[BioPython] Parsing of phd file names in Ace

[Andrew Nunberg]

Something else I noticed.

If you make an ace file with phd2Ace.perl in the consed package, the
resulting ace file breaks the parser

Andy

Oh, yes I will be using it quite a bit for  a while.

Also, has someone implimented a python API for Primer3 ? Something that will
execute and parse the results?

I am currently using the Perl one and don¹t have time to switch that script
to python

-- 
Andrew Nunberg
Bioinformagician
Orion Genomics
(314)-615-6989
www.oriongenomics.com


> From: Frank Kauff <fkauff at duke.edu>
> Organization: Duke University
> Date: Fri, 06 Feb 2004 10:46:13 -0500
> To: Andrew Nunberg <anunberg at oriongenomics.com>
> Subject: Re: [BioPython] Parsing of phd file names in Ace
> 
> Hi Andy,
> 
> hey, somebody is using it :-)
> Well spotted. I changed it. Anyway, the previous parser had some bugs
> when rt tages were interspersed between the reads of a contig. Better
> don't use it any more. I just emailed Brad the new version which I
> tested with a lot of my contigs and it seems it can handle them nicely.
> I'd be thankful if you give the ace parser a good workout and let me
> know of more bugs.
> 
> Frank
> 
> On Thu, 2004-02-05 at 18:47, Andrew Nunberg wrote:
>> In the following snipet of code
>> Ace_record is the acerecordfile from an entire parsing of an ace file
>> 
>> ace_phd_list=[]
>>     for record in ace_record.records:
>>         for ds in record.ds:
>>             ace_phd_list.append(ds.phd_file)
>> 
>> In my case the list looks like this
>> 
>> [' fvlc001f001d16f0.abd.phd.1 ', ' fvlc001f001d16k0.abd.phd.1 ']
>> There appears to be trailing white space on either side, might want strip it
>> before adding
>> 
>> Andy
> -- 
> Frank Kauff
> Dept. of Biology
> Duke University
> Box 90338
> Durham, NC 27708
> USA
> 
> Phone 919-660-7382
> Fax 919-660-7293
> 
>