[BioPython] sequences description in Expasy

[Alessandro S. Nascimento]

Hi Sebastian,


here is a fragment of the the seqfile. I've put a "infile.readline" at 
the beginning of the script to skip the information line....

Hope you will be able to test....


thanks


alessandro




Sequences in NR_asn.aln with network comprising ['W', 'R', 'R'] residues 
in [13, 72, 251] positions
Q61RZ3_CAEBR/179-386
O16963_CAEEL/229-435
O16676_CAEEL/221-428
Q966A2_CAEEL/177-390
NHR59_CAEEL/202-415
O18087_CAEEL/172-352
Q3I5Q0_GECLA/203-349
Q3I5P9_GECLA/237-418
Q3I5Q1_GECLA/236-417
Q3I5Q2_GECLA/241-422
O76241_UCAPU/270-451
Q9U7D9_LOCMI/201-382
Q6V7U7_LOCMI/223-404
Q4GZT9_BLAGE/247-428
Q4GZU0_BLAGE/224-405
Q86LU9_9HYME/111-283
Q52ZN8_9HYME/98-258
Q86LU7_9HYME/113-285
Q52ZN9_POLFU/91-272
Q9NG48_APIME/239-420
Q5MBF7_9HYME/239-420
Q86LV1_LITFO/134-305
Q9NFY1_TENMO/220-401
Q4W6C8_LEPDE/196-377
Q3HYJ8_STRPU/132-294
Q8T5C6_BIOGL/247-428
Q5I7G2_LYMST/247-428
Q66TQ0_9CAEN/241-422
RXRB_MOUSE/331-512
RXRB_RAT/269-450
Q499T0_RAT/296-477
Q6MGB3_RAT/262-443
Q5JP90_HUMAN/248-389
O97864_PIG/18-187
RXRB_HUMAN/344-525
Q32S23_BOVIN/343-524
Q4VXY7_HUMAN/293-474
Q5STP9_HUMAN/344-525
RXRB_CANFA/344-525
Q95L53_MUSVI/336-517
Q2PZU8_PIG/185-366
RXRA_HUMAN/273-454
RXRA_MOUSE/278-459
RXRA_RAT/278-459
Q2V504_HUMAN/263-444
Q3UMU4_MOUSE/278-459
Q5VYG4_HUMAN/273-454
Q6LC96_MOUSE/250-431
Q6P3U7_HUMAN/327-508
RXRA_XENLA/299-480
Q804B5_CARAU/108-289
RXRAB_BRARE/190-371
Q7T2G7_DICLA/92-273
RXRA_BRARE/252-433
Q90Y66_PAROL/116-291
Q6DHP9_BRARE/263-444
Q90Y01_PETMA/65-237




Sebastian Bassi wrote:
> Hello,
>
> Could you please provide me a sample "seq_file" like the one your
> program uses, just to test your code.
> Best regards.
> SB.
>
> On 8/30/06, Alessandro S. Nascimento <as_nascimento at yahoo.com.br> wrote:
>> Hi all,
>>
>>
>> I am trying to write something to read a list of sequences and search
>> some descriptions of them in expasy. I wrote something as follows:
>>
>> def sequence_retriever(seq_file):
>>     from Bio.WWW import ExPASy
>>     infile=open(seq_file, 'r')
>>     infile.readline()
>>     result=[]
>>     for line in infile:
>>         i=0
>>         while line[i:i+1] != '/':
>>             i=i+1
>>
>>         else:
>>             result.append(line[0:i])
>>     all_results=''
>>     for res in result:
>>         detail=ExPASy.get_sprot_raw(res)
>> ==>      print detail.read()
>>         all_results=all_results+detail.read()
>>     print all_results
>>
>>
>> And it is working (at least until this moment!) but I would be very
>> helpful if there was how to get something like detail.description that
>> could print out the line that starts with DE and contains the
>> informations about the sequence.... I've looked in documentation and
>> tutorials but didn't find anything.  Does anyone have any clue?
>>
>> Thanks
>>
>>
>> alessandro
>> _______________________________________________
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>>
>
>