diff --git a/sdrf_pipelines/__init__.py b/sdrf_pipelines/__init__.py index 5a6b518d..15331024 100644 --- 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 index 4e6c876a..a01a8b6f 100644 --- 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 index 59d02e16..18b9223c 100644 --- 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 index f4f34abc..52816c8a 100644 --- 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 index ace77e15..a19a890e 100644 --- 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