On 15/12/10 20:39, Peter wrote:
On Wed, Dec 15, 2010 at 2:42 AM, Florent Anglyflorent.angly@gmail.com wrote:
Hi,
I was wondering if there is a tool in Galaxy to put mate pair reads located in two files inside a single file? I made the error of believing that the FASTQ joiner does that, but it does not.
If this feature is not planned, I am willing to work on it. Which of the following would be better for integration into Galaxy?
- a clean Python implementation like the other utilities in tools/fastq/,
i.e. fastq_groomer.py and fastq_paired_end_joiner.py
- a wrapper around the Velvet utilities, shuffleSequences_fastq.pl and
shuffleSequences_fasta.pl, given that Velvet already has a wrapper in Galaxy
Hi Peter,
Are you asking for a tool to interleave to FASTQ or FASTA files with matching entries (with matching names in the same order) into one file which alternates forward then reverse read?
Yes, indeed, this is what I am proposing.
Would you prefer it with or without error checking?
Error checking is best.
I think the scripts in velvet are fast but will fail horribly with bad input... note there is a simple Biopython script to do this included with velvet already (simple version with no error checking, I have written a more robust version too - it looks like I haven't sent it to Daniel to include in velvet though).
I rolled my own FASTQ paired read interlacer and deinterlacer today, using the Galaxy Python modules in lib/galaxy_utils/. I must say these modules made it quite convenient and efficient to implement error-checking in the (de)interlacing. You can find the scripts here if you're interested: http://bitbucket.org/fangly/galaxy-central I'll make the XML wrappers tomorrow and test them. Hopefully after this is done, my changes can be pulled into the official Galaxy repository.
Best,
Florent