RJE GenBank Module
Copyright © 2011 Richard J. Edwards - See source code for GNU License Notice
This module is for parsing information out of GenBank files and converting them to other formats.
See also rje.py generic commandline options.
History Module Version History
# 0.0 - Initial Compilation. # 0.1 - Modified and Tidied output a little. # 0.2 - Added details to skip and option to use different detail for protein accession number. # 0.3 - Added reloading of features. # 1.0 - Basic functioning version. Added fetchuid=LIST Genbank retrieval to generate seqin=FILE. # 1.1 - Added use of rje_taxonomy for getting Species Code from TaxID. # 1.2 - Modified to deal with genbank protein entries. # 1.2.1 - Fixed feature bug that was breaking parser and removing trailing '*' from protein sequences. # 1.2.2 - Fixed more features that were breaking parser. # 1.3.0 - Added split viral output. # 1.3.1 - Fixed bug in split viral output. # 1.3.2 - Fixed bug in reverse complement sequences with introns. # 1.4.0 - Added addtags=T/F : Add locus_tag identifiers if missing - needed for gene/cds/prot fasta output [False] # 1.4.1 - Fixed genetic code warning. # 1.5.0 - Added setupRefGenome() method based on PAGSAT code. # 1.5.1 - Fixed logskip append locus sequence file bug. # 1.5.2 - Fixed addtag(s) bug. # 1.5.3 - Fixed https genbank download issue. # 1.5.4 - Added recognition of *.gbff for genbank files. # 1.5.5 - Fixed bug to use Locus for *.full.fas and thus link to Feature table properly.
© 2015 RJ Edwards. Contact: firstname.lastname@example.org.