Raj: Created page with 'Category:Bioinformatics #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequenc…'

2010-07-22T08:38:31Z

Created page with 'Category:Bioinformatics <source lang=perl> #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequenc…'

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[[Category:Bioinformatics]]

<source lang=perl>
#! /usr/bin/perl -w
# *************************************************************
# This Programme does the following in sequence
# -> Parses a multi fasta
# -> Makes the separate file with completely 'N', >80 Ns and <80 Ns
# -> Written as individual files.
# Author : Rajkumar (itc@rajkumar.in)
# Release: JUL 2009
# *************************************************************

# Libraries
use strict;
use Bio::Perl;
use Bio::SeqIO;

# Variables
my $path = "/home/raj/bio";
my $path1 = "$path/user/raja";
my $path2 = "$path1/blast/BES-NR";
my $multifasta = "$path2/BES.fa";

my $outfile1 = "$path2/BES_All_N.fa";
my $outfile2 = "$path2/BES_MoreThan_80N.fa";
my $outfile3 = "$path2/BES_LessThan_81N.fa";
my $outfile4 = "$path2/BES_withNo_N.fa";
my $outfile5 = "$path2/BES_Atlest_1N.fa";
my $stat = "$path2/stat.txt";

# Getting the Grip of folders
if (-e $outfile1) {`rm $outfile1`;}
if (-e $outfile2) {`rm $outfile2`;}
if (-e $outfile3) {`rm $outfile3`;}
if (-e $outfile4) {`rm $outfile4`;}
if (-e $outfile5) {`rm $outfile5`;}

# making several Fasta files of GDNA
my $in = Bio::SeqIO->new(-file => "$multifasta", -format => 'Fasta');
my $identifier;
my $sequence;

while ( my $seq = $in->next_seq() ) {
$identifier = $seq->id;
$sequence = $seq->seq;

#Trim the identifier
#$identifier =~ s/_Size:[0-9]+bp//g;

my ($fasta) = $_;
$fasta = ">$identifier\n$sequence\n";

my $count_seq = length($sequence);
my $count_N = ($sequence =~ tr/N//);

if ($count_seq eq $count_N) {

open (FASTA, ">>".$outfile1);
print FASTA $fasta;
close FASTA;
}

if ($count_N >80) {

open (FASTA, ">>".$outfile2);
print FASTA $fasta;
close FASTA;
}

if ($count_N <=80) {

open (FASTA, ">>".$outfile3);
print FASTA $fasta;
close FASTA;
}

if ($count_N <1) {

open (FASTA, ">>".$outfile4);
print FASTA $fasta;
close FASTA;
}

if ($count_N >=1) {

open (FASTA, ">>".$outfile5);
print FASTA $fasta;
close FASTA;
}

}

# Generating STAT

my $c_outfile1 = `grep -c ">" $outfile1`; chomp $c_outfile1;
my $c_outfile2 = `grep -c ">" $outfile2`; chomp $c_outfile2;
my $c_outfile3 = `grep -c ">" $outfile3`; chomp $c_outfile3;
my $c_outfile4 = `grep -c ">" $outfile4`; chomp $c_outfile4;
my $c_outfile5 = `grep -c ">" $outfile5`; chomp $c_outfile5;
my $total = `grep -c ">" $multifasta`; chomp $total;

my $stat_content = "Total sequences:\t$total\nBES with No 'N':\t$c_outfile4\nBES with atleast one 'N':\t$c_outfile5\nBES with all 'N':\t$c_outfile1\nBES with more than 80 'N's:\t$c_outfile2\nBES with less than 81 'N's:\t$c_outfile3\n";
open (F, ">$stat");
print F $stat_content;
close F;

# END

</source>

N stat fasta.pl - Revision history

Raj: Created page with 'Category:Bioinformatics #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequenc…'