Created
August 3, 2018 15:42
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So running the below with the pathological case ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/ARCHIVE/BUILD.37.3/CHR_01/hs_ref_GRCh37.p5_chr1.fa.gz
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#!/usr/bin/env perl6 | |
use Compress::Zlib; | |
use IO::String; | |
my $DATA_DIR = %*ENV<DATA_DIR> // '/Users/matt/data/reference/GRCh37/sequence/dna'; | |
for dir($DATA_DIR).grep(/chr\d+\.fa\.gz/) -> $file { | |
my $out_file = $file.IO.extension('txt', :2parts).open(:w); | |
my $chromosome = IO::String.new(buffer=>gzslurp($file)); | |
for $chromosome.lines -> $line { | |
FIRST { next } | |
chomp $line; | |
$out_file.print($line); | |
} | |
} |
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