Opened by paidopoieo at 2005-12-02 02:27
User since
2003-08-04
7321 Artikel
ModeratorIn
2003-08-04
7321 Artikel
ModeratorIn
ich hab den code mal ge-perltidy-ed und ihn dann auf die daten losgelassen...
und hier der output
Code: (dl
)
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#!/usr/bin/perl -w
use strict;
use warnings;
use Bio::SeqIO;
use Bio::Tools::Run::RemoteBlast;
use Bio::Seq;
use IO::String;
use Bio::SearchIO;
my $prog = 'blastp';
my $db = 'swissprot';
my $e_val = '20000';
my $matrix = 'PAM30';
#my $outfile = 'Output';
my @data;
my $line_dataArray;
my $rid;
my $count = 1;
my @params = (
'-prog' => $prog,
'-data' => $db,
'-expect' => $e_val,
'-matrix' => $matrix
);
my $seqio_obj = Bio::SeqIO->new(
-file => "Perm.txt",
-format => "raw",
);
print "entering blast....";
my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
print "Blast entered successfully \n";
while ( my $query = $seqio_obj->next_seq ) {
print "submit Sequence...just do it....\n";
my $r = $factory->submit_blast($query);
print $query->seq;
print "\n";
# Wait for the reply and save the output file
print "entering while loop for saving Output.... \n";
while ( my @rids = $factory->each_rid ) {
foreach my $rid (@rids) {
my $rc = $factory->retrieve_blast($rid);
if ( !ref($rc) ) {
print '$rc is not a ref!', "\n";
if ( $rc < 0 ) {
print "Remove rid ...\n";
$factory->remove_rid($rid);
}
# sleep 5;
}
else {
print "retrieved Results successfully \n";
print $rid;
print "\n";
my $filename = "$count.out";
$factory->save_output($filename);
print "File saved successfully \n";
$count++;
$factory->remove_rid($rid);
}
}
print "\n";
print "\n";
}
}
und hier der output
Code: (dl
)
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entering blast....Blast entered successfully
submit Sequence...just do it....
RKKWWWRW
entering while loop for saving Output....
-------------------- WARNING ---------------------
MSG: <HTML>
<HEAD>
</HEAD>
<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
<IMG SRC="images/head_results.gif" ALT="Header of the page" BORDER="0"NAME="BlastHeaderGif" WIDTH="600" HEIGHT="45" ALIGN="middle">
<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST"><hr><font color="red">ERROR: Invalid RID: 1133551880-19615-126416106060</font
---------------------------------------------------
$rc is not a ref!
Remove rid ...
submit Sequence...just do it....
RKKWWWKW
entering while loop for saving Output....
-------------------- WARNING ---------------------
MSG: <HTML>
<HEAD>
</HEAD>
<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
<IMG SRC="images/head_results.gif" ALT="Header of the page" BORDER="0"NAME="BlastHeaderGif" WIDTH="600" HEIGHT="45" ALIGN="middle">
<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST"><hr><font color="red">ERROR: Invalid RID: 1133551883-28224-102103062411</font
---------------------------------------------------
$rc is not a ref!
Remove rid ...
submit Sequence...just do it....
KRKWKRKW
entering while loop for saving Output....
-------------------- WARNING ---------------------
MSG: <HTML>
<HEAD>
</HEAD>
<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
<IMG SRC="images/head_results.gif" ALT="Header of the page" BORDER="0"NAME="BlastHeaderGif" WIDTH="600" HEIGHT="45" ALIGN="middle">
<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST"><hr><font color="red">ERROR: Invalid RID: 1133551891-20159-118320711185</font
---------------------------------------------------
$rc is not a ref!
Remove rid ...
submit Sequence...just do it....
RKRKWKRR
entering while loop for saving Output....
-------------------- WARNING ---------------------
MSG: <HTML>
<HEAD>
</HEAD>
<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
<IMG SRC="images/head_results.gif" ALT="Header of the page" BORDER="0"NAME="BlastHeaderGif" WIDTH="600" HEIGHT="45" ALIGN="middle">
<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST"><hr><font color="red">ERROR: Invalid RID: 1133551897-20419-66770204654</font>
---------------------------------------------------
$rc is not a ref!
Remove rid ...
submit Sequence...just do it....
RKRKWKRW
entering while loop for saving Output....
-------------------- WARNING ---------------------
MSG: <HTML>
<HEAD>
</HEAD>
<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
<IMG SRC="images/head_results.gif" ALT="Header of the page" BORDER="0"NAME="BlastHeaderGif" WIDTH="600" HEIGHT="45" ALIGN="middle">
<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST"><hr><font color="red">ERROR: Invalid RID: 1133551905-20883-151607413394</font
---------------------------------------------------
$rc is not a ref!
Remove rid ...
submit Sequence...just do it....
RKRKWKWK
entering while loop for saving Output....
-------------------- WARNING ---------------------
MSG: <HTML>
<HEAD>
</HEAD>
<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
<IMG SRC="images/head_results.gif" ALT="Header of the page" BORDER="0"NAME="BlastHeaderGif" WIDTH="600" HEIGHT="45" ALIGN="middle">
<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST"><hr><font color="red">ERROR: Invalid RID: 1133551910-29540-201656722897</font
---------------------------------------------------
$rc is not a ref!
Remove rid ...
submit Sequence...just do it....
KRKWKWRW
entering while loop for saving Output....
-------------------- WARNING ---------------------
MSG: <HTML>
<HEAD>
</HEAD>
<BODY BGCOLOR="#FFFFFF" LINK="#0000FF" VLINK="#660099" ALINK="#660099">
<IMG SRC="images/head_results.gif" ALT="Header of the page" BORDER="0"NAME="BlastHeaderGif" WIDTH="600" HEIGHT="45" ALIGN="middle">
<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" method="POST"><hr><font color="red">ERROR: Invalid RID: 1133551913-21163-178685964119</font
---------------------------------------------------
$rc is not a ref!
Remove rid ...