HI to all, I have a file with lots of sequences but I want to extract sequences only with the keyword "FULL-LENGTH". I dont want sequences with keywords NON-FULL-LENGTH.I have a text file that has 8,000 sequences distributed in equal amount with these 2 keywords Can anybody suggest a perl program for this problem?
>isotig07104 FULL-LENGTH (BLAST)
GGTGAGTACTAAATTATaCGAAAGATTGAaGTCCAGTTATAGCTCTGCCT
ATAaTTAAAGCATGAATATCGTGAGTTCCTTCGTATGTGTTTACAGTTTC
>isotig07106 NON-FULL-LENGTH (BLAST)
TTAGCATATTCTAtCTTTTTtAGAcTAAGGAAaGATGGAAgTGtAaTtAA
aGAATTTGAaCCAAAAATTCATAGAtCTGTtATTAAGTCATGTGCTAAaT
Thank u raghul
"Hi to neilfws & all others Thanks for the response. I made-up the code, please correct it. Can you people suggest me tutorial links or textbooks for Bioperl.
!/usr/bin/perl -w
use strict;
use Bio::SeqIO;
my $seqin = Bio::SeqIO->new(-file => "euplotes.txt", -format => "fasta");
my $seqout = Bio::SeqIO->new(-file => ">outfile.txt", -format => "fasta");
while(my $seq = $seqin->next_seq)
{
if($seq->desc) =~/^FULL-LENGTH\s+/ {
$seqout->write_seq($seq);
}
}
".
My answer with awk, not perl. If the lines starting with '>' contains "NON-FULL-LENGTH" then don't print the remaining lines.
cat biostar7114.fasta | awk '/^>/ {
ok=(index($0,"NON-FULL-LENGTH")==0);
if(ok) print $0;
next;
}
{
if(ok) print $0;
}'
>isotig07104 FULL-LENGTH (BLAST)
GGTGAGTACTAAATTATaCGAAAGATTGAaGTCCAGTTATAGCTCTGCCT
ATAaTTAAAGCATGAATATCGTGAGTTCCTTCGTATGTGTTTACAGTTTC
You can use my answer to your previous question as a starting point.
In this case, the Bioperl method to use is $seq->desc. In your sample sequence fasta header:
>isotig07104 FULL-LENGTH (BLAST)
The description is everything after the first space. Since you are looking for descriptions that begin with the words "FULL-LENGTH", then something like:
if($seq->desc) =~/^FULL-LENGTH\s+/ {
# write sequence to file as per my previous answer
}
should work.
I suggest investing some effort in learning at least a few of the Bioperl methods (and regular expressions); it will make solving these "variations on a theme" problems very easy indeed.
I made as u have told & I am giving the code below, please correct it
#!/usr/bin/perl -w
use strict;
use Bio::SeqIO;
my $seqin = Bio::SeqIO->new(-file => "inputfile.txt", -format => "fasta");
my $seqout = Bio::SeqIO->new(-file => ">full_length.txt", -format => "fasta");
while(my $seq = $seqin->next_seq) {
if($seq->desc) =~/^FULL-LENGTHs+/ {
$seqout->write_seq($seq);
}
}
Hi I made up the code, please correct it.
Can u please give me some tutorial links for bioperl(for beginners) or suggest textbook
thank you
#!/usr/bin/perl -w
use strict;
use Bio::SeqIO;
my $seqin = Bio::SeqIO->new(-file => "euplotes.txt", -format => "fasta");
my $seqout = Bio::SeqIO->new(-file => ">outfile.txt", -format => "fasta");
while(my $seq = $seqin->next_seq)
{
if($seq->desc) =~/^FULL-LENGTHs+/ {
$seqout->write_seq($seq);
}
}
Hi to neilfws & all others
Thanks for the response.
I made-up the code, please correct it.
Can you people suggest me tutorial links or textbooks for Bioperl.
#!/usr/bin/perl -w
use strict;
use Bio::SeqIO;
my $seqin = Bio::SeqIO->new(-file => "euplotes.txt", -format => "fasta");
my $seqout = Bio::SeqIO->new(-file => ">outfile.txt", -format => "fasta");
while(my $seq = $seqin->next_seq)
{
if($seq->desc) =~/^FULL-LENGTHs+/ {
$seqout->write_seq($seq);
}
}
AFAIK, it won't work. Test your script with a set of sequences in FASTA format.
Log in to answer this question.
Hi to neilfws & all others Thanks for the response. I made-up the code, please correct it. Can you people suggest me tutorial links or textbooks on Bioperl.
!/usr/bin/perl -w
use strict; use Bio::SeqIO;
my $seqin = Bio::SeqIO->new(-file => "euplotes.txt", -format => "fasta"); my $seqout = Bio::SeqIO->new(-file => ">outfile.txt", -format => "fasta"); while(my $seq = $seqin->next_seq) { if($seq->desc) =~/^FULL-LENGTHs+/ { $seqout->write_seq($seq); } }
Your code looks fine. As for Bioperl, everything you need is right there on the website - http://www.bioperl.org/wiki/Main_Page. Link to tutorials - http://www.bioperl.org/wiki/Tutorials.