[Bioperl-l] boulder batch retrieve error

Tue, 5 Jun 2001 14:28:36 -0500

<html><head><meta Name='keywords' Content='commtouch, pronto, mail, free email, free, branded, web based, free web based email, communications, internet, software, advertising banners, e-mail, free software'></head><body   ><div align='left'><font   ><blockquote><blockquote><TT>Hi, <BR>
<BR>
I just installed the boulder package. I can use <BR>
it to retrive entries from Genbank when <BR>
accession nubmers are spelled out. However, <BR>
none of the other methods, such as <BR>
<BR>
-fetch $query, <BR>
-fetch local file,<BR>
-fetch @array, <BR>
<BR>
works for me (they all return the same error <BR>
message). <BR>
<BR>
For example, the following script results in an <BR>
error message: Can't use string <BR>
(&quot;/home/hao/Desktop/UniGene/Handpi&quot;) as an <BR>
ARRAY ref while &quot;strict refs&quot; in use at <BR>
/usr/lib/perl5/site_perl/5.6.0/Boulder/Genbank.pm <BR>
line 1092.<BR>
==========<BR>
use Boulder::Genbank<BR>
 &nbsp; $gb = Boulder::Genbank-&gt;newFh (-accessor=&gt; <BR>
'Entrez',<BR>
 &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; <BR>
-param &nbsp;=&gt; <BR>
'/home/hao/Desktop/UniGene/Handpick.refseq');<BR>
<BR>
while ($data = &lt;$gb&gt;) {<BR>
 &nbsp; &nbsp; &nbsp; print $data-&gt;Accession;<BR>
<BR>
}<BR>
===========<BR>
<BR>
Any suggestions?<BR>
<BR>
Thanks.<BR>
<BR>
Hao Chen<BR>
Univ. Tennessee at Memphis, USA<BR>
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