coalispr.resources.share.genbank2gtf

Script to enerate gtf from genbank file.

Attributes

exts

convtab

Functions

genbank2gtf(file_name, conversion_table, otherpath, ...)

Generate gtf from genbank file for chosen features. Requires biopython.

main(args)

Module Contents

coalispr.resources.share.genbank2gtf.exts = ['.dat', '.gbff', '.gbk', '.gb', '.gz']
coalispr.resources.share.genbank2gtf.convtab = '_conv.tab'
coalispr.resources.share.genbank2gtf.genbank2gtf(file_name, conversion_table, otherpath, selected_features, gtf_name, include_lengths)

Generate gtf from genbank file for chosen features. Requires biopython.

Parameters:

  • file_name (str) – Full/relative path to (compressed, ‘gz’) genbank file (‘.gbff’, ‘.gbk’, ‘.gb’).

  • conversion_table (str) – Start of name of conversion table (.tab file) to simplify chromosome names (these should be the same as used in the fasta file; see clean_fasta.py)

  • otherpath (str) – Path to conversion table if not in default folder.

  • selected_features (int) – Number for list of scanned features/types

  • gtf_name (str) – Filename for output gtf.

  • include_lengths (int {0.1}) – Flag to indicate whether to create a file with chromosome lengths; 0: No; 1: Yes

Return type:

Downloaded genbank file information translated to GTF.

coalispr.resources.share.genbank2gtf.main(args)