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Commit 173d4627 authored by Hottlet Valentin's avatar Hottlet Valentin
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test2.py

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NP_031768.2 OS=Mus musculus OX=10090 GN=COL1A1
NP_031769.2 OS=Mus musculus OX=10090 GN=COL1A2
XP_032768589.1 OS=Rattus rattus OX=10117 GN=COL1A1
XP_032762867.1 OS=Rattus rattus OX=10117 GN=COL1A2
NP_445756.1 OS=Rattus norvegicus OX=10116 GN=COL1A1
NP_445808.2 OS=Rattus norvegicus OX=10116 GN=COL1A2
constraints:0
hard sequences:6
soft sequences:0
soft constraints:0
NP_031768.2 OS=Mus musculus OX=10090 GN=COL1A1
NP_031769.2 OS=Mus musculus OX=10090 GN=COL1A2
XP_032768589.1 OS=Rattus rattus OX=10117 GN=COL1A1
XP_032762867.1 OS=Rattus rattus OX=10117 GN=COL1A2
NP_445756.1 OS=Rattus norvegicus OX=10116 GN=COL1A1
NP_445808.2 OS=Rattus norvegicus OX=10116 GN=COL1A2
constraints:0
hard sequences:6
soft sequences:0
soft constraints:0
No taxonomy provided. Unable to apply TAXONOMY completion. No taxonomy provided. Unable to apply TAXONOMY completion.
NP_031768.2 OS=Mus musculus OX=10090 GN=COL1A1 NP_031768.2 OS=Mus musculus OX=10090 GN=COL1A1
NP_031769.2 OS=Mus musculus OX=10090 GN=COL1A2 NP_031769.2 OS=Mus musculus OX=10090 GN=COL1A2
...@@ -41,7 +21,6 @@ hard sequences:6 ...@@ -41,7 +21,6 @@ hard sequences:6
soft sequences:0 soft sequences:0
soft constraints:0 soft constraints:0
No taxonomy provided. Unable to apply TAXONOMY completion. No taxonomy provided. Unable to apply TAXONOMY completion.
No taxonomy provided. Unable to apply TAXONOMY completion.
File test/table_mouse_ABC.tsv, line 5: wrong mass, 1592,8. Ignored. File test/table_mouse_ABC.tsv, line 5: wrong mass, 1592,8. Ignored.
NP_031768.2 OS=Mus musculus OX=10090 GN=COL1A1 NP_031768.2 OS=Mus musculus OX=10090 GN=COL1A1
NP_031769.2 OS=Mus musculus OX=10090 GN=COL1A2 NP_031769.2 OS=Mus musculus OX=10090 GN=COL1A2
...@@ -54,18 +33,6 @@ hard sequences:6 ...@@ -54,18 +33,6 @@ hard sequences:6
soft sequences:0 soft sequences:0
soft constraints:0 soft constraints:0
No taxonomy provided. Unable to apply TAXONOMY completion. No taxonomy provided. Unable to apply TAXONOMY completion.
File test/table_mouse_ABC.tsv, line 5: wrong mass, 1592,8. Ignored.
NP_031768.2 OS=Mus musculus OX=10090 GN=COL1A1
NP_031769.2 OS=Mus musculus OX=10090 GN=COL1A2
XP_032768589.1 OS=Rattus rattus OX=10117 GN=COL1A1
XP_032762867.1 OS=Rattus rattus OX=10117 GN=COL1A2
NP_445756.1 OS=Rattus norvegicus OX=10116 GN=COL1A1
NP_445808.2 OS=Rattus norvegicus OX=10116 GN=COL1A2
constraints:0
hard sequences:6
soft sequences:0
soft constraints:0
File test/table_mouse_ABC.tsv, line 5: wrong mass, 1592,8. Ignored.
NP_031768.2 OS=Mus musculus OX=10090 GN=COL1A1 NP_031768.2 OS=Mus musculus OX=10090 GN=COL1A1
NP_031769.2 OS=Mus musculus OX=10090 GN=COL1A2 NP_031769.2 OS=Mus musculus OX=10090 GN=COL1A2
XP_032768589.1 OS=Rattus rattus OX=10117 GN=COL1A1 XP_032768589.1 OS=Rattus rattus OX=10117 GN=COL1A1
...@@ -76,15 +43,5 @@ constraints:0 ...@@ -76,15 +43,5 @@ constraints:0
hard sequences:6 hard sequences:6
soft sequences:0 soft sequences:0
soft constraints:0 soft constraints:0
Mus musculus: multiple peptides found for 1592.8.
No taxonomy provided. Unable to apply TAXONOMY completion. No taxonomy provided. Unable to apply TAXONOMY completion.
File test/table_mouse_ABC.tsv, line 5: wrong mass, 1592,8. Ignored.
