker	Gene
+Meles meles	GLPGEFGLPGPAGPR	2H	COL1A2-484/B	COL1A2
+Meles meles	GLPGVSGSVGEPGPLGIAGPPGAR	3H	COL1A2-793/D	COL1A2
+Meles meles	GLTGPIGPPGPAGAPGDKGEAGPSGPAGPTGAR	2H	COL1A1-586/F	COL1A1
+Meles meles	GLTGPIGPPGPAGAPGDKGEAGPSGPAGPTGAR	3H	COL1A1-586/F	COL1A1
+Meles meles	GPNGEAGSTGPSGPPGLR	2H	COL1A2-292/P2	COL1A2
+Meles meles	GPPGESGAAGPSGPIGSR	1H	COL1A2-502/C	COL1A2
+Meles meles	GPSGEAGTAGPPGTPGPQGLLGAPGILGLPGSR	4H	COL1A2-757/G	COL1A2
+Meles meles	GPSGEAGTAGPPGTPGPQGLLGAPGILGLPGSR	5H	COL1A2-757/G	COL1A2
+Meles meles	GVQGPPGPAGPR	1H	COL1A1-508/P1	COL1A1
+Meles meles	TGHPGTVGPAGIR	0H	COL1A2-978/A	COL1A2
+Meles meles	TGHPGTVGPAGIR	1H	COL1A2-978/A	COL1A2
\ No newline at end of file