in reply to how do i obtain blast result from the given file
Your homepage says you're new to programming, so I thought I'd add some missing bits of code (in bold) in case you were not aware that they should be there.
NB I have not changed/fixed the logic of your code.
eg
If you're looking for some good books, I can highly recommend these 3 books which form a 3 part series:
Learning Perl: Making Easy Things Easy and Hard Things Possible
Intermediate Perl: Beyond The Basics of Learning Perl
Mastering Perl: Creating Professional Programs with Perl
I just happened to notice this. I have no idea what it it like, but it might be just what you want:
Mastering Perl for Bioinformatics
NB I have not changed/fixed the logic of your code.
--------------------------------------------------------------------- #!usr/bin/perl -w use strict; use warnings; open(IN,"/home/maize/sequence-ID.txt") || die $!; open(OUT,">abc.txt") || die $!; open(OUT1,">blastresults.txt") || die $!; while(my $id=<IN>) { $id=~s/\n|\r//g; open(BLAST,"output/$id") || die $!; while(my $file=<BLAST>) { if ($file=~ m/No hits found/) { print OUT "$id \n"; } } close(BLAST) || die $!; } close(IN) || die $!; close(OUT) || die $!; close(OUT1) || die $!; ---------------------------------------------------------------------If you prefer you can use normal Perl variables instead of file handles
eg
--------------------------------------------------------------------- open(my $blast,"output/$id") || die $!; while(my $file=<$blast>) { if ($file=~ m/No hits found/) { print OUT "$id \n"; } } close($blast) || die $!; ---------------------------------------------------------------------
If you're looking for some good books, I can highly recommend these 3 books which form a 3 part series:
Learning Perl: Making Easy Things Easy and Hard Things Possible
Intermediate Perl: Beyond The Basics of Learning Perl
Mastering Perl: Creating Professional Programs with Perl
I just happened to notice this. I have no idea what it it like, but it might be just what you want:
Mastering Perl for Bioinformatics
|
---|
Replies are listed 'Best First'. | |
---|---|
Re^2: how do i obtain blast result from the given file
by bingalee (Acolyte) on Jun 18, 2013 at 19:56 UTC |
In Section
Seekers of Perl Wisdom