| Previous changeset 1:0b09345fa632 (2020-09-14) Next changeset 3:dd0f4da5f68f (2020-09-15) |
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Commit message:
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modified:
src/General_functions.py |
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| diff -r 0b09345fa632 -r ccca6ad98f78 src/General_functions.py --- a/src/General_functions.py Mon Sep 14 13:16:28 2020 +0000 +++ b/src/General_functions.py Mon Sep 14 13:17:45 2020 +0000 |
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| @@ -1,5 +1,6 @@ import re import numpy as np +import galaxy.model def get_column_names( file_path, toNotConsider=-1, each=1): options=[] @@ -76,7 +77,7 @@ def get_condition_file_names( file_list, toNotConsider=-1, each=1): options=[] - if not isinstance(file_list,list):#if input file is a tabular file, act as get_column_names + if not (isinstance(file_list,list) or isinstance(file_list,galaxy.model.HistoryDatasetCollectionAssociation) or isinstance(file_list,galaxy.model.DatasetCollection)) :#if input file is a tabular file, act as get_column_names inputfile = open(file_list.file_name) firstLine = next(inputfile).strip().split("\t") cpt=0 @@ -88,13 +89,17 @@ if cpt==each: cpt=0 inputfile.close() - else:#if input file is a .cel file list or a collection - if not hasattr(file_list[0],'collection'):#if it is not a collection, get name easily - for i, field_component in enumerate( file_list ): - options.append( ( field_component.name, field_component.name, False ) ) - else:#if the file is a collection, have to get deeper in the corresponding HistoryDatasetCollectionAssociation object - for i, field_component in enumerate( file_list[0].collection.elements ): - options.append( ( field_component.element_identifier, field_component.element_identifier, False ) ) + else:#if input file is a .cel file list, a DatasetCollection or a HistoryDatasetCollectionAssociation + if isinstance(file_list,list):#if it is a list, retrieve names easily + for i, field_component in enumerate( file_list ): + options.append( ( field_component.name, field_component.name, False ) ) + else:#if the file is a DatasetCollection, have to get deeper in the corresponding DatasetCollection object + if isinstance(file_list,galaxy.model.DatasetCollection):#if it is a list, retrieve names easily + for i, field_component in enumerate( file_list.elements ): + options.append( ( field_component.element_identifier, field_component.element_identifier, False ) ) + else:#if the file is a HistoryDatasetCollectionAssociation, have to get a little bit deeper in the corresponding HistoryDatasetCollectionAssociation object + for i, field_component in enumerate( file_list.collection.elements ): + options.append( ( field_component.element_identifier, field_component.element_identifier, False ) ) return options def generateFactorFile( file_list, factor_list, outputFileName, logFile): @@ -102,10 +107,7 @@ outputfile = open(outputFileName, 'w') outputLog = open(logFile, 'w') sampleList=[] - if not isinstance(file_list,list): - conditionNames=get_condition_file_names(file_list,0) #unique expression file, remove the first column (index=0) - else : - conditionNames=get_condition_file_names(file_list) #.CEL files + conditionNames=get_condition_file_names(file_list,0) #if it's a unique expression file, remove the first column (index=0) for iSample, sample_component in enumerate (conditionNames): sampleList.append(str(sample_component[1])) outputLog.write("[INFO] "+str(len(sampleList))+" sample are detected as input\n") |