Mercurial > repos > rlegendre > ribo_tools

comparison metagene_readthrough.py @ 14:344bacf6acb8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author rlegendre
date Fri, 10 Apr 2015 03:18:56 -0400
parents 7c944fd9907e
children 702e60e819c2
comparison
equal deleted inserted replaced
13:7c944fd9907e 14:344bacf6acb8
119 119
120 120
121 def check_homo_coverage(gene,GFF,start,stop, aln) : 121 def check_homo_coverage(gene,GFF,start,stop, aln) :
122 122
123 chrom = GFF[gene]['chrom'] 123 chrom = GFF[gene]['chrom']
124 ## compute nunber of nucleotides in CDS with a coverage equal to zero 124 ## compute number of nucleotides in CDS with a coverage equal to zero
125 nt_cds_cov = 0 125 nt_cds_cov = 0
126 nt_cds_num = 0 126 nt_cds_num = 0
127 for i in range(1,GFF[gene]['exon_number']+1) : 127 for i in range(1,GFF[gene]['exon_number']+1) :
128 for z in range(GFF[gene]['exon'][i]['start'],GFF[gene]['exon'][i]['stop']): 128 for z in range(GFF[gene]['exon'][i]['start'],GFF[gene]['exon'][i]['stop']):
129 nt_cds_num += 1 129 nt_cds_num += 1
130 if aln.count(chrom,z,z+1) == 0 : 130 if aln.count(chrom,z,z+1) == 0 :
131 nt_cds_cov += 1 131 nt_cds_cov += 1
132 132
133 ## compute percent of CDS no covering 133 ## compute percent of CDS no covering
134 percent = nt_cds_cov*100/nt_cds_num 134 if nt_cds_cov == 0 or nt_cds_num == 0:
135 percent = 0
136 else:
137 percent = nt_cds_cov*100/nt_cds_num
135 138
136 ## compute number of nucleotides with no coverage in extension 139 ## compute number of nucleotides with no coverage in extension
137 nt_no_cover = 0 140 nt_no_cover = 0
138 for pos in range(start,stop,1) : 141 for pos in range(start,stop,1) :
139 if aln.count(chrom,pos,pos+1) == 0 : 142 if aln.count(chrom,pos,pos+1) == 0 :