Raj: Created page with 'Category: Bioinformatics #!/usr/bin/perl -w # Libraries use strict; use Bio::SearchIO; # Variables my ($i, $j, $inFile, $result, $hit, $report, $temp…'

2010-07-22T12:01:00Z

Created page with 'Category: Bioinformatics <source lang=perl> #!/usr/bin/perl -w # Libraries use strict; use Bio::SearchIO; # Variables my ($i, $j, $inFile, $result, $hit, $report, $temp…'

New page

[[Category: Bioinformatics]]

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

# Libraries
use strict;
use Bio::SearchIO;

# Variables
my ($i, $j, $inFile, $result, $hit, $report, $temp, $filecontent) = $_;

my $path = "/home/raj/bio";
my $path1 = "$path/user/raja";
my $path2 = "$path1/parse_blast";

# Input prompt

if (! $ARGV[0]) {
print "What is the BLAST file to parse? ";
chomp ($inFile = <STDIN>);
}
else {
$inFile = $ARGV[0];
}

my $outfile = "$path2/$inFile.hits.txt";
$temp = "$path2/temp";

# Parsing Function

$report = new Bio::SearchIO(
-file=>"$inFile",
-format => "blast");

$i = 0;
while($result = $report->next_result) {

$i++;
my $query = $result->query_accession;

$j = 0;
while ( $hit = $result->next_hit) {

$j++;
}

$filecontent = "$i\t$query\t$j\n";

open (F, ">>".$temp);
print F "$filecontent";
close F;

}

# Sort the temp File
$filecontent = `sort -t '\t' -k3 -nr $temp`;

# Making the outfile
open (FH, ">".$outfile);
print FH "Query_No\tQuery_Name\tNumber of Hits\n$filecontent";
close FH;

if (-e $temp) {`rm $temp`};

# END

</source>

Parse blast stat.pl - Revision history

Raj: Created page with 'Category: Bioinformatics #!/usr/bin/perl -w # Libraries use strict; use Bio::SearchIO; # Variables my ($i, $j, $inFile, $result, $hit, $report, $temp…'