FILE: 1.clean.tab2.20171115.pl
#! /usr/bin/perl
# usage:
# ~/pypeworks/biogrid/00_cleanup_biogrid_table.pl BIOGRID-ORGANISM-Homo_sapiens-3.2.117.tab2.txt > BIOGRID-ORGANISM-Homo_sapiens-3.2.117.tab2.clean.txt
# can use bash to apply it to more species as needed
while ( <>) {
chomp;
@aux = split "\t";
@new = ();
foreach (@aux) {
$blah = $_;
$blah =~ s/\s//g;
($blah eq '-') && ($blah='');
if (! $blah) {
push @new, 'NA';
} else {
# somebody in BioGRID thought it would be cute to use backslash
# as quotes
$blah = $_;
$blah =~ s/\\//g;
push @new, $blah;
}
}
print join ("\t", @new), "\n";
}
Based on
https://github.com/ivanamihalek/biogrid/blob/master/00_cleanup_biogrid_table.pl
Based on
https://github.com/ivanamihalek/biogrid/blob/master/00_cleanup_biogrid_table.pl
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