Converting FASTA/qual file pair from 454 to FASTQ

[oiiio]

Hi all,

Is there anything out there that can convert FASTA/qual file pairs from 454 to a single FASTQ file? I have seen plenty of tools that do the opposite already in my search...

[maubp]

Biopython can a few lines, see "Converting FASTA and QUAL files into FASTQ files" in the tutorial,

from Bio import SeqIO
from Bio.SeqIO.QualityIO import PairedFastaQualIterator
handle = open("temp.fastq", "w") #w=write
records = PairedFastaQualIterator(open("example.fasta"), open("example.qual"))
count = SeqIO.write(records, handle, "fastq")
handle.close()
print "Converted %i records" % count

[maasha]

With Biopieces you can do:

read_454 -i test.fna -q test.fna.qual | write_fastq -o test.fq -x

[TonyBrooks]

This has already been covered in a previous post

http://seqanswers.com/forums/showthread.php?t=15862&highlight=454+FASTQ

[maubp]

This has already been covered in a previous post

http://seqanswers.com/forums/showthr...ight=454+FASTQ

Relevant, but not quite the same - that thread was about SFF to FASTQ or FASTA+QUAL.

This thread is about FASTA+QUAL to FASTQ.

[TonyBrooks]

Relevant, but note quite the same - that thread was about SFF to FASTQ or FASTA+QUAL.

This thread is about FASTA+QUAL to FASTQ.

Sorry. There is definitely a thread on FASTA+QUAL to FASTQ though. Someone ended up posting a perl script that did it without the need for any specific software. I just posted the wrong link.

Here it is:

http://seqanswers.com/forums/showthread.php?t=2775

Check out post #17

[essvee]

You can also use galaxy... under NGS: QC and Manipulation there is a tool called 'Combine FASTA and QUAL into FASTQ'

[oiiio]

Thanks everyone. I ended up using the maubp's biopython suggestion and it is working great. Sorry I didn't see the other thread earlier, it is titled 'fastq sequence converter' and I must have skipped over it.

[xApple]

Taking on maubp's suggestion and making a better script to place in your ~/bin folder:

#!/usr/bin/env python

"""
Convert FASTA + QUAL file pairs to a single FASTQ file
http://seqanswers.com/forums/showthread.php?t=16925

You can use this script from the shell like this::
$ ./fasta_to_fastaq reads.fna reads.qual reads.fastq
"""

# The libraries we need #
import sys, os
from Bio import SeqIO
from Bio.SeqIO.QualityIO import PairedFastaQualIterator
# Get the shell arguments #
fa_path = sys.argv[1]
qa_path = sys.argv[2]
fq_path = sys.argv[3]
# Check that the paths are valid #
if not os.path.exists(fa_path): raise Exception("No file at %s." % fa_path)
if not os.path.exists(qa_path): raise Exception("No file at %s." % qa_path)
# Do it #
with open(fq_path, "w") as handle:
    records = PairedFastaQualIterator(open(fa_path), open(qa_path))
    count = SeqIO.write(records, handle, "fastq")
# Report success #
print "Converted %i records" % count

[mossman]

FASTA to FASTQ

Many thanks to all - was looking for something specific to a Mac but I can use several of these suggestions - my first post and it was a definite help for me - again many thanks