chapmanb

#!/usr/bin/perl

###################################################################
# FindSomatic.pl
#
# Tool for detecting somatic mutations in normal/tumor pair 
# using microassembly
# 
#  Author: Giuseppe Narzisi 
#    Date: December 11, 2013

chapmanb

track name="tb_knownGene" description="table browser query on knownGene" visibility=3 url= 
1	2985741	3355185	uc001akc.3	0	+	2985823	3350375	0	17	119,350,51,135,103,208,148,154,1417,85,170,78,170,175,237,175,4888,	0,116947,174909,315974,327313,333613,335561,336317,342206,345385,348650,349489,356403,356873,361694,362788,364556,
1	2985741	3355185	uc001ake.3	0	+	2985823	3350375	0	17	119,350,51,135,103,208,148,154,1417,88,170,78,170,175,237,175,4888,	0,116947,174909,315974,327313,333613,335561,336317,342206,345382,348650,349489,356403,356873,361694,362788,364556,
1	2985741	3355185	uc001akf.3	0	+	2985823	3350375	0	17	119,350,51,135,103,208,148,154,1417,88,170,78,170,175,237,175,4945,	0,116947,174909,315974,327313,333613,335561,336317,342206,345382,348650,349489,356403,356873,361694,362788,364499,
1	28929608	28969604	uc001bqx.3	0	-	28930050	28948593	0	6	478,89,115,78,252,438,	0,2275,10150,14856,18817,39558,
1	28929608	28969604	uc001bqy.3	0	-	28930050	28948593	0	6	478,89,115,78,252,101,	0,2275,10150,14856,18817,3989

chapmanb

class ORFFinder:
    """Find the longest ORF in a given sequence
    "seq" is a string, if "start" is not provided any codon can be the start of
    and ORF. If muliple ORFs have the longest length the first one encountered
    is printed
    """
    def __init__(self, seq, start=[], stop=["TAG", "TAA", "TGA"]):
        self.seq = seq
        self.start = start
        self.stop = stop