[Bioperl-l] Blast server: checking seq prior to job submission

[Hilmar Lapp]

We could also by default just remove all digits in fasta.pm -- I'm not  
sure they'd be useful in some case (you'd have an option to turn this  
off).

Any opinions on that?

	-hilmar

On Wednesday, February 12, 2003, at 06:45  AM, Charles Hauser wrote:

> Jason,
>
> (background for list): trying to code a cgi to either warn users that
> their sequences while properly formatted FASTA are flawed, OR to
> reformat seq post submission
>
> On Wed, 2003-02-12 at 08:20, Jason Stajich wrote:
>> See the problem is they are all technically valid FASTA...  You can  
>> put
>> whatever you want on the line after the >  and then it must be  
>> sequence
>> after the next newline.
>> I'll think if there are any other ways to get at what you want.
>>
>> BTW if you run that sequence through SeqIO::fasta, does it complain,  
>> or
>> work?
>
> No, this is my concern - the queries do not match what users think they
> are submitting.
>
> seqIO fasta correctly returns the seq following the first newline.
> Somehow I need to warn users that their seq while FASTA is flawed.
>
> $in  = Bio::SeqIO->new(-file => "$infile" , '-format' => 'fasta');
>
> while ( my $seq = $in->next_seq() ) {
>     print "Sequence ",$seq->id," first 10 bases
> ",$seq->subseq(1,10),"\n";
> }
>
>
>> 13560  MLINKLWLLL VTLCLTEELA AAGEKSYGKP CGGQDCSGSC QCFPEKGARG  
>> RPGPIGIQGP
> 	TGPQGFTGST GLSGLKGERG FPGLLGPYGP KGDKGPMGVP GFLGINGIPG HPGQPGPRGP
> Sequence 13560 first 10 bases TGPQGFTGST
>
>> 14062MASEGPREPESEGIKLSADVKPFVPRFAGLNVAWLESSEACVFPSSAATYYPFVQEPPVTEQKIY 
>> TEDMA
> FGASTFPPQYLSSEITLHPYAYSPYTLDSTQNVYSVPGSQYLYNQPSCYRGFQTVKHRNENTCPLPQEMK
> Sequence  
> 14062MASEGPREPESEGIKLSADVKPFVPRFAGLNVAWLESSEACVFPSSAATYYPFVQEPPVTEQKIYT 
> EDMA first 10 bases FGASTFPPQY
>
>
>
>
> Chuck
>
>
>
>
>
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-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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