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#!/usr/bin/perl
#-------------------------------------------------------------------------------
# Split a tab-separated (or space-separated) file based on the
# first column (chromosome name)
#
# Note: Lines starting with "#" are ignored.
#
# Usage: cat file.vcf | ./splitChr.pl [name [ext]]
#
# Pablo Cingolani
#-------------------------------------------------------------------------------
$chrPrev = "";
$name = "chr";
$ext = "txt";
if( $ARGV[0] ne '' ) { $name = $ARGV[0]; }
if( $ARGV[1] ne '' ) { $ext = $ARGV[1]; }
# Iterate on STDIN
for( $i=1 ; $l = <STDIN> ; $i++ ) {
if( $l =~/^#/ ) {
# Ignore headers
} else {
($chr) = split /\t/, $l;
# Different chromosome? => Create new file
if( $chr ne $chrPrev ) {
$fileName = "$name$chr.$ext";
print "Input line $i. Creating file '$fileName'\n";
open CHR, ">$fileName";
$chrPrev = $chr;
}
print CHR $l;
}
}
close CHR;
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