perl - Searching FASTA file for motif and returning title line for each sequence containing the motif -

below code have searching fasta file entered @ command line user-provided motif. when run , enter motif know in file returns 'motif not found'. i'm beginner in perl, , can't fugure out how print motif found, let alone return title line. appreciate in resolving this.

thanks.

use warnings; use strict;   $motif;   $filename;   @seq;    #my $motif_found;   $scalar;    $filename = $argv[0];    open (dnafile,$filename) || die "cannot open file\n"; @seq = split(/[>]/, $filename); print "enter motif search for; ";  $motif = <stdin>;    chomp $motif;   foreach $scalar(@seq) {       if ($scalar =~ m/$motif/ig) {         print "motif found in following sequences\n";           print $scalar;       } else {         print "motif not found\n";       }   }   close dnafile; 

there no point in "rolling own" fasta parser. bioperl has spent years developing one, , silly not use it.

use strict; use bio::seqio;  $usage = "perl dnamotif.pl <fasta file> <motif>"; $fasta_filename = shift(@argv) or die("usage: $usage $!"); $motif = shift(@argv) or die("usage: $usage $!");  $fasta_parser = bio::seqio->new(-file => $fasta_filename, -format => 'fasta'); while(my $seq_obj = $fasta_parser->next_seq()) {   printf("searching sequence '%s'...", $seq_obj->id);   if((my $pos = index($seq_obj->seq(), $motif)) != -1)   {     printf("motif found @ position %d!\n", $pos + 1);   }   else   {     printf("motif not found.\n");   } } 

this program finds (1-based) position of first motif match in each sequence. can edited find position of each match. may not print things in format want/need. i'll leave these issues "an exercise reader." :)

if need download bioperl, try this link. let me know if have issues.

for bioinformatics questions this, i've found biostar forum helpful.