Commit 64a72f6d authored by Mathieu Courcelles's avatar Mathieu Courcelles

Fixes support for Kojak 1.6.1 (Issue #27)

Issue with intra-peptide cross-link
parent 1760bc1b
Pipeline #15071256 passed with stage
in 2 minutes and 18 seconds
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......@@ -162,8 +162,7 @@ class KojakParser:
fields['display_protein2'] = result.group(1)
fields['peptide_position2'] = int(result.group(2)) - int(fields['pep2_link_pos']) + 1
if fields['peptide_position2'] == -1 and fields['pep2_link_pos'] != -1:
fields['peptide_position2'] = fields['peptide_position1']
fields['autovalidated'] = False
fields['validated'] = ''
......@@ -212,6 +211,9 @@ class KojakParser:
clpep.peptide_position2 = clpep.fs_prot2_id.sequence.find(fields['peptide_wo_mod2']) + 1
pep_pos_dict[key] = clpep.peptide_position2
if fields['peptide_position2'] == -1 and fields['pep2_link_pos'] != -1:
fields['peptide_position2'] = fields['peptide_position1']
clpep.guessLinkType()
# clpep.id = next_id
......
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