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<p>Jason,<br>
Thanks for responding. <br>
So I produce my sim4cc file with ./sim4cc <filename1> <filename2> A=4 > output_file<br>
<br>
My code is very simple <br>
<br>
#!/usr/bin/perl<br>
use Bio::Seq;<br>
use Bio::SearchIO;<br>
use Bio::SeqIO;<br>
<br>
my $sim4 = new Bio::SearchIO(-format => 'sim4',<br>
-file => 'c:\\perl\\sim4cc.result');<br>
<br>
while( my $result = $sim4->next_result ) {<br>
## $result is a Bio::Search::Result::ResultI compliant object<br>
<br>
while( my $hit = $result->next_hit ) {<br>
## $hit is a Bio::Search::Hit::HitI compliant object<br>
while( my $hsp = $hit->next_hsp ) {<br>
## $hsp is a Bio::Search::HSP::HSPI compliant object<br>
<br>
print "Query string ", $hsp->query_string , "\n";<br>
print "Hit string " , $hsp->hit_string , "\n";<br>
<br>
}<br>
}<br>
}<br>
exit;<br>
<br>
<br>
The hit string is always blank but the query string is what you would expect.<br>
<br>
I've attached a sim4cc output file. <br>
<br>
btw - I installed regular sim4 ran a gene through it; parsed with the above and it too is missing the hit string?<br>
<br>
I'm not sure if I'm doing something wrong or it something with the parsing process<br>
<br>
thanks,<br>
jeff kittrell<br>
<br>
<i>(See attached file: sim4.results)</i><br>
<br>
<br>
<br>
<br>
<img width="16" height="16" src="cid:0__=09BBFC47DFE60E668f9e8a93df93869@unmc.edu" border="0" alt="Inactive hide details for Jason Stajich ---02/24/2010 01:50:37 PM---sending an example can help -- I guess the formats are diff"><font color="#424282">Jason Stajich ---02/24/2010 01:50:37 PM---sending an example can help -- I guess the formats are different enough that the parser doesn't wor</font><br>
<br>
<table width="100%" border="0" cellspacing="0" cellpadding="0">
<tr valign="top"><td width="1%"><img width="96" height="1" src="cid:1__=09BBFC47DFE60E668f9e8a93df93869@unmc.edu" border="0" alt=""><br>
<font size="2" color="#5F5F5F">From:</font></td><td width="100%"><img width="1" height="1" src="cid:1__=09BBFC47DFE60E668f9e8a93df93869@unmc.edu" border="0" alt=""><br>
<font size="2">Jason Stajich <jason@bioperl.org></font></td></tr>
<tr valign="top"><td width="1%"><img width="96" height="1" src="cid:1__=09BBFC47DFE60E668f9e8a93df93869@unmc.edu" border="0" alt=""><br>
<font size="2" color="#5F5F5F">To:</font></td><td width="100%"><img width="1" height="1" src="cid:1__=09BBFC47DFE60E668f9e8a93df93869@unmc.edu" border="0" alt=""><br>
<font size="2">Jeff S Kittrell <jskittrell@unmc.edu></font></td></tr>
<tr valign="top"><td width="1%"><img width="96" height="1" src="cid:1__=09BBFC47DFE60E668f9e8a93df93869@unmc.edu" border="0" alt=""><br>
<font size="2" color="#5F5F5F">Cc:</font></td><td width="100%" valign="middle"><img width="1" height="1" src="cid:1__=09BBFC47DFE60E668f9e8a93df93869@unmc.edu" border="0" alt=""><br>
<font size="2">bioperl-l <bioperl-l@lists.open-bio.org></font></td></tr>
<tr valign="top"><td width="1%"><img width="96" height="1" src="cid:1__=09BBFC47DFE60E668f9e8a93df93869@unmc.edu" border="0" alt=""><br>
<font size="2" color="#5F5F5F">Date:</font></td><td width="100%"><img width="1" height="1" src="cid:1__=09BBFC47DFE60E668f9e8a93df93869@unmc.edu" border="0" alt=""><br>
<font size="2">02/24/2010 01:50 PM</font></td></tr>
<tr valign="top"><td width="1%"><img width="96" height="1" src="cid:1__=09BBFC47DFE60E668f9e8a93df93869@unmc.edu" border="0" alt=""><br>
<font size="2" color="#5F5F5F">Subject:</font></td><td width="100%"><img width="1" height="1" src="cid:1__=09BBFC47DFE60E668f9e8a93df93869@unmc.edu" border="0" alt=""><br>
<font size="2">Re: [Bioperl-l] sim4cc vs sim4</font></td></tr>
<tr valign="top"><td width="1%"><img width="96" height="1" src="cid:1__=09BBFC47DFE60E668f9e8a93df93869@unmc.edu" border="0" alt=""><br>
<font size="2" color="#5F5F5F">Sent by:</font></td><td width="100%"><img width="1" height="1" src="cid:1__=09BBFC47DFE60E668f9e8a93df93869@unmc.edu" border="0" alt=""><br>
<font size="2">Jason Stajich <jason.stajich@gmail.com></font></td></tr>
</table>
<hr width="100%" size="2" align="left" noshade style="color:#8091A5; "><br>
<br>
<br>
<font size="4">sending an example can help -- I guess the formats are different enough that the parser doesn't work. Why people don't just generate a GFF or simple tab format when they write a new tool, I don't know....<br>
<br>
-jason<br>
<br>
Jeff S Kittrell wrote: </font>
<ul>
<ul><font size="4">Has anyone used the sim4 file parser on a sim4cc? When I parse the file with SearchIO(-format => 'sim4') or Bio::Tools::Sim4::Results the query string returns a null. I assume there is some slight difference between the two file formats? Any help is appreciated.<br>
<br>
Jeff</font>
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