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gpertea |
23 |
#!/bin/tcsh -f |
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if ("x"$1 == "x-h") then |
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echo "Usage: gtfcount [-g][-c][-l] <gtfile>" |
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echo " Show the count of distinct transcript names.\n Options:" |
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echo " -g : report distinct gene names count (gene_id attribute)" |
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echo " -c : report transcript counts per reference sequence" |
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gpertea |
71 |
echo " -C : show count of coding transcripts" |
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gpertea |
23 |
echo " -l : list transcripts" |
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gpertea |
71 |
echo " -Cl : list coding transcripts" |
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gpertea |
23 |
echo " -f : report transcript counts per gene_id" |
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exit 1 |
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endif |
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if ("x"$1 == "x-g") then |
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shift |
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perl -ne 'print "$1\n" if m/gene_id "([^"]+)/' $1 | sort -u | wc -l |
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exit |
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endif |
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if ("x"$1 == "x-l") then |
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shift |
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perl -ne 'print "$1\n" if m/transcript_id "([^"]+)/' $1 | sort -u |
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exit |
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endif |
| 23 |
gpertea |
71 |
if ("x"$1 == "x-Cl") then |
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shift |
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perl -ne 'print "$1\n" if m/\tCDS\t/ && m/transcript_id "([^"]+)/' $1 | sort -u |
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exit |
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endif |
| 28 |
gpertea |
23 |
if ("x"$1 == "x-c") then |
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shift |
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perl -ne '@t=split(/\t/);print "$t[0]\t$1\n" if $t[8]=~m/transcript_id "([^"]+)/' $1 | sort -u | cut -f1 | uniq -c |
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exit |
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endif |
| 33 |
gpertea |
71 |
if ("x"$1 == "x-C") then |
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shift |
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perl -ne 'print "$1\n" if m/\tCDS\t/ && m/transcript_id "([^"]+)/' $1 | sort -u | wc -l |
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exit |
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endif |
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| 39 |
gpertea |
23 |
if ("x"$1 == "x-f") then |
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shift |
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perl -ne '($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 |
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exit |
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endif |
| 44 |
gpertea |
71 |
|
| 45 |
gpertea |
23 |
perl -ne 'print "$1\n" if m/transcript_id "([^"]+)/' $1 | sort -u | wc -l |
