extract_anno

#!/usr/bin/perl
use strict;
use warnings;
use Getopt::Long 'HelpMessage';
use List::MoreUtils qw(firstidx);

my $usage=<<_EOH_;;
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This script is used to extract the annotation information of selected genes

Usage: 
extract_anno --genes Blenny_Control_Vent.DEGs.txt \
--anno unprot_name_description_orthgroup.txt \
--col col

Input files:

1. --genes Blenny_Control_Vent.DEGs.txt

OG0004527
OG0057108
OG0058317
OG0049323
OG0031955

2. --anno unprot_name_description_orthgroup.txt (this file should be seperated by Tabular form)

Orth_id	Uni_id	Gene_des
OG0000007	sp|Q9Y3S1|WNK2_HUMAN	Serine/threonine-protein kinase WNK2
OG0000012	sp|P18729|ZG57_XENLA	Gastrula zinc finger protein XlCGF57.1 (Fragment)
OG0000019	sp|P03360|POL_AVIRE	Gag-Pol polyprotein (Fragment)
OG0000020	sp|O60284|ST18_HUMAN	Suppression of tumorigenicity 18 protein

3. --col the column of annotation file (--anno unprot_name_description_orthgroup.txt) 
		 that includes the elements in selected genes (--genes Blenny_Control_Vent.DEGs.txt)



											Kang 2021-09-24
------------------------------------------------------------------------------------------
_EOH_
;

GetOptions(
	'genes:s', \my $gene,	# the file has genes (one id per line)
	'anno:s', \ my $ann,	# the annotaion file
	'col:i', \ my $col, # the column (should be number: 1, 2, 3 ...) of annotation including gene id in gene file
	'help', \ my $help
	);

if ($help || (! $gene) || (! $ann) && (! $col)) {
	die $usage; # all of these options are mandatory requirements
}

my %ano;
open ANN, "$ann" or die "can not open $ann\n";
while (<ANN>) {
	chomp;
	s/\r//g;
	my @a=split /\t/;
	my $info;
	for (my $i = 0; $i < @a; $i++) {
		$a[$i]=~s/^\s+//;
		$a[$i]=~s/\s+$//;
		unless ($i==$col-1) {
			$info.=$a[$i]."\t";
		}
	}
	$info=~s/\s+$//;
	$ano{$a[$col-1]}=$info;
}

open GENE, "$gene" or die "can not open $gene\n";
while (<GENE>) {
	chomp;
	s/\r//g;
	s/^\s+//;
	s/\s+$//;
	print "$_\t$ano{$_}\n";
}