[BioPython] BLAST/tutorial problems

Thu Jul 22 19:30:21 EDT 2004

I recently started having my program hang during the part that does 
BLAST queries.  I traced the problem to this section of my code:

--------

b_results = NCBIWWW.blast('blastp', 'nr', f_record, format_type = 
"HTML")

save_file = open(data_path_prefix + file_unique_id + 'blast', 'w')

--------
which was pretty much taken verbatim from the tutorial. However instead 
of getting my results back in a usable format, I get the HTML below 
saved to a file.  My server logs just say 'unexpected end of stream' 
(this is running as part of a CGI script)

has anyone encountered an error like this before?

thanks in advance,

Aaron Zschau

--------

<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" H
EIGHT="45" ALIGN="middle">
<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" 
method="POST"><input name="ALIGNMENT
S" type="hidden" value="50"><input name="AUTO_FORMAT" type="hidden" 
value="on"><input name="CLIENT" type=
"hidden" value="web"><input name="DESCRIPTIONS" type="hidden" 
value="100"><input name="EXPECT" type="hidd
en" value="10"><input name="FORMAT_TYPE" type="hidden" 
value="HTML"><input name="HITLIST_SIZE" type="hidd
en" value="100"><input name="I_THRESH" type="hidden" 
value="0.001"><input name="LAYOUT" type="hidden" val
ue="OneWindow"><input name="NCBI_GI" type="hidden" value="yes"><input 
name="PAGE" type="hidden" value="Pr
oteins"><input name="PID" type="hidden" value="8571"><input name="RID" 
type="hidden" value="1090538237-85
71-194036110105.BLASTQ4"><input name="RTOE" type="hidden" 
value="20"><input name="SHOW_OVERVIEW" type="hi
dden" value="checked"><input name="STEP_NUMBER" type="hidden" 
value="1"><input name="_PGR" type="hidden"
value="2"><input name="_PGR" type="hidden" value="2"><input name="CMD" 
type="hidden" value="Get"></form>
<form action="Blast.cgi" enctype="application/x-www-form-urlencoded" 
method="POST" TARGET=""><input name=
"ALIGNMENTS" type="hidden" value="50"><input name="AUTO_FORMAT" 
type="hidden" value="on"><input name="CLI
ENT" type="hidden" value="web"><input name="DESCRIPTIONS" type="hidden" 
value="100"><input name="EXPECT"
type="hidden" value="10"><input name="FORMAT_TYPE" type="hidden" 
value="HTML"><input name="HITLIST_SIZE"
type="hidden" value="100"><input name="I_THRESH" type="hidden" 
value="0.001"><input name="LAYOUT" type="h
idden" value="OneWindow"><input name="NCBI_GI" type="hidden" 
value="yes"><input name="PAGE" type="hidden"
  value="Proteins"><input name="PID" type="hidden" value="8571"><input 
name="RID" type="hidden" value="109
0538237-8571-194036110105.BLASTQ4"><input name="RTOE" type="hidden" 
value="20"><input name="SHOW_OVERVIEW
" type="hidden" value="checked"><input name="STEP_NUMBER" type="hidden" 
value="1"><input name="_PGR" type
="hidden" value="2"><input name="CMD" type="hidden" value="Get">WAITING
<HTML>
<p></p>
<!--
QBlastInfoBegin
         Status=WAITING
QBlastInfoEnd
--><p></p>
<SCRIPT LANGUAGE="JavaScript"><!--
setTimeout('document.forms[0].submit();',12000);
//--></SCRIPT>
<P><table>
<tr><td>Request ID</td><td> 
<b>1090538237-8571-194036110105.BLASTQ4</b></td></tr>
<tr><td>Status</td><td>Searching</td></tr>
<tr><td>Submitted at</td><td>Thu Jul 22 19:17:17 2004</td></tr>
<tr><td>Current time</td><td>Thu Jul 22 19:18:15 2004</td></tr>
<P></table>
<p><hr>This page will be automatically updated in <b>12</b> seconds 
until search is done<BR>

</form>