Convert sequence files to extended OBITools fasta format

convert2fasta.py [options] [filename 1] [filename 2] ...

Convert sequence files to the extended OBITools fasta format. If no file name are specified data are read from standard input.

obitools common options

-h, --help
show this help message and exit
--DEBUG
Set logging in debug mode
--no-psyco
Don’t use psyco even if it installed

convert2fasta.py specific options

--genbank
input file is in genbank format
--embl
input file is in embl format
--fna
input file is in fasta nucleic format produced by 454 sequencer pipeline
--nuc
input file contains nucleic sequences
--prot
input file contains protein sequences

example

for converting a genbank file to fasta

% convert2fasta.py --genbank --nuc sequences.gb > sequences.fasta