Parse blast.pl - Revision history

Raj at 18:33, 28 December 2009

2009-12-28T18:33:21Z

← Older revision		Revision as of 18:33, 28 December 2009
Line 81:		Line 81:
	# Filters only the top hit scaffold		# Filters only the top hit scaffold
	next if ($scaf_ids[0] ne "$scaf_id");		next if ($scaf_ids[0] ne "$scaf_id");
			#cutoff if the alignment length is less than 70
			next if ($aln_length < 70);

	open (F, ">>".$resdir."/".$file);		open (F, ">>".$resdir."/".$file);

Raj at 18:05, 27 December 2009

2009-12-27T18:05:34Z

← Older revision		Revision as of 18:05, 27 December 2009
Line 6:		Line 6:
	# -> Parse the Blast output of scaffold mapping		# -> Parse the Blast output of scaffold mapping
	# -> Write the results into a seperate folder with each EST		# -> Write the results into a seperate folder with each EST
			# -> Write the statistics files (est_scaf_hit.stat, unique_scaf_hit.stat)
	# Author : Rajkumar (itc@rajkumar.in)		# Author : Rajkumar (itc@rajkumar.in)
	# Release: DEC 2009		# Release: DEC 2009
Line 19:		Line 20:

	# Variables		# Variables
	my $path = "/home/raj/bio";		my $path = "/home/raj/bio";
	my $infile = "$path/euca/blast/est_scaffold.txt";		my $infile = "$path/euca/blast/est_scaffold.txt";
	my $tempdir = "$path/euca/blast/temp";		my $tempdir = "$path/euca/blast/temp";
	my $resdir = "$path/euca/blast/result";		my $resdir = "$path/euca/blast/result";
	my $statfile = "$path/euca/blast/blast.stat";		my $statfile = "$path/euca/blast/est_scaf_hit.stat";
			my $uniquescaf= "$path/euca/blast/unique_scaf_hit.stat";

	my ($i) = $_;		my ($i) = $_;
	my (@files,@esthits) = @_;		my (@files,@esthits, @uniquescaf, @uniquescaf_ ) = @_;

	# Parsing Functions		# Parsing Functions
Line 108:		Line 110:

	push(@esthits, "$est_id\t$scaf_id\n");		push(@esthits, "$est_id\t$scaf_id\n");
			push(@uniquescaf, "$scaf_id\n");

	}		}
	}		}


			# Writing the EST vs scaffolds
	@esthits = sort(@esthits);		@esthits = sort(@esthits);


	open (H, ">".$statfile);		open (H, ">".$statfile);
	print H "@esthits";		print H "@esthits";
	close H;		close H;

			#Writing the unique scaffold names
			my %seen;
			@uniquescaf_ = grep !$seen{$_}++, @uniquescaf;
			@uniquescaf_ = sort(@uniquescaf_);

			open (H1, ">".$uniquescaf);
			print H1 "@uniquescaf_";
			close H1;


	print "\nDone!\n\n";		print "\nDone!\n\n";

Raj at 17:24, 27 December 2009

2009-12-27T17:24:23Z

← Older revision		Revision as of 17:24, 27 December 2009
Line 1:		Line 1:
	<source ~~land~~=perl>		<source lang=perl>
	#! /usr/bin/perl -w		#! /usr/bin/perl -w

Raj: New page: #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Parse the Blast output of scaff...

2009-12-27T17:24:05Z

New page: <source land=perl> #! /usr/bin/perl -w # ************************************************************* # This Programme does the following in sequence # -> Parse the Blast output of scaff...

New page

<source land=perl>
#! /usr/bin/perl -w

# *************************************************************
# This Programme does the following in sequence
# -> Parse the Blast output of scaffold mapping
# -> Write the results into a seperate folder with each EST
# Author : Rajkumar (itc@rajkumar.in)
# Release: DEC 2009
# *************************************************************

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

# At the top: Time Start
my ($sec,$min,$hour,$mday,$mon,$year,$wday,$yday,$isdst) = localtime(time);

# Variables
my $path = "/home/raj/bio";
my $infile = "$path/euca/blast/est_scaffold.txt";
my $tempdir = "$path/euca/blast/temp";
my $resdir = "$path/euca/blast/result";
my $statfile = "$path/euca/blast/blast.stat";

my ($i) = $_;
my (@files,@esthits) = @_;

# Parsing Functions

# Having the required dir
if (-e "$tempdir") {`rm -fr $tempdir`;}
if (! -e "$tempdir") {`mkdir $tempdir`;}
if (-e "$resdir") {`rm -fr $resdir`;}
if (! -e "$resdir") {`mkdir $resdir`;}

# Let's Parse the file to have files written for indiavidual ESTs

foreach my $line (split ("\n", `cat $infile`)) {

next if ($line !~ m/^CL|gi/);
next if ($line =~ m/^#/);

foreach my $tab (split ("\t", $line)) {
next if ($tab !~ m/^CL|gi|sca/);
$tab =~ s/\|/_/g;

if ($tab =~ m/^CL|gi/) {

open (FH, ">>".$tempdir."/".$tab.".gff");
print FH "$line\n";
close FH;
}
}
}

# Work woth the temp file to pick only the top hits with one scaffold
opendir (DIR, "$tempdir") or die $!;
@files = readdir(DIR);
close(DIR);

foreach my $file(@files) {
next if ($file eq "." or $file eq "..");

# Clearing the array
my @scaf_ids = ();

foreach my $line_ (split ("\n", `cat $tempdir/$file`)) {

my ($est_id, $scaf_id) = split(/\t/, $line_);
push(@scaf_ids, "$scaf_id");

# Filters only the top hit scaffold
next if ($scaf_ids[0] ne "$scaf_id");

open (F, ">>".$resdir."/".$file);
print F "$line_\n";
close F;
}
}

# cleaning the temp dir
if (-e "$tempdir") {`rm -fr $tempdir`;}

# Generating statistics
opendir (DIR, "$resdir") or die $!;
@files = readdir(DIR);
close(DIR);

foreach my $file(@files) {
next if ($file eq "." or $file eq "..");

$i = 0;
foreach my $line__ (split ("\n", `cat $resdir/$file`)) {

$i++;
my ($est_id, $scaf_id) = split(/\t/, $line__);
next if ( $i>1 );

push(@esthits, "$est_id\t$scaf_id\n");
}
}

@esthits = sort(@esthits);

open (H, ">".$statfile);
print H "@esthits";
close H;

print "\nDone!\n\n";

# At the End: Time Calculation
my ($sec_,$min_,$hour_,$mday_,$mon_,$year_,$wday_,$yday_,$isdst_) = localtime(time);
my $days = $mday_-$mday;
my $hours = $hour_-$hour;
my $mins = $min_-$min;
my $secs = $sec_-$sec;
print "\n------------------------\nDuration: ";
if ($days>0) { print "$days days";}
if ($hours>0) { print ": $hours hours";}
if ($mins>0) { print ": $mins mins";}
if ($secs>0) { print ": $secs secs";}
print "\n------------------------\n";

# END
</source>