Created
December 6, 2016 07:01
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map2.pl
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use strict; | |
use warnings; | |
use Text::CSV_XS; | |
use Data::Printer; | |
my $csv = Text::CSV_XS->new({ binary => 1, sep_char => "\t" }); | |
open my $fh, "<", $ARGV[0] or die $!; | |
open my $fh2, "<", $ARGV[1] or die $!; | |
# 1. 키맵 생성 | |
my %map = (); | |
while(my $row = $csv->getline($fh)) { | |
$map{$row->[0]} = $row->[1]; | |
} | |
my $count = 0; | |
while(my $row = $csv->getline($fh2)) { | |
if ($row->[2] && $row->[2] eq 'gene') { | |
my ($name_str) = $row->[8] =~ /Name=([^;]+);/; | |
my ($alias_str) = $row->[8] =~ /Alias=([^;]+);/; | |
$name_str .= '0'; | |
$alias_str = join(",", map { $_.'0' } split ',', $alias_str); | |
$row->[8] =~ s/Name=([^;]+);/Name=$name_str;/; | |
$row->[8] =~ s/Alias=([^;]+);/Alias=$alias_str;/; | |
} | |
elsif ($row->[2] && $row->[2] eq 'exon') { | |
my ($parent_str) = $row->[8] =~ /Parent=([^;]+);/; | |
for my $parent_col (split ",", $parent_str) { | |
$row->[8] =~ s/Parent=([^;]+);/Parent=$parent_col;/; | |
print join("\t", @{ $row })."\n"; | |
} | |
next; | |
} | |
print join("\t", @{ $row })."\n"; | |
} |
Author
JEEN
commented
Dec 6, 2016
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