Commit 9f5a7d5c authored by Mathieu Courcelles's avatar Mathieu Courcelles

Rollback changes for dead-end (Issue #27)

Dead end peptides are handled in Kojak parser and not in guess link
type.
parent 29a518a2
Pipeline #15351586 passed with stage
in 1 minute and 23 seconds
...@@ -522,8 +522,7 @@ class CLPeptide(AdminURLMixin, models.Model): ...@@ -522,8 +522,7 @@ class CLPeptide(AdminURLMixin, models.Model):
self.link_type = 'Linear peptide' self.link_type = 'Linear peptide'
deadend_keywords = ['bs3', 'bs2g', 'adh_oh', deadend_keywords = ['bs3', 'bs2g', 'adh_oh']
'[156.08]']
pepseq = self.peptide1 pepseq = self.peptide1
pepseq = re.sub('Cm', 'C', pepseq) pepseq = re.sub('Cm', 'C', pepseq)
......
...@@ -196,7 +196,7 @@ class KojakParser: ...@@ -196,7 +196,7 @@ class KojakParser:
clpep.peptide_position1 = clpep.fs_prot1_id.sequence.find(fields['peptide_wo_mod1']) + 1 clpep.peptide_position1 = clpep.fs_prot1_id.sequence.find(fields['peptide_wo_mod1']) + 1
pep_pos_dict[key] = clpep.peptide_position1 pep_pos_dict[key] = clpep.peptide_position1
# Check DSS dead end - this could be improved # Check DSS dead end - this could be improved
pepseq = re.sub('(K\[.+?\])', 'k', row['Peptide #1']) pepseq = re.sub('(K\[.+?\])', 'k', row['Peptide #1'])
pepseq = re.sub('(\[.+?\])', '', pepseq) pepseq = re.sub('(\[.+?\])', '', pepseq)
......
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