[Bioperl-l] [Bug 2937] Strand in fasta35 output does not seem to be parsed

[Dave Messina]

Hi Mick,

Did you try running the test case that you had originally attached to the bug report? Or is the below from different code and a diffrent fasta output file?

In any case, I'll need to look at the fasta35 output file and the parse2.pl you ran in order to reproduce and fix this -- could you please open a new bug report and attach them to it?

Thanks,
Dave



On Nov 30, 2009, at 17:49, michael watson (IAH-C) wrote:

> Hi Dave
> 
> Just got round to looking at this.
> 
> In bioperl-1.6.0, the strand didn't get parsed, but the module only warned about something:
> 
> --------------------- WARNING ---------------------
> MSG: Unrecognized alignment line (1) ' /usr/local/fasta3/bin/fasta35 -n -U -Q -H -A -E 2.0 -C 19 -m 0 -m 9i -O iltv_pre.fasta35 iltv_pre.fasta clusters.fasta'
> ---------------------------------------------------
> 
> However, in the bioperl-live I just downloaded, this had turned into a full-on stack trace:
> 
> ------------- EXCEPTION -------------
> MSG: Unrecognized alignment line (1) ' /usr/local/fasta3/bin/fasta35 -n -U -Q -H -A -E 2.0 -C 19 -m 0 -m 9i -O iltv_pre.fasta35 iltv_pre.fasta clusters.fasta'
> STACK Bio::SearchIO::fasta::next_result /usr/local/bioperl-live_301109//Bio/SearchIO/fasta.pm:1347
> STACK toplevel parse2.pl:20
> -------------------------------------
> 
> I'm not sure if this is even related to the strand issue (I suspect not, but you never know) but something changed between bioperl-1.6.0 and the live trunk I downloaded today to ensure I still can't use the module.
> 
> Is this another bug report?
> 
> Thanks again for all your help
> 
> Mick
> 
> -----Original Message-----
> From: Dave Messina [mailto:David.Messina at sbc.su.se] 
> Sent: 23 November 2009 17:46
> To: michael watson (IAH-C)
> Subject: Re: [Bug 2937] Strand in fasta35 output does not seem to be parsed
> 
> Hi Mick,
> 
> Sure thing -- the current build from subversion is packaged up every  
> night and available here:
> http://www.bioperl.org/DIST/nightly_builds/
> 
> Just grab bioperl-live.tar.gz from there and you'll get the changes.
> 
> 
> Dave
> 
> 
> 
> 
> On Nov 23, 2009, at 6:34 PM, michael watson (IAH-C) wrote:
> 
>> Hi Dave
>> 
>> Thanks for the hard work.
>> 
>> Trying to get the latest updates so I can use this... don't have svn  
>> on my server, tried to install it and I don't have python either,  
>> which is needed to install it.
>> 
>> I face about 3 weeks whilst my IT department sort this out, unless I  
>> can access the changes any other way?
>> 
>> Thanks
>> Mick
>> 
>> -----Original Message-----
>> From: bugzilla-daemon at portal.open-bio.org [mailto:bugzilla- 
>> daemon at portal.open-bio.org]
>> Sent: 20 November 2009 15:12
>> To: michael watson (IAH-C)
>> Subject: [Bug 2937] Strand in fasta35 output does not seem to be  
>> parsed
>> 
>> http://bugzilla.open-bio.org/show_bug.cgi?id=2937
>> 
>> 
>> online at davemessina.com changed:
>> 
>>          What    |Removed                     |Added
>> ----------------------------------------------------------------------------
>>            Status|NEW                         |RESOLVED
>>        Resolution|                            |FIXED
>> 
>> 
>> 
>> 
>> ------- Comment #7 from online at davemessina.com  2009-11-20 10:12 EST  
>> -------
>> Fixed in r16394.
>> 
>> Michael, thanks for the report. Your test cases pass, but please  
>> reopen the bug
>> if needed.
>> 
>> 
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