[Bioperl-l] parsing interproscan result

[Dave Messina]

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On Thu, May 12, 2011 at 11:32, Shachi Gahoi <shachigahoimbi at gmail.com>wrote:

> How to use Bio::SeqIO::interpro<http://search.cpan.org/%7Ecjfields/BioPerl-1.6.900/Bio/SeqIO/interpro.pm>module of bioperl.
>

As I said in my previous, email, see the SeqIO HOWTO:
http://www.bioperl.org/wiki/HOWTO:SeqIO



> In bioperl site only following code is available. Where is test file
> "t/SeqIO/interpro". Please help me.
>

It's part of the BioPerl distribution.
https://github.com/bioperl/bioperl-live/blob/master/t/SeqIO/interpro.t


Dave






> ################################################
>
> use strict;
>   use Bio::SeqIO;
>
>   my $io = Bio::SeqIO->new(-format => "interpro",
>
>                            -file   => $interpro_file);
>
>   while (my $seq = $io->next_seq) {
>
>
>     # use the Sequence object
>   }
>
> ##################################################
>
>
>
>
>
> On Thu, May 12, 2011 at 1:02 PM, Dave Messina <David.Messina at sbc.su.se>wrote:
>
>> Hi Shachi,
>>
>> There is a SeqIO module for parsing InterProScan XML which I think will do
>> what you want. Bio::SeqIO::interpro
>>
>> The basic structure of your code will follow the SeqIO idiom (see the
>> SeqIO HOWTO), and the test file t/SeqIO/interpro.t has some bits of example
>> code that might be helpful for the interpro-specific stuff.
>>
>> Dave
>>
>>
>>
>>
>> On Thu, May 12, 2011 at 08:22, Shachi Gahoi <shachigahoimbi at gmail.com>wrote:
>>
>>> I want to parse interproscan result and through parsing of interproscan
>>> result I want PROSITE signature as an output.
>>>
>>> Like, I entered a particular sequence in Interproscan and now i want to
>>> parse a domain signature it contains.
>>>
>>> So how can i parse a particular domain signature from interproscan
>>> output.
>>>
>>> Is there any module in bioperl to parse a domain signature from
>>> interproscan
>>> output.
>>>
>>> Please tell me if anyone knows.
>>>
>>>
>>>
>>> Thanks in advance
>>>
>>> --
>>> Regards,
>>> Shachi
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>
>>
>
>
> --
> Regards,
> Shachi
>