Read split.pl - Revision history

Raj at 16:37, 8 April 2010

2010-04-08T16:37:03Z

← Older revision		Revision as of 16:37, 8 April 2010
Line 19:		Line 19:

	# Variables		# Variables
	my $path = "/home/raj/bio/user/raja";		my $file = "set9"; # change this for each file
	my $multifasta = "$path/~~set_1~~.txt";		my $path = "/home/raj/bio/user/raja";
	my $file1 = "reads_0bp.txt";		my $multifasta = "$path/data/$file.txt";
	my $file2 = "reads_1-80bp.txt";		my $file1 = "$file.reads_0bp.txt";
	my $file3 = "reads_80+bp.txt";		my $file2 = "$file.reads_1-80bp.txt";
	my $statfile = "stat.txt";		my $file3 = "$file.reads_80+bp.txt";
	my $idfile = "id_size.txt";		my $statfile = "$file.stat.txt";
			my $idfile = "$file.id_size.txt";

	# Getting the grip of files		# Getting the grip of files
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	if (-e "$file3") {`rm $file3`;}		if (-e "$file3") {`rm $file3`;}
	if (-e "$idfile") {`rm $idfile`;}		if (-e "$idfile") {`rm $idfile`;}

	# Let's Hack		# Let's Hack
	my $in = Bio::SeqIO->new(-file => "$multifasta", -format => 'Fasta');		my $in = Bio::SeqIO->new(-file => "$multifasta", -format => 'Fasta');
Line 40:		Line 41:
	$sequence = $seq->seq;		$sequence = $seq->seq;


	my $count_seq = length($sequence);		my $count_seq = length($sequence);
	my $fasta = ">".$identifier."_Size:".$count_seq."bp\n".$sequence."\n";		my $fasta = ">".$identifier."_Size:".$count_seq."bp\n".$sequence."\n";
Line 49:		Line 50:
	print FH $fasta ;		print FH $fasta ;
	close FH ;		close FH ;

	open (FH, ">>".$idfile);		open (FH, ">>".$idfile);
	print FH $id_size ;		print FH $id_size ;
	close FH ;		close FH ;

	}		}

Line 60:		Line 61:
	print FH $fasta ;		print FH $fasta ;
	close FH ;		close FH ;

	open (FH, ">>".$idfile);		open (FH, ">>".$idfile);
	print FH $id_size ;		print FH $id_size ;
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	print FH $fasta ;		print FH $fasta ;
	close FH ;		close FH ;


	open (FH, ">>".$idfile);		open (FH, ">>".$idfile);
	print FH $id_size ;		print FH $id_size ;

Raj at 03:31, 8 April 2010

2010-04-08T03:31:08Z

← Older revision		Revision as of 03:31, 8 April 2010
Line 1:		Line 1:
	[[Category:Bioinformatics ]]		[[Category:Bioinformatics ]]
	<source lang=perl>		<source lang=perl>

	#! /usr/bin/perl -w		#! /usr/bin/perl -w
	# *************************************************************		# *************************************************************
	# This Programme does the following in sequence		# This Programme does the following in sequence
	# -> Parses a multi fasta		# -> Parses a multi fasta
	# -> ~~count~~ characters and splits as (1) 0 (2) <80 (3) >80		# -> Count characters and splits as (1) 0 (2) <=80 (3) >80
	# -> Capture the results		# -> Capture the results in files in 3 catogories
			# -> Generates the statistics
			# -> Generates Tab delimited file with ID and size
	# Author : Rajkumar (itc@rajkumar.in)		# Author : Rajkumar (itc@rajkumar.in)
	# Release: MAR 2010		# Release: MAR 2010
Line 19:		Line 19:

	# Variables		# Variables
	my $path = "/home/raj/bio/user/raja";		my $path = "/home/raj/bio/user/raja";
	my $multifasta = "$path/set_1.txt";		my $multifasta = "$path/set_1.txt";
	my $file1 = "reads_0bp.txt";		my $file1 = "reads_0bp.txt";
	my $file2 = "reads_1-80bp.txt";		my $file2 = "reads_1-80bp.txt";
	my $file3 = "reads_80+bp.txt";		my $file3 = "reads_80+bp.txt";
	my $statfile = "stat.txt";		my $statfile = "stat.txt";
			my $idfile = "id_size.txt";

	# ~~spliting~~		# Getting the grip of files
	if (-e "$file1") {`rm $file1`;}		if (-e "$file1") {`rm $file1`;}
	if (-e "$file2") {`rm $file2`;}		if (-e "$file2") {`rm $file2`;}
	if (-e "$file3") {`rm $file3`;}		if (-e "$file3") {`rm $file3`;}
			if (-e "$idfile") {`rm $idfile`;}

