parseFeatureCounts module

parseFeatureCounts.parse_featureCounts(files, genes)[source]

Read a file and the sample ID and save gene_ids and tmp_values

Parameters

  • files – list of files

  • genes – dict mapping gene_ids to gene_names

Returns

counts_all_files list of lists

Returns

gene_dict of unique genes

Returns

geneLengths_all_files dict mapping ids to lengths

parseFeatureCounts.write_lengths(geneLengths_all_files, outpath)[source]

Create mini-table with gene-lengths from RNAseq pipeline from FeatureCounts output

Parameters

  • geneLengths_all_files – gene_ids mapped to gene_lengths

  • outpath – path where to store outfile, txt