mgkit.workflow.fasta_utils module

New in version 0.3.0.

Scripts that includes some functionality to help use FASTA files with the framework

split command

Used to split a fasta file into smaller fragments

translate command

Used to translate nucleotide sequences into amino acids.

uid command

Used to change a FASTA file headers to a unique ID. A table (tab separated) with the changes made can be kept, using the –table option.

Changes

New in version 0.3.0.

Changed in version 0.3.1: added translate and uid command

mgkit.workflow.fasta_utils.load_trans_table(table_name)

Loads translation table

mgkit.workflow.fasta_utils.main()

Main function

mgkit.workflow.fasta_utils.set_parser()

Sets command line arguments parser

mgkit.workflow.fasta_utils.set_split_parser(parser)

mgkit.workflow.fasta_utils.set_translate_parser(parser)

mgkit.workflow.fasta_utils.set_uid_parser(parser)

mgkit.workflow.fasta_utils.split_command(options)

mgkit.workflow.fasta_utils.translate_command(options)

mgkit.workflow.fasta_utils.translate_seq(name, seq, trans_table)

Tranlates sequence into the 6 frames

mgkit.workflow.fasta_utils.uid_command(options)