Extract sequence from multi fasta file with PERL - Page 2

julianeishida · 03-13-2012, 12:51 AM

Thanks.

I didn`t know about Biopieces. It is really useful. Highly recommended for those whose programing ability is low

swaraj · 03-13-2012, 03:21 AM

A quick way to do in bioperl
http://biostar.stackexchange.com/que...3gb-fasta-file

pjyoti · 05-06-2012, 09:40 PM

hello everyone...

I am using the following perl script for retrieving sequences in fasta format.....

use Bio::Perl;
$database="genbank";
$format="fasta";
$pipe ="\\|";
$space = " ";
open(INPUTFILE, "<1.txt");
while(<INPUTFILE>)
{
my($line) = $_;
chomp($line);
$line=~ s/$space/:/;
$line=~ s/$pipe/$space/;
$line=~ s/g/G/;
$line=~ s/i/I/;
$id= "$line";
#print "$id";
#print "\n";
$sequence = get_sequence($database, $id);
$test = write_sequence( ">>sequences_1.txt", $format, $sequence);
open (CHK , ">>checking.txt");
print CHK <<HERE;
$test
HERE
close CHK;
}
exit;

after getting some sequences i am getting an error messege....

-----------Exception-------------
MSG: WebDBSeqI Request Error:
HTTP/1.1 502 Bad Gateway
connection: close
Date:
.
.
.
.
.
.
<?xml version="1.0" encoding="ISO-8859-1"?

The proxy server received an invalid response from an upstream server.

plz help me out...

pjyoti · 05-06-2012, 09:47 PM

hello everyone...

I am using the following perl script for retrieving sequences in fasta format.....

use Bio::Perl;
$database="genbank";
$format="fasta";
$pipe ="\\|";
$space = " ";
open(INPUTFILE, "<1.txt");
while(<INPUTFILE>)
{
my($line) = $_;
chomp($line);
$line=~ s/$space/:/;
$line=~ s/$pipe/$space/;
$line=~ s/g/G/;
$line=~ s/i/I/;
$id= "$line";
#print "$id";
#print "\n";
$sequence = get_sequence($database, $id);
$test = write_sequence( ">>sequences_1.txt", $format, $sequence);
open (CHK , ">>checking.txt");
print CHK <<HERE;
$test
HERE
close CHK;
}
exit;

after getting some sequences i am getting an error messege....

-----------Exception-------------
MSG: WebDBSeqI Request Error:
HTTP/1.1 502 Bad Gateway
connection: close
Date:
.
.
.
.
.
.
<?xml version="1.0" encoding="ISO-8859-1"?
<!DOCTYPE html PUBLIC "-//W#C//DTD XHTML 1.0 Strict//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="htttp://www.org/1999/xhtml" lang="en" xm:lang="en"
<head>
<title>Bad Gateway!</title> <link rev="made" href="mailto:info@ncbi.nlm.nih.gov"/>

The proxy server received an invalid response from an upstream server.

plz help me out...

vivek · 07-12-2012, 04:54 AM

Dear ......,

I follow the same steps but it is not working ...

Vivek

Quote:

Originally Posted by apc2010

If you need sequences extracted from a multi-FASTA and are open to using a pre-existing tool, I would also suggest either the faSomeRecords or faOneRecord command line utilities from UCSC.

They have versions of this tool for OSX and Linux. Here is a link to the executable downloads:

http://hgdownload.cse.ucsc.edu/admin/exe/

The difference between the two: faOneRecord takes the sequence name to extract from the command line, faSomeRecords reads in a file of 1 or more sequence names to extract from the multi-FASTA.

Usage:

Code:

================================================================
========   faOneRecord   ====================================
================================================================
faOneRecord - Extract a single record from a .FA file
usage:
   faOneRecord in.fa recordName

================================================================
========   faSomeRecords   ====================================
================================================================
faSomeRecords - Extract multiple fa records
usage:
   faSomeRecords in.fa listFile out.fa
options:
   -exclude - output sequences not in the list file.

yzzhang · 01-31-2013, 01:27 PM

don't contain > in the file list, the script faSomeRecords can work well.

Quote:

Originally Posted by mghita

I have given up. I replaced the @ with > and still didn't work. I have combined a little awk and R and does my job just fine. Thanks a lot for the effort!

Madalina

ML1975 · 12-05-2017, 10:51 PM

Quote:

Originally Posted by boetsie

Hi,

I've attached a script which can do this. If i understand it correctly you have a file like;

>chr1
AGCTGATGATAGT...
>chr2
ACAAAATAGTCGAT....
>chr3
....

And your perl script would be something like;

perl extractSequence.pl genomefile.fa chr1

where 'chr1' corresponds to a sequence named chr1 (indicated by chr1)?

