#Perl script used to extract list 
# of Gene Ontologies associated with morphology 
# from Mantidactylus betsileanus annotated transcripts, 
# based on list defined on morphology-associated 
# GO terms list in Xenopus laevis. 


! /usr/bin/perl -w

 program to search index in database 
 print search index and line matched

@idarray1=();
$filegoanno = $ARGV[0];
open(IN, $filegoanno) || die "File with index not found"; 

while (<IN>) {
	chomp;
	/(^\S+)/;
	push (@idarray1, $1); push index into array
}

$numele=@idarray1;
$filedb = $ARGV[1];
open (INN, $filedb) || die "File with database not found";
open(OUT,">result.txt") || die "cannot open file " ; open input file for reading.

	@filedata= <GET_FILE_DATA>;
	$text = "@filedata";

$ct=0;
while ($ct<$numele) { counter
	`grep '$idarray1[$ct]' $filedb > resulttmp.txt`;  temporary file
	open (IN2, "resulttmp.txt");
	while (<IN2>) {
		chomp;
		$line=$_;
		print "$idarray1[$ct]\t$line\n";
	
	}
		$ct++;
}

`rm resulttmp.txt`;