Question: Extracting, Stitching, Converting Maf Files: Interval_Maf_To_Merged_Fasta.Py: Command Line Usage?
gravatar for Anton Kratz
6.4 years ago by
Anton Kratz10
Anton Kratz10 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 I believe the actual stitcher is "" 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 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/ -G -i ../foo.bed -m ../chr1.maf -d hg18 -o stdout Traceback (most recent call last): File "./tools/maf/", line 196, in <module> if __name__ == "__main__": __main__() File "./tools/maf/", 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)
galaxy • 2.7k views
ADD COMMENTlink modified 2.9 years ago by Thomas0 • written 6.4 years ago by Anton Kratz10
gravatar for Thomas
2.9 years ago by
Thomas0 wrote:

Take a look at this thread:

ADD COMMENTlink written 2.9 years ago by Thomas0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 175 users visited in the last hour