Say you have a more complicated file like;

>chr1_coverage1000_length100
AGATGTATGTTAGA

You can do something like;

perl extractSequence.pl genomefile.fa chr1_.

which will extract all the sequences containing the header chr1_

To store the results, do;

perl extractSequence.pl genomefile.fa chr1 > filename.txt

If this is what you want, you can use my script.

Boetsie

7 years later and I have used your script - thanks for sharing

Works a treat!

brojee · 07-07-2019, 08:45 AM

On the off chance that you need groupings separated from a multi-FASTA and are available to utilizing a prior instrument, I would likewise recommend either the faSomeRecords or faOneRecord direction line utilities from UCSC.

They have renditions of this apparatus for OSX and Linux. Here is a connection to the executable downloads:

http://hgdownload.cse.ucsc.edu/administrator/exe/

The distinction between the two: faOneRecord takes the grouping name to separate from the order line, faSomeRecords peruses in a record of at least 1 succession names to remove from the multi-FASTA.

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07-07-2019, 08:45 AM	#28
brojee Member Location: Bhopal Join Date: Jul 2019 Posts: 19	On the off chance that you need groupings separated from a multi-FASTA and are available to utilizing a prior instrument, I would likewise recommend either the faSomeRecords or faOneRecord direction line utilities from UCSC. They have renditions of this apparatus for OSX and Linux. Here is a connection to the executable downloads: http://hgdownload.cse.ucsc.edu/administrator/exe/ The distinction between the two: faOneRecord takes the grouping name to separate from the order line, faSomeRecords peruses in a record of at least 1 succession names to remove from the multi-FASTA. __________________ Best SEO Company in Bhopal, Best Web Development Company in Bhopal

03-13-2012, 12:51 AM	#21
julianeishida Junior Member Location: Japan Join Date: Mar 2012 Posts: 1	Thanks. I didn`t know about Biopieces. It is really useful. Highly recommended for those whose programing ability is low

03-13-2012, 03:21 AM	#22
swaraj Member Location: Naples, Italy Join Date: Feb 2012 Posts: 50	A quick way to do in bioperl http://biostar.stackexchange.com/que...3gb-fasta-file

05-06-2012, 09:40 PM	#23
pjyoti Junior Member Location: india Join Date: Nov 2011 Posts: 2	hello everyone... I am using the following perl script for retrieving sequences in fasta format..... use Bio::Perl; $database="genbank"; $format="fasta"; $pipe ="\\\|"; $space = " "; open(INPUTFILE, "<1.txt"); while(<INPUTFILE>) { my($line) = $_; chomp($line); $line=~ s/$space/:/; $line=~ s/$pipe/$space/; $line=~ s/g/G/; $line=~ s/i/I/; $id= "$line"; #print "$id"; #print "\n"; $sequence = get_sequence($database, $id); $test = write_sequence( ">>sequences_1.txt", $format, $sequence); open (CHK , ">>checking.txt"); print CHK <<HERE; $test HERE close CHK; } exit; after getting some sequences i am getting an error messege.... -----------Exception------------- MSG: WebDBSeqI Request Error: HTTP/1.1 502 Bad Gateway connection: close Date: . . . . . . <?xml version="1.0" encoding="ISO-8859-1"? The proxy server received an invalid response from an upstream server. plz help me out...

05-06-2012, 09:47 PM	#24
pjyoti Junior Member Location: india Join Date: Nov 2011 Posts: 2	hello everyone... I am using the following perl script for retrieving sequences in fasta format..... use Bio::Perl; $database="genbank"; $format="fasta"; $pipe ="\\\|"; $space = " "; open(INPUTFILE, "<1.txt"); while(<INPUTFILE>) { my($line) = $_; chomp($line); $line=~ s/$space/:/; $line=~ s/$pipe/$space/; $line=~ s/g/G/; $line=~ s/i/I/; $id= "$line"; #print "$id"; #print "\n"; $sequence = get_sequence($database, $id); $test = write_sequence( ">>sequences_1.txt", $format, $sequence); open (CHK , ">>checking.txt"); print CHK <<HERE; $test HERE close CHK; } exit; after getting some sequences i am getting an error messege.... -----------Exception------------- MSG: WebDBSeqI Request Error: HTTP/1.1 502 Bad Gateway connection: close Date: . . . . . . <?xml version="1.0" encoding="ISO-8859-1"? <!DOCTYPE html PUBLIC "-//W#C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="htttp://www.org/1999/xhtml" lang="en" xm:lang="en" <head> <title>Bad Gateway!</title> <link rev="made" href="mailto:info@ncbi.nlm.nih.gov"/> The proxy server received an invalid response from an upstream server. plz help me out...