Anybody know about bioperl?

[norainib]

is there anyone who can teach me how to translate perl script? it is on how to call data from wordpad and import it to perl script?


Use file called swissprot.txt. Write a Perl program ( sp.pl) that extracts the following information from each entry:
• idenfication line (starts with ``ID'')
• sequence definition line (starts with ``SQ'')
• protein sequence (lines between ``SQ'' and ``//'')


How can i extract data from notepad to perl script.

for example:
ID 3BHS_BOVIN STANDARD; PRT; 372 AA.
AC P14893;
DT 01-APR-1990 (Rel. 14, Created)
DT 01-APR-1990 (Rel. 14, Last sequence update)
DT 15-JUL-1999 (Rel. 38, Last annotation update)
DE 3 BETA-HYDROXYSTEROID DEHYDROGENASE/DELTA 5-->4-ISOMERASE (3BETA-HSD)
DE [INCLUDES: 3-BETA-HYDROXY-DELTA(5)-STEROID DEHYDROGENASE
DE (EC 1.1.1.145) (3-BETA-HYDROXY-5-ENE STEROID DEHYDROGENASE)
DE (PROGESTERONE REDUCTASE); STEROID DELTA-ISOMERASE (EC 5.3.3.1) (DELTA-
DE 5-3-KETOSTEROID ISOMERASE)].
GN HSD3B.
OS Bos taurus (Bovine).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Mammalia; Eutheria; Cetartiodactyla ; Ruminantia; Pecora; Bovoidea;
OC Bovidae; Bovinae; Bos.
OX NCBI_TaxID=9913 ;
RN [1]
RP SEQUENCE FROM N.A.
RC TISSUE=OVARY;
RX MEDLINE=9009251 7; PubMed=2599102;
RA Zhao H.-F., Simard J., Labrie C., Breton N., Rheaume E., Luu-The V.,
RA Labrie F.;
RT "Molecular cloning, cDNA structure and ...

how can i use this as my data. and get output from perl just give the output of ID, SEQ,

Can anybody help or just give some link to refer this problem.?

Tq..

[KevinADC]

open(FILE, 'swissprot.txt') or die "$!";
while(<FILE>){
   do something with each line of the file
}
close(FILE);

[norainib]

open(FILE, 'swissprot.txt') or die "$!";
while(<FILE>){
   do something with each line of the file
}
close(FILE);

thanks for ur code but im not sure what doyou mean by {do something with each line to the file}


please explain to me, i really dont know....i'm still in learning stage?

[KevinADC]

maybe you should start at the beginning:

http://www.perl.org/books/beginning-perl/

[kershell]

maybe you should start at the beginning:

http://www.perl.org/books/beginning-perl/

Certainly. And go through the bioperl tutorial at http://www.bioperl.org/wiki/Bptutorial.pl