Delete src/main_build.py

src/main_build.py

-"""
-main_build.py
-
-building new markers and new peptide tables
-""" 
-import os
-import time
-import sys
-
-# local import
-from src import markers
-from src import sequences 
-from src import known_markers 
-from src import fasta_parsing as fa
-from src import peptide_table as pt
-
-def escape(message):
-    print("\n "+message)
-    sys.exit(" Stopping execution.\n\n Type <pampa build -h> for more help.\n")
-
-
-def check_and_update_parameters(peptide_table, fasta, directory, limit, output):
-    """
-    Parameters checking and fixing
-    """
-    
-    if output is None:
-        escape("Missing parameter: output (-o).")
-    output_dir, output_file = os.path.split(output)
-    # Ensure the output directory exists
-    if len(output_dir)>0 and not os.path.exists(output_dir):
-        os.makedirs(output_dir)
-    extension=output_file[-4:].lower()
-    if extension!=".tsv":
-        output_file=output_file+".tsv"
-    else:
-        output_file=output_file[:-4]+".tsv"
-    output=os.path.join(output_dir, output_file)
-    report_file="report_"+output_file.replace("tsv", "txt")
-    report=os.path.join(output_dir, report_file)
-
-    if peptide_table is None:
-        escape("Missing parameter: peptide_table (-p)")
-    for pep in peptide_table:
-            if not os.path.isfile(pep):
-                escape("File "+pep+" not found.")    
-    if limit:
-        if not os.path.isfile(limit):
-            escape("File "+limit+" not found (-l).")            
-        
-    q = (fasta, directory)
-    if not (q[0] or q[1] ):
-        escape("Missing target sequences (-f or -d).")
-    if (q[0] and q[1])  :
-        escape("Options -f (fasta file) and -d (directory of fasta files) are mutually exclusive.")
-    if q[0]:
-        if not os.path.isfile(fasta):
-           escape("File "+fasta+" not found (-f).")
-    if q[1]:
-        if not os.path.isdir(directory):
-            escape("Directory "+directory+" not found (-d).")
-            
-    return (peptide_table, fasta, directory, limit, output, report)
-
-
-def create_report(report, output, peptide_table, fasta,  directory, limit,  set_of_markers, set_of_new_markers):
-    
-    sys.stdout=open(report, 'w')
-    print (time.ctime())
-    print("")
-    print("---------------------------------")
-    print("   PARAMETERS")
-    print("---------------------------------\n")
-    if peptide_table:
-        print("  Peptide table for model markers : ", end="")
-        for file in peptide_table:
-            print(file, end=" ")
-        print("")
-    if fasta:
-        print("  Fasta file for new markers      : "+str(fasta))
-    else:
-        print("  Fasta file for new markers      : "+str(directory))
-    if limit:
-        print("  Limited to                      : "+ limit)
-        
-    print("")
-    print("---------------------------------")
-    print("   OUTPUT FILES")
-    print("---------------------------------\n")
-    print("  Main result file (TSV)   : "+output)
-    print("  Report (this file)       : "+report)
-
-    print("")
-    print("---------------------------------")
-    print("  NEW MARKERS FOR FASTA FILES ")
-    print("---------------------------------\n")
-    markers.colinearity(set_of_new_markers)
-    markers.check_set_of_markers(set_of_new_markers)
-    
-    sys.stdout = sys.__stdout__
-    
-
-
-# a faire : calcul de la masse en option ?
-
-def main(peptide_table=None, fasta=None, directory=None, limit=None, output=None):
-    
-    (peptide_table, fasta, directory, limit, output, report)=check_and_update_parameters(peptide_table, fasta, directory, limit, output)
-
-    set_of_markers= pt.parse_peptide_tables(peptide_table, None, None)
-    set_of_sequences = fa.build_set_of_sequences(fasta, directory, limit, None)      
-    set_of_new_markers=known_markers.find_markers_all_sequences(set_of_sequences, set_of_markers)
-
-    pt.build_peptide_table_from_set_of_markers(set_of_new_markers,output,"")
-
-    create_report(report, output, peptide_table, fasta, directory, limit, set_of_markers, set_of_new_markers)
-
-    print("")
-    print("   Job completed.")
-    print("   All results are available in the two following files.") 
-    print("")
-    print(f"   - New markers       : {output}")
-    print(f"   - Report on the run : {report}")
-    print("")