Hi, im pretty new to perl, and could really do with some help;
i have a text file with over 50 Fasta sequences (genetic sequences that start with the > symbol
for example here are 2 fasta sequences - this is how it appears in my text file:
mm4_blastzTightHg16_none_knownGene_chr21 range=chr17:31141192-31141355 5'pad=0 3'pad=0 revComp=FALSE strand=+ repeatMasking=none
ACTGCCATTATCCAGGACCCTTAGGGAAGAAATCCCGCAGGAGATGAACT CACAGAGGGACCTTGTTAGGCTCTGGCTCCAGTAAAATGCATAAAAGTGA CCTCTATCTCCTCTTAGAATTCAGAAAGCCAAAAAGAACATTATTCCCAC ACAATTAAGGAGAA
mm4_blastzTightHg16_none_knownGene_chr21 range=chr17:31195588-31195813 5'pad=0 3'pad=0 revComp=FALSE strand=+ repeatMasking=none
TGGGCTCATATATAATGCATAAGTCTGGGTAATGGATACTTTTCGTTAGT CATAAAATGTTCAAATGACTCACAGATGTGTGGCCCTCGCAGCTGTTCCT CCCCAGCTAATGGTGCTGGCTTCCAGTCAGAGGACTTTTGTACCAAAGGA GTCTGGCAGCGACAGAGGTTCTTGTGATATTCCCATTGAGAGAATCATTC ACTGTCAGCAGAGACAACAATGACAA
what i need to do is
a) open the text file
b) read through the text file, for each fasta sequence (starts with an >, and ends before the next >), i want to perform the following:
(i) copy the sequence into an online submission form, hit the submit button
(ii) retrieve the results from the following webpage, and store them into another file
it doesnt seem the hardest task in the world but im pretty stuck, firstly on how to tell perl how to recognise each fasta sequnce, and then all the online submission stuff
has anyone any ideas
thanks
stuart gillies
_________________________________________________________________
Want to block unwanted pop-ups? Download the free MSN Toolbar now! http://toolbar.msn.co.uk/
-- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED] <http://learn.perl.org/> <http://learn.perl.org/first-response>