			# Let's Hack

	my $in = Bio::SeqIO->new(-file => "$multifasta", -format => 'Fasta');		my $in = Bio::SeqIO->new(-file => "$multifasta", -format => 'Fasta');
	my ($identifier, $sequence) = $_;		my ($identifier, $sequence) = $_;
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	$identifier = $seq->id;		$identifier = $seq->id;
	$sequence = $seq->seq;		$sequence = $seq->seq;


	~~my $fasta = ">$identifier\n$sequence\n";~~
	my $count_seq = length($sequence);		my $count_seq = length($sequence);
			my $fasta = ">".$identifier."_Size:".$count_seq."bp\n".$sequence."\n";
			my $id_size = "$identifier\t$count_seq\n";

	if ($count_seq eq 0){		if ($count_seq eq 0){
	open (FH, ">>".$file1);		open (FH, ">>".$file1);
	print FH $fasta ;		print FH $fasta ;
	close FH ;		close FH ;

			open (FH, ">>".$idfile);
			print FH $id_size ;
			close FH ;

	}		}

	if ( $count_seq < 81 && $count_seq > 0){		if ( $count_seq < 81 && $count_seq > 0){
	open (FH, ">>".$file2);		open (FH, ">>".$file2);
	print FH $fasta ;		print FH $fasta ;
			close FH ;

			open (FH, ">>".$idfile);
			print FH $id_size ;
	close FH ;		close FH ;
	}		}

	if ( $count_seq > 80){		if ( $count_seq > 80){
	open (FH, ">>".$file3);		open (FH, ">>".$file3);
	print FH $fasta ;		print FH $fasta ;
			close FH ;


			open (FH, ">>".$idfile);
			print FH $id_size ;
	close FH ;		close FH ;
	}		}
Line 64:		Line 81:
	my $stat2 = `grep -c ">" $file2`; chomp $stat2;		my $stat2 = `grep -c ">" $file2`; chomp $stat2;
	my $stat3 = `grep -c ">" $file3`; chomp $stat3;		my $stat3 = `grep -c ">" $file3`; chomp $stat3;


	my $stat = "Statistics\n==========\n$file1 $stat1 sequences\n$file2 $stat2 sequences\n$file3 $stat3 sequences\n";		my $stat = "Statistics\n==========\n$file1 $stat1 sequences\n$file2 $stat2 sequences\n$file3 $stat3 sequences\n";
	open (FH, ">".$statfile);		open (FH, ">".$statfile);
	print FH $stat ;		print FH $stat ;
	close FH ;		close FH ;

			# END



	~~# END~~
	</source>		</source>

Raj at 17:59, 7 April 2010

2010-04-07T17:59:20Z

← Older revision		Revision as of 17:59, 7 April 2010
Line 1:		Line 1:
			[[Category:Bioinformatics ]]
	<source lang=perl>		<source lang=perl>

Raj: Created page with ' #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Parses a multi fasta …'

2010-04-07T17:57:50Z

Created page with '<source lang=perl> #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Parses a multi fasta …'

New page

<source lang=perl>

#! /usr/bin/perl -w
# *************************************************************
# This Programme does the following in sequence
# -> Parses a multi fasta
# -> count characters and splits as (1) 0 (2) <80 (3) >80
# -> Capture the results

# Author : Rajkumar (itc@rajkumar.in)
# Release: MAR 2010
# *************************************************************

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

# Variables
my $path = "/home/raj/bio/user/raja";
my $multifasta = "$path/set_1.txt";
my $file1 = "reads_0bp.txt";
my $file2 = "reads_1-80bp.txt";
my $file3 = "reads_80+bp.txt";
my $statfile = "stat.txt";

# spliting
if (-e "$file1") {`rm $file1`;}
if (-e "$file2") {`rm $file2`;}
if (-e "$file3") {`rm $file3`;}

my $in = Bio::SeqIO->new(-file => "$multifasta", -format => 'Fasta');
my ($identifier, $sequence) = $_;
while ( my $seq = $in->next_seq() ) {
$identifier = $seq->id;
$sequence = $seq->seq;

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

if ($count_seq eq 0){
open (FH, ">>".$file1);
print FH $fasta ;
close FH ;
}

if ( $count_seq < 81 && $count_seq > 0){
open (FH, ">>".$file2);
print FH $fasta ;
close FH ;
}

if ( $count_seq > 80){
open (FH, ">>".$file3);
print FH $fasta ;
close FH ;
}
}
# statistics
my $stat1 = `grep -c ">" $file1`; chomp $stat1;
my $stat2 = `grep -c ">" $file2`; chomp $stat2;
my $stat3 = `grep -c ">" $file3`; chomp $stat3;

my $stat = "Statistics\n==========\n$file1 $stat1 sequences\n$file2 $stat2 sequences\n$file3 $stat3 sequences\n";
open (FH, ">".$statfile);
print FH $stat ;
close FH ;

# END
</source>