Merge pull request #446 from Proteobench/444-replace-mass-shifts-in-p…

…eptide-proforma-strings-during-fragpipe-and-sage-parsing-with-modification-names homogenise peptidoform strings in DDA result files
Proteobench · Nov 22, 2024 · 1e1710e · 1e1710e
2 parents 498fa27 + f4ec6cb
commit 1e1710e
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/proteobench/io/parsing/io_parse_settings/parse_settings_fragpipe.toml b/proteobench/io/parsing/io_parse_settings/parse_settings_fragpipe.toml
@@ -29,7 +29,7 @@
 "before_aa" = false
 "isalpha" = true
 "isupper" = true
-"pattern"="\\[([^]]+)\\]"
+"pattern"="(?<=\\[).+?(?=\\])"
 "modification_dict" = {"57.0215" = "Carbamidomethyl", "57.0216" = "Carbamidomethyl", "15.9949" = "Oxidation", "-17.026548" = "Gln->pyro-Glu", "-18.010565" = "Glu->pyro-Glu", "42.0106" = "Acetyl"}
 
 [general]

diff --git a/proteobench/io/parsing/io_parse_settings/parse_settings_sage.toml b/proteobench/io/parsing/io_parse_settings/parse_settings_sage.toml
@@ -29,7 +29,7 @@
 "before_aa" = false
 "isalpha" = true
 "isupper" = true
-"pattern"="\\[([^]]+)\\]"
+"pattern"="(?<=\\[).+?(?=\\])"
 "modification_dict" = {"+57.0215" = "Carbamidomethyl", "+15.9949" = "Oxidation", "-17.026548" = "Gln->pyro-Glu", "-18.010565" = "Glu->pyro-Glu", "+42" = "Acetyl"}
 
 [general]

diff --git a/proteobench/io/parsing/parse_ion.py b/proteobench/io/parsing/parse_ion.py
@@ -13,7 +13,7 @@ def load_input_file(input_csv: str, input_format: str) -> pd.DataFrame:
     if input_format == "MaxQuant":
         input_data_frame = pd.read_csv(input_csv, sep="\t", low_memory=False)
     elif input_format == "AlphaPept":
-        input_data_frame = pd.read_csv(input_csv, low_memory=False)
+        input_data_frame = pd.read_csv(input_csv, low_memory=False, dtype={"charge": int})
     elif input_format == "Sage":
         input_data_frame = pd.read_csv(input_csv, sep="\t", low_memory=False)
     elif input_format == "FragPipe":