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.
E.g. here I tried to get the stitched FASTA conversion for a region defined in foo.bed out