fileUtils package

Submodules

fileUtils.file_handling module

fileUtils.file_handling.get_files(inpath, ext)[source]

Create list of files

Parameters

  • inpath – to folder

  • ext – of files

Returns

files: list

fileUtils.file_handling.get_files_and_sample_ids(inpath, ext)[source]

Create list of files

Parameters

  • inpath – to files

  • ext – file extension

Returns

files: as list

Returns

sample_ids: as list

fileUtils.file_handling.parse_csv(files)[source]

Parse csv files

Parameters

files – list of files

Returns

srr_metadata: metadata dictionary

fileUtils.file_handling.read_tpm(infile)[source]

Reads TPM values from merged file into floats

Parameters

infile – merged TPM values

Returns

sample_ids

Returns

gene_ids

Returns

gene_names

Returns

data_list

fileUtils.file_handling.read_unique_genes(genes)[source]

Read genes from rnaseq pipeline

Parameters

genes – genes_id mapped to name

Returns

gene_dict: mapping ids to names

fileUtils.file_handling.write_table(gene_dict, sample_ids, all_files, outpath)[source]

Create tab separated table with merged values, adapted from Steffen Lemke

Parameters

  • gene_dict – gene_ids mapped to gene_names

  • sample_ids – array

  • all_files – dict

  • outpath – path where to store outfile, tsv

fileUtils.metadata_handling module

fileUtils.metadata_handling.read_metadata(metadata, sample_ids)[source]

Read in metadata file csv format FileID, SampleType, CaseID, Project

Returns

meta_dict

Returns

target_names: dict

Returns

target: array

Returns

annotation: pd.DataFrame

Returns

project_arr

Returns

color_list