Merge pull request #20 from wfondrie/mod_parsing

Fixed problem with parsing modifications from pepXML.
wfondrie · Mar 11, 2021 · 50431f1 · 50431f1
2 parents 2aa978c + 7ca986f
commit 50431f1
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,10 +1,12 @@
 # Changelog for mokapot  
 
-## [Unreleased]
+## [0.6.1] - 2021-03-11
 ### Fixed
 - Parsing Percolator tab-delimited files with a "DefaultDirection" line.
 - `Label` column is now converted to boolean during PIN file parsing. 
   Previously, problems occurred if the `Label` column was of dtype `object`.
+- Parsing modifications from pepXML files were indexed incorrectly on the
+  peptide string.
 
 ## [0.6.0] - 2021-03-03  
 ### Added  

diff --git a/mokapot/parsers/pepxml.py b/mokapot/parsers/pepxml.py
@@ -253,6 +253,7 @@ def _parse_psm(psm_info, spec_info, decoy_prefix):
                 idx = offset + int(mod.get("position"))
                 mass = mod.get("mass")
                 mod_pep = mod_pep[:idx] + "[" + mass + "]" + mod_pep[idx:]
+                offset += 2 + len(mass)
 
             psm["peptide"] = mod_pep