NP_031768.2 OS=Mus musculus OX=10090 GN=COL1A1
NP_031769.2 OS=Mus musculus OX=10090 GN=COL1A2
XP_032768589.1 OS=Rattus rattus OX=10117 GN=COL1A1
XP_032762867.1 OS=Rattus rattus OX=10117 GN=COL1A2
NP_445756.1 OS=Rattus norvegicus OX=10116 GN=COL1A1
NP_445808.2 OS=Rattus norvegicus OX=10116 GN=COL1A2
constraints:0
hard sequences:6
soft sequences:0
soft constraints:0
Taxon name Marker Sequence Mass PTM Hel Length Gene Digestion Taxon name Marker Sequence Mass PTM Hel Length Gene Digestion
Mus musculus P2 GSPGEAGSAGPAGPPGLR 1566.75067512066 2H 292 18 COL1A2 Yes Mus musculus P2 GSPGEAGSAGPAGPPGLR 1566.75067512066 2H 292 18 COL1A2 Yes
Rattus norvegicus P2 GSPGEPGSAGPAGPPGLR 1608.7612401848 3H 292 18 COL1A2 Yes
Rattus rattus P2 GSPGEPGSAGPAGPPGLR 1608.7612401848 3H 292 18 COL1A2 Yes
...@@ -4,11 +4,70 @@ ...@@ -4,11 +4,70 @@
============================================ ============================================
Fri Mar 21 13:30:02 2025 Fri Mar 21 14:46:48 2025
--------------------------------- ---------------------------------
PARAMETERS PARAMETERS
--------------------------------- ---------------------------------
Incomplete fields Incomplete fields
{'Sequence', 'End', 'PTM', 'SeqID', 'Begin', 'Mass', 'GN', 'Hel'} {'Digestion', 'Sequence', 'PTM', 'Mass', 'OS'}
DIGESTION
Mode : SUPPLEMENT
---------------------------------
INPUT PEPTIDE TABLE
---------------------------------
['test/table_P2.tsv']
---------------------------------
INPUT SEQUENCES
---------------------------------
NP_031769.2 COL1A2 Mus musculus
NP_445808.2 COL1A2 Rattus norvegicus
NP_031768.2 COL1A1 Mus musculus
XP_032768589.1 COL1A1 Rattus rattus
XP_032762867.1 COL1A2 Rattus rattus
NP_445756.1 COL1A1 Rattus norvegicus
---------------------------------
NEW PEPTIDE TABLE
---------------------------------
Total number of species: 3
Gene : COL1A2
P2 - 2H P2 - 3H
Mus musculus NP_031769.2 388[1566.7507]
Rattus norvegicus NP_445808.2 388[1608.7612]
Rattus rattus XP_032762867.1 388[1608.7612]
---------------------------------
UNDISTINGUISHABLE SPECIES
---------------------------------
- Rattus rattus Rattus norvegicus
---------------------------------
INCLUSION OF SPECIES
---------------------------------
None
---------------------------------
WARNINGS
---------------------------------
Warnings were raised regarding your inputs.
- No taxonomy provided. Unable to apply TAXONOMY completion.
---------------------------------
OUTPUT FILES
---------------------------------
Main result file (TSV) : test/result/output_P2.tsv
Report (this file) : test/result/report_output_P2.txt
...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
============================================ ============================================
Fri Mar 21 13:29:56 2025 Fri Mar 21 14:42:08 2025
--------------------------------- ---------------------------------
PARAMETERS PARAMETERS
...@@ -32,5 +32,5 @@ Incomplete fields ...@@ -32,5 +32,5 @@ Incomplete fields
OUTPUT FILES OUTPUT FILES
--------------------------------- ---------------------------------
Main result file (TSV) : output_dog_G.tsv Main result file (TSV) : test/result/output_dog_G.tsv
Report (this file) : report_output_dog_G.txt Report (this file) : test/result/report_output_dog_G.txt
...@@ -4,11 +4,66 @@ ...@@ -4,11 +4,66 @@
============================================ ============================================
Fri Mar 21 13:30:38 2025 Fri Mar 21 14:49:54 2025
--------------------------------- ---------------------------------
PARAMETERS PARAMETERS
--------------------------------- ---------------------------------
Incomplete fields Incomplete fields
{'End', 'GN', 'Mass', 'Begin', 'PTM', 'Hel', 'Sequence', 'SeqID'} {'PTM', 'End', 'Hel', 'Begin', 'Sequence', 'SeqID'}
Mode : SUPPLEMENT
---------------------------------
INPUT PEPTIDE TABLE
---------------------------------
['test/table_mouse_ABC.tsv']
---------------------------------
INPUT SEQUENCES
---------------------------------
NP_031769.2 COL1A2 Mus musculus
XP_032762867.1 COL1A2 Rattus rattus
NP_031768.2 COL1A1 Mus musculus
NP_445808.2 COL1A2 Rattus norvegicus
XP_032768589.1 COL1A1 Rattus rattus
NP_445756.1 COL1A1 Rattus norvegicus
---------------------------------
NEW PEPTIDE TABLE
---------------------------------
Total number of species: 1
Gene : COL1A2
A - 0H A - 1H B - 2H C - 2H C - 3H
Mus musculus NP_031769.2 1074[1178.6276] 1074[1194.6226] 580[1453.7434] 985[1592.8027] 316[1592.8391]
---------------------------------
UNDISTINGUISHABLE SPECIES
---------------------------------
None
---------------------------------
INCLUSION OF SPECIES
---------------------------------
None
---------------------------------
WARNINGS
---------------------------------
Warnings were raised regarding your inputs.
- Mus musculus: multiple peptides found for 1592.8.
- No taxonomy provided. Unable to apply TAXONOMY completion.
---------------------------------
OUTPUT FILES
---------------------------------
Main result file (TSV) : test/result/output_mouse_ABC.tsv
Report (this file) : test/result/report_output_mouse_ABC.txt
Taxon name Marker Sequence Mass PTM Hel Length Gene Digestion Taxon name Marker Sequence Mass PTM Hel Length Gene Digestion
Mus musculus P2 292 18 COL1A2 P2 292 18 COL1A2
Taxon name Marker Sequence Mass PTM Hel Gene SeqID Begin End Taxon Marker Sequence Mass PTM Hel Gene SeqID Begin End
Mus musculus A 1178.6 COL1A2 Mus musculus A 1178.6 COL1A2
Mus musculus A 1194.6 COL1A2 Mus musculus A 1194.6 COL1A2
Mus musculus B 1453.7 COL1A2 Mus musculus B 1453.7 COL1A2
Mus musculus C 1592,8 COL1A2 Mus musculus C 1592.8 COL1A2
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