GENSCAN 1.0	Date run: 11-Mar-109	Time: 00:29:37

Sequence scaffold_2 : 47583 bp : 37.42% C+G : Isochore 1 ( 0 - 100 C+G%)

Parameter matrix: test.smat

Predicted genes/exons:

Gn.Ex Type S .Begin ...End .Len Fr Ph I/Ac Do/T CodRg P.... Tscr..
----- ---- - ------ ------ ---- -- -- ---- ---- ----- ----- ------

 1.01 Init -   2604   2462  143  0  2   77   96   184 0.883  20.81
 1.00 Prom -   3677   3638   40                               2.82

 2.00 Prom +   4382   4421   40                               1.62
 2.01 Init +   6395   6399    5  1  2   73   84     0 0.122  -0.16
 2.02 Intr +   8270   8412  143  2  2   74   82   110 0.141  12.00
 2.03 Term +   8516   8523    8  0  2   46   46     0 0.473  -8.05
 2.04 PlyA +   9723   9728    6                               2.27

Predicted peptide sequence(s):

Predicted coding sequence(s):


>scaffold_2|GENSCAN_predicted_peptide_1|48_aa
MDRSHQIWDEKLMDQKCVLYPVCLWHEQESEMNWEAEKAERLRTEQKX

>scaffold_2|GENSCAN_predicted_CDS_1|144_bp
atggatcggagtcatcagatatgggatgagaagctgatggatcagaagtgcgtcctctac
cccgtctgcctctggcacgagcaggagagcgagatgaactgggaggctgagaaagctgag
aggctaaggactgaacagaaaggn

>scaffold_2|GENSCAN_predicted_peptide_2|51_aa
MRKNEGVDDADPLIEGMKEITLKDSATPEDKDQEDKQDERGEEIQEQPQEM

>scaffold_2|GENSCAN_predicted_CDS_2|156_bp
atgaggaagaatgagggtgttgatgatgcagatccactaatagaaggtatgaaggagatc
actctgaaagattcagcaactccagaagacaaggatcaagaagacaaacaagatgagaga
ggtgaagaaattcaagaacaacctcaagagatgtag


##</code><code>##

#!/usr/bin/perl

open(OUT1,">seqfile1_lc.out");
open(OUT2,">seqfile2_uc.out");

opendir(DIR,"/home/user/Desktop/resultfolder");
while(($filename=readdir(DIR))) {
open(FILE,"/home/user/Desktop/resultfolder/$filename");
while(<FILE>){
	if($_ =~ m/^>/) && $_=~m/GENSCAN_predicted_CDS/ || $_=~m/GENSCAN_predicted_peptide/) {
		push(@seq,$seq) if $seq;
		$seq=();
		push(@seq,"\n$_");
	} else {
		$_ =~ s/\s*$//;
		$seq = $seq."$_";
	}
	}
}
push(@seq,$seq);

while($_= shift @seq){
	if($_ =~ m/^>/) && $_=~m/GENSCAN_predicted_CDS/ ){
	$header=$_;
	$seq=shift @seq;
	print OUT1 $header;
	print OUT1 $seq;
	}
	if($_ =~ m/^>/) && $_=~m/GENSCAN_predicted_peptide/ ){
	$header=$_;
	$seq=shift @seq;
	print OUT2 $header;
	print OUT2 $seq;


	}
}

##</code><code>##

seqfile1_uc.out
>scaffold_2|GENSCAN_predicted_CDS_1|144_bp
atggatcggagtcatcagatatgggatgagaagctgatggatcagaagtgcgtcctctac
cccgtctgcctctggcacgagcaggagagcgagatgaactgggaggctgagaaagctgag
aggctaaggactgaacagaaaggn
>scaffold_2|GENSCAN_predicted_CDS_2|156_bp
atgaggaagaatgagggtgttgatgatgcagatccactaatagaaggtatgaaggagatc
actctgaaagattcagcaactccagaagacaaggatcaagaagacaaacaagatgagaga
ggtgaagaaattcaagaacaacctcaagagatgtag
........... so on... from all the 40,000 files.

seqfile2_uc.out
>scaffold_2|GENSCAN_predicted_peptide_1|48_aa
MDRSHQIWDEKLMDQKCVLYPVCLWHEQESEMNWEAEKAERLRTEQKX
>scaffold_2|GENSCAN_predicted_peptide_2|51_aa
MRKNEGVDDADPLIEGMKEITLKDSATPEDKDQEDKQDERGEEIQEQPQEM
....... so on...from all the 40,000 files.