extract-data.pl

# sample data:
#
# row_num,gene_id,ensembl_gene_symbol,gene_symbol,entrez_id
# 1,66982,"ENSG00000000003","TSPAN6",7105
# 2,66983,"ENSG00000000005","TNMD",64102
# 3,66984,"ENSG00000000419","DPM1",8813
# 4,66985,"ENSG00000000457","SCYL3",57147
# ...

#!/usr/bin/perl
use strict;
use warnings;

my ($gene, $info, @info, $row, $data, @data, $opt);

$gene = $ARGV[0]; $opt = $ARGV[1];
$info = `cat genes_rows_metadata.csv |egrep -w $gene`;
chomp($info);
@info = split(",",$info);
$row = $info[0];
$info = join("\t",@info);
$data = `cat genes_matrix.csv |head -$row |tail -1`;
chomp($data);
@data = split(",",$data);
$data = join("\t",@data[1..$#data]);

if ($opt == 2 && $info[1] == $data[0]) {
  print "$info[3]\t$data\n";
}
elsif ($opt == 1) {
  print "$info\t$data[0]\n";
}