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root/gclib/scripts/gtfcount
Revision: 23
Committed: Tue Jul 26 21:44:38 2011 UTC (8 years, 2 months ago) by gpertea
Original Path: ann_bin/gtfcount
File size: 1034 byte(s)
Log Message:
adding misc scripts

Line User Rev File contents
1 gpertea 23 #!/bin/tcsh -f
2     if ("x"$1 == "x-h") then
3     echo "Usage: gtfcount [-g][-c][-l] <gtfile>"
4     echo " Show the count of distinct transcript names.\n Options:"
5     echo " -g : report distinct gene names count (gene_id attribute)"
6     echo " -c : report transcript counts per reference sequence"
7     echo " -l : list transcripts"
8     echo " -f : report transcript counts per gene_id"
9     exit 1
10     endif
11     if ("x"$1 == "x-g") then
12     shift
13     perl -ne 'print "$1\n" if m/gene_id "([^"]+)/' $1 | sort -u | wc -l
14     exit
15     endif
16     if ("x"$1 == "x-l") then
17     shift
18     perl -ne 'print "$1\n" if m/transcript_id "([^"]+)/' $1 | sort -u
19     exit
20     endif
21     if ("x"$1 == "x-c") then
22     shift
23     perl -ne '@t=split(/\t/);print "$t[0]\t$1\n" if $t[8]=~m/transcript_id "([^"]+)/' $1 | sort -u | cut -f1 | uniq -c
24     exit
25     endif
26     if ("x"$1 == "x-f") then
27     shift
28     perl -ne '($g)=(m/gene_id\s+"([^"]+)/); ($t)=(m/transcript_id\s+"([^"]+)/); print "$g\t$t\n" if $g && $t' $1 | sort -u | cut -f1 | uniq -c
29     exit
30     endif
31     perl -ne 'print "$1\n" if m/transcript_id "([^"]+)/' $1 | sort -u | wc -l

Properties

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svn:executable *