Dear Galaxy team / user mailing list,

my question is with respect to command line usage, not about interactive / web-based Galaxy usage. Regarding the publication [1], section "2.3 Stitchers".

I want to use the stitcher to extract a given region from MAF files, stitch it together and convert it to FASTA.

I downloaded and installed Galaxy according to the instructions from http://wiki.g2.bx.psu.edu/Admin/Get%20Galaxy

I believe the actual stitcher is "interval_maf_to_merged_fasta.py" in the /tools/maf directory (not clear from the paper or docs but I belive this is the tool that implements this functionality).

How can I actually extract, stitch, convert with interval_maf_to_merged_fasta.py?

I have difficulties figuring all necessary command line parameters out by reading the source code.

F.e. here I tried to get the stiched FASTA conversion for a region defined in "foo.bed" out of "chr1.maf":

$ python ./tools/maf/interval_maf_to_merged_fasta.py -G -i ../foo.bed -m ../chr1.maf -d hg18 -o stdout Traceback (most recent call last): File "./tools/maf/interval_maf_to_merged_fasta.py", line 196, in <module> if __name__ == "__main__": __main__() File "./tools/maf/interval_maf_to_merged_fasta.py", line 107, in __main__ if options.mafSourceType.lower() in ["cached"]: AttributeError: 'NoneType' object has no attribute 'lower'

Is it necessary to index the MAF files first somehow? Do I have to set the type of MAF file, and to what?

Would be great if someone could give a short overview how to stitch MAF files command-line based.

Thank you!

Anton

References [1] Blankenberg, D., Taylor, J., Nekrutenko, A. & Galaxy Team. Making whole genome multiple alignments usable for biologists. *Bioinformatics (Oxford, England)* *27*, 2426-2428 (2011)