Question: Extracting, Stitching, Converting Maf Files: Interval_Maf_To_Merged_Fasta.Py: Command Line Usage?
0
Anton Kratz • 10 wrote:
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)
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modified 2.9 years ago
by
Thomas • 0
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written
6.4 years ago by
Anton Kratz • 10
