Convert FRG files back to fastq paired end reads

Question

[arnstrm]

Hello,

Is there a script somewhere that I can use to convert the FRGfiles back to paired end fastqfiles?

If not, what info can I use to find the pairs? First 2 records for my FRG file are as follows:

{FRG
act:A
acc:aa202
rnd:1
sta:G
lib:aa
pla:0
loc:0
src:
.
seq:
GCACATGTGCATAGATTTCACGGACCTCAATCGCGCCTGTCCGAAAGATGACTTCCCTTTGCCCCGGATAGATCAACTGGTCGATTCTACGGCCGGCTGCGAAGCGATGAGTTTCTTGGATGCTTATTCTGGCTACCACCAGATTAGCAT
.
qlt:
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
.
hps:
.
clr:0,150
}
{FRG
act:A
acc:aa203
rnd:1
sta:G
lib:aa
pla:0
loc:0
src:
.
seq:
TTGCCCTTGAAAGGTCTTTGTCATGAGTCTCTGGAAGGTTGCTCCGGCGTTTTTCAAGCCGAATGGCATTCGGACGTAGTAGAAAGTACCCACAGGAGTGATGAAACTAGTCTTCTCTTCATCTTCCGGGATCATGCTAATCTGGTGGTA
.
qlt:
EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEE
.
hps:
.
clr:0,150
}

Thanks for any help!

EDIT: I can easily parse the FRG file to fastq, but still don't know how to find pairs. If you any of you have experience working with frg/celera assembler, please provide any insights. Thanks.

Answer 1

[thackl]

There is a conversion script in celera:

celera/src/AS_GPK/frg-to-fastq.pl

Judging from the output file names, it is PE aware.

my $outAname  = "$outPrefix.1.fastq";
my $outBname  = "$outPrefix.2.fastq";
my $outIname  = "$outPrefix.i.fastq";
my $outSname  = "$outPrefix.s.fastq";

There is also one in the AMOS package (not sure if this does PE though)

amos/bin/frg2fastq

[arnstrm]

Thanks for the reply. Can you please tell me which version of CA you're using? I couldn't find those lines in WGS 6.1 to 8.3. All I have in wgs-6.1/src/AS_REF/frg-to-fasta.pl is

#!/usr/bin/perl
use strict;

while (!eof(STDIN)) {
    $_ = <STDIN>;
    chomp;

    if (m/^acc:(.*)$/) {
        print ">$1\n";
    }

    if (m/^seq:$/) {

        $_ = <STDIN>;
        chomp;

        while ($_ ne ".") {
            print "$_\n";
            $_ = <STDIN>;
            chomp;
        }
    }
}

Thank you for you help and sorry for the late reply!

[thackl]

It's part of the latest source release wgs-8.3rc1.tar.bz2.

wgs-8.3rc1/src/AS_GKP/frg-to-fastq.pl

[arnstrm]

Ah, I see they moved that script. Thanks for pointing it out. I'll give it a try to see if it works.

[thackl]

No, actually it was my mistake. I copied the path to frg-to-fasta which is in REF and than just changed a to q... I fixed it, thanks