Sequence annotation pipeline user Kantale
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[edit] Documentation
Documentation for Sequence annotation pipeline
[edit] Parameters
<inputs> </inputs>
[edit] Return
[edit] See also
[edit] Code
def Sequence_annotation_pipeline_user_Kantale( input_filename = None, constants = None, temp_dir = None, results_dir = None, chromosome_column_of_input = 0, start_column_of_input = 1, end_column_of_input = 2, reference_column_of_input = 3, observed_column_of_input = 4, use_first_line_from_input_as_header = True, buildver = "hg18", gene_based_annotations = "refgene,knowngene,ensgene", region_based_annotations = "band,segdup,dgv,gwascatalog", filter_based_annotations = "snp130", custom_annotations = None, ): #Input check if type(use_first_line_from_input_as_header).__name__ != "bool": raise Exception("use_first_line_from_input_as_header need to be defined") if not use_first_line_from_input_as_header: raise Exception("use_first_line_from_input_as_header should be True. Input should have a header.") if buildver != "hg18": raise Exception("Build version: " + str(buildver) + " is not supported") lock_filename = temp_dir + "/delete.me" lock_file = open(lock_filename, "w") lock_file.close() pipeline = [] pipeline += [{ "name" : "push the button", "command" : "Wait_while_file_exists", "params" : { "filename" : lock_filename }, "prereq" : [], "mem" : "1GB", "walltime" : "1:00:00", }] pipeline += [{ "name" : "Annotate with annovar", "command" : "AnnotateTABFilenameViaANNOVAR", "params" : { "pathToANNOVAR" : constants["path_to_annovar"], "outputDirectory" : results_dir, "outputFilename" : "output_annovar.txt", "buildver" : buildver, "inputFilename" : input_filename, "chromosomeColumnOfInputFilename" : chromosome_column_of_input, "startColumnOfInputFilename" : start_column_of_input, "endColumnOfInputFilename" : end_column_of_input, "referenceColumnOfInputFilename" : reference_column_of_input, "observedColumnOfInputFilename" : observed_column_of_input, "useFirstLineFromInputAsHeader" : use_first_line_from_input_as_header, "annotationDirectory" : constants["path_to_annovar_annotation_files_hg18"], "geneBasedAnnotations" : gene_based_annotations, "regionBasedAnnotations" : region_based_annotations, "filterBasedAnnotations" : filter_based_annotations, "customAnnotations" : custom_annotations, "pbsStats" : None, }, "prereq" : ["push the button"], "mem" : "4GB", "walltime" : "4:00:00", }] pipeline += [{ "name" : "Geno Ontology Annotation", "command" : "AnnotateListOfChromosomePositionFilesWithGOFromBioMartEnsembl", "params" : { "listOfFilesToAnnotate" : [results_dir + "/output_annovar.txt"], "numberOfFirstLinesToIgnoreInFileToAnnotate" : [1], "chromosomeColumnOfFilesToAnnotate" : [0], "positionColumnOfFilesToAnnotate" : [1], "fileWithGOAnnotation" : constants["path_to_gene_ontology_36"], "fileWithGOAnnotationChromosomeColumn" : 1, "fileWithGOAnnotationStartColumn" : 2, "fileWithGOAnnotationEndColumn" : 3, "columnsWithGOAnnotationComaSeparated" : "4,5,6,7,8,9", "numberOfFirstLinesToIgnoreInGOAnnotationFile" : 1, "outputDirectory" : results_dir, "outputFilename" : "output_GO", }, "prereq" : ["Annotate with annovar"], "mem" : "4GB", "walltime" : "4:00:00", }] pipeline += [{ "name" : "Allele Frequencies Annotation", "command" : "AnnotateTABFileWithAlleleFrequencies", "params" : { "filesToBeAnnotated" : [results_dir + "/output_GO.GO"], "chromosomeColumnOfFileToBeAnnotated" : 0, "positionColumnOfFileToBeAnnotated" : 1, "readHeaderFromFirstLineFromFileToBeAnnotated" : True, "alleleFrequencyFiles" : None, "outputFilenames" : results_dir + "/output.txt", }, "prereq" : ["Geno Ontology Annotation"], "mem" : "4GB", "walltime" : "4:00:00", }] return pipeline
[edit] Unit Tests
def uni1(): return True
[edit] Development Code
def Sequence_annotation_pipeline_user_Kantale(): pass
[edit] Permissions
[edit] Documentation Permissions
Kantale
[edit] Code Permissions
Kantale
[edit] Unit Tests Permissions
Kantale
