[Bio] View of /FigTutorial/seq

Revision 1.1 - (download) (as text) (annotate)
Thu Jun 10 14:51:56 2004 UTC (15 years, 6 months ago) by disz
Branch: MAIN
CVS Tags: merge-bodev_news-3, rast_rel_2014_0912, rast_rel_2008_06_18, rast_rel_2008_06_16, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, Root-bobdev_news, rast_rel_2008_09_30, caBIG-13Feb06-00, rast_rel_2010_0526, rast_rel_2014_0729, merge-trunktag-bobdev_news-1, rast_rel_2009_05_18, caBIG-05Apr06-00, rast_rel_2009_0925, rast_rel_2010_1206, rast_rel_2010_0118, caBIG-00-00-00, rast_rel_2009_02_05, rast_rel_2011_0119, rast_rel_2008_12_18, merge-trunktag-bodev_news-3, merge-bobdev_news-2, merge-bobdev_news-1, rast_rel_2008_10_09, rast_release_2008_09_29, rast_rel_2008_04_23, rast_rel_2008_08_07, rast_rel_2009_07_09, rast_rel_2010_0827, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, rast_rel_2008_10_29, rast_rel_2009_03_26, merge-trunktag-bobdev_news-2, rast_rel_2008_11_24, HEAD
Branch point for: Branch-bobdev_news

Python version of tutorial code

from FigKernelPackages import FIG
import sys

fig = FIG.FIG()

def die(msg):
	print msg
	sys.exit(0)

if len(sys.argv) != 3:
	die("usage: seq_utils Genome Location")

genome = sys.argv[1]
loc = sys.argv[2]

seq = fig.dna_seq(genome, loc)

if seq:
    seqR = fig.reverse_comp(seq);

    tran  = fig.translate(seq);
    tranR = fig.translate(seqR);

    fig.display_id_and_seq("plus_strand",seq);
    #fig.display_id_and_seq("plus_strand_translated",\$tran,\*STDERR);


    fig.display_id_and_seq("minus_strand",seqR);
    #fig.display_id_and_seq("minus_strand_translated",\$tranR,\*STDERR);

View of /FigTutorial/seq_utils.py