[Bioperl-l] regexp / protein database

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Wed Aug 30 13:21:34 EDT 2006


Correcting myself, that should have been:

my @regexps = ("regexp1", "regexp2", "regexp3");
for my $i (0 .. $#regexps) {
     my $regexp = $regexps[$i];
     while ($record =~ /$regexp/g) {
         # Do something fancy
     }
}

Apologies,
Mauricio.

Mauricio Herrera Cuadra wrote:
> Supposing that you have an array with all the desired regexps you want 
> to search on a record, you can try something like this:
> 
> my @regexp = ("regexp1", "regexp2", "regexp3");
> for my $i (0 .. $#regexp) {
>      while ($record =~ /$i/g) {
>          # Do something fancy
>      }
> }
> 
> Regards,
> Mauricio.
> 
> Chris Fields wrote:
>> Funny, I was thinking along the lines of a motif search.  Didn't even think
>> of this solution!
>>
>> Chris
>>
>>> -----Original Message-----
>>> From: Cook, Malcolm [mailto:MEC at stowers-institute.org]
>>> Sent: Tuesday, August 29, 2006 10:43 AM
>>> To: Chris Fields; Hubert Prielinger
>>> Cc: bioperl-l at bioperl.org
>>> Subject: RE: [Bioperl-l] regexp / protein database
>>>
>>> For swissprot, you might try SwissKnife
>>> (http://swissknife.sourceforge.net/docs/)
>>>
>>> This will let you write something like this (based on example snippet
>>> provided):
>>>
>>>
>>> use SWISS::Entry;
>>> # Read an entire record at a time
>>> $/ = "\/\/\n";
>>> while (<>){
>>>   $entry = SWISS::Entry->fromText($_);
>>>   next unless $entry->SQs->seq =~ m/$YourRegExp/o;
>>>   DO WHAT YOU WANT TO THE SEQUENCE
>>> }
>>>
>>>
>>>
>>>> -----Original Message-----
>>>> From: bioperl-l-bounces at lists.open-bio.org
>>>> [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Chris Fields
>>>> Sent: Monday, August 28, 2006 8:41 PM
>>>> To: Hubert Prielinger
>>>> Cc: bioperl-l at bioperl.org
>>>> Subject: Re: [Bioperl-l] regexp / protein database
>>>>
>>>> Hubert,
>>>>
>>>> This is answered in the FAQ.  You might also check the mail list
>>>> archives via gmane.
>>>>
>>>> http://www.bioperl.org/wiki/FAQ#Utilities
>>>>
>>>> http://search.gmane.org/?
>>>> query=&email=&group=gmane.comp.lang.perl.bio.general&sort=relev
>>>> ance&DEFA
>>>> ULTOP=and&query=
>>>>
>>>> Chris
>>>>
>>>> On Aug 28, 2006, at 8:15 PM, Hubert Prielinger wrote:
>>>>
>>>>> Hi,
>>>>> Is it possible to scan a protein database (e.g: swissprot..) directly
>>>>> with regular expression. I have taken a look at
>>>>> Bio::Tools::SeqPattern,
>>>>> but it seems it isn't a proper solution.
>>>>> like it is done on that webpage: http://scansite.mit.edu/
>>>>> dbsequence_reg.html
>>>>>
>>>>> thanks
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>> Christopher Fields
>>>> Postdoctoral Researcher
>>>> Lab of Dr. Robert Switzer
>>>> Dept of Biochemistry
>>>> University of Illinois Urbana-Champaign
>>>>
>>>>
>>>>
>>>> _______________________________________________
>>>> Bioperl-l mailing list
>>>> Bioperl-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
> 

-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM



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