Merge pull request #165 from bigbio/ypriverol-patch-1

Update openms.py
bigbio · Apr 6, 2024 · fe1851e · fe1851e
2 parents 07c1dea + e9f50fe
commit fe1851e
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Showing 5 changed files with 7 additions and 8 deletions.
diff --git a/sdrf_pipelines/__init__.py b/sdrf_pipelines/__init__.py
@@ -1 +1 @@
-__version__ = "0.0.25"
+__version__ = "0.0.26"
diff --git a/sdrf_pipelines/normalyzerde/normalyzerde.py b/sdrf_pipelines/normalyzerde/normalyzerde.py
@@ -25,7 +25,6 @@ def convert_normalyzerde_design(
         sdrf.columns = map(str.lower, sdrf.columns)  # convert column names to lower-case
         data = {}
         condition = []
-        replicates = []
         runs = sdrf["comment[data file]"].tolist()
         source_names = sdrf["source name"].tolist()
 

diff --git a/sdrf_pipelines/openms/openms.py b/sdrf_pipelines/openms/openms.py
@@ -126,7 +126,9 @@ def __init__(self) -> None:
         self.enzymes = {
             "Glutamyl endopeptidase": "glutamyl endopeptidase",
             "Trypsin/p": "Trypsin/P",
+            "Trypchymo": "TrypChymo",
             "Lys-c": "Lys-C",
+            "Lys-c/p": "Lys-C/P",
             "Lys-n": "Lys-N",
             "Arg-c": "Arg-C",
             "Arg-c/p": "Arg-C/P",
@@ -424,7 +426,7 @@ def openms_convert(
 
         if not split_by_columns:
             # output of search settings for every row in sdrf
-            self.save_search_settings_to_file("openms.tsv", sdrf, f2c, extension_convert=extension_convert)
+            self.save_search_settings_to_file("openms.tsv", sdrf, f2c)
 
             # output one experimental design file
             if one_table:
@@ -458,7 +460,7 @@ def openms_convert(
                 # extract rows from sdrf for current condition
                 split_sdrf = sdrf.loc[sdrf["_conditions_from_factors"] == c]
                 output_filename = "openms.tsv." + str(index)
-                self.save_search_settings_to_file(output_filename, split_sdrf, f2c, extension_convert=extension_convert)
+                self.save_search_settings_to_file(output_filename, split_sdrf, f2c)
 
                 # output of experimental design
                 output_filename = "experimental_design.tsv." + str(index)
@@ -976,7 +978,7 @@ def writeOneTableExperimentalDesign(
         with open(output_filename, "w+") as of:
             of.write(f)
 
-    def save_search_settings_to_file(self, output_filename, sdrf, f2c, extension_convert):
+    def save_search_settings_to_file(self, output_filename, sdrf, f2c):
         f = ""
         open_ms_search_settings_header = [
             "URI",

diff --git a/sdrf_pipelines/sdrf/sdrf.py b/sdrf_pipelines/sdrf/sdrf.py
@@ -3,8 +3,6 @@
 import logging
 
 import pandas as pd
-from pandas import DataFrame
-from pandas._typing import PythonFuncType
 
 from sdrf_pipelines.sdrf.sdrf_schema import CELL_LINES_TEMPLATE
 from sdrf_pipelines.sdrf.sdrf_schema import HUMAN_TEMPLATE

diff --git a/sdrf_pipelines/zooma/ols.py b/sdrf_pipelines/zooma/ols.py
@@ -198,7 +198,7 @@ def search(
                                 bytype=bytype,
                                 rows=rows,
                                 num_retries=num_retries,
-                                start=(rows + (start)),
+                                start=(rows + start),
                             )
                         )
                         return docs_found