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root/gclib/scripts/gtfcount
Revision: 71
Committed: Fri Sep 23 19:23:49 2011 UTC (8 years ago) by gpertea
File size: 1389 byte(s)
Log Message:
gridx fixed to export PERL5LIB and PYTHONPATH

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 gpertea 71 echo " -C : show count of coding transcripts"
8 gpertea 23 echo " -l : list transcripts"
9 gpertea 71 echo " -Cl : list coding transcripts"
10 gpertea 23 echo " -f : report transcript counts per gene_id"
11     exit 1
12     endif
13     if ("x"$1 == "x-g") then
14     shift
15     perl -ne 'print "$1\n" if m/gene_id "([^"]+)/' $1 | sort -u | wc -l
16     exit
17     endif
18     if ("x"$1 == "x-l") then
19     shift
20     perl -ne 'print "$1\n" if m/transcript_id "([^"]+)/' $1 | sort -u
21     exit
22     endif
23 gpertea 71 if ("x"$1 == "x-Cl") then
24     shift
25     perl -ne 'print "$1\n" if m/\tCDS\t/ && m/transcript_id "([^"]+)/' $1 | sort -u
26     exit
27     endif
28 gpertea 23 if ("x"$1 == "x-c") then
29     shift
30     perl -ne '@t=split(/\t/);print "$t[0]\t$1\n" if $t[8]=~m/transcript_id "([^"]+)/' $1 | sort -u | cut -f1 | uniq -c
31     exit
32     endif
33 gpertea 71 if ("x"$1 == "x-C") then
34     shift
35     perl -ne 'print "$1\n" if m/\tCDS\t/ && m/transcript_id "([^"]+)/' $1 | sort -u | wc -l
36     exit
37     endif
38    
39 gpertea 23 if ("x"$1 == "x-f") then
40     shift
41     perl -ne '($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
42     exit
43     endif
44 gpertea 71
45 gpertea 23 perl -ne 'print "$1\n" if m/transcript_id "([^"]+)/' $1 | sort -u | wc -l

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