Oct 27, 2009, 4:07 AM
Post #1 of 3
Hello to all,
Perl for bioinformatrics...
My name is Alvaro and I´m new here (and also in perl programming). I´ve started my PhD studies in Molecular Biology, and my supervisor has encouraged me to learn Perl in order to use it to perform some bioinformatic tasks.
I´m a Biologists with no programming experience, and its being very hard to me learn Perl programming at the moment.
It seems that since my programming background was null at the moment, I cannot run a perl program correctly since I came across "syntax" errors all the time and you (people in this forum) are the only expertise advice I can get, so please forgive me if any script I ask you about has what you may call as "basic mistakes"...
I tried to create a program that reads a list of Protein Accesion Numbers (PAN) from a plain text file, assign those PAN to an array. Then using a loop, each of these PAN should be extracted from a database using a Bioperl script.
My program doesn´t seem to work at all, and I wonder if you could take a look at it an tell me what I´m doing wrong.
You will save my neck if you help me.
Here is the program I´ve written:
# Enter the list trough STDIN
print "Enter your list name:";
@list = <STDIN>;
# The loop to retrieve each of the list PAN
# and write them to a file
foreach $list (@list)
my $out = new Bio::SeqIO (-file => ">remote_seqs.fasta",
-format => 'fasta');
$db = new Bio::DB::GenPept();
$seq = $db->get_Seq_by_acc('');
Thanks in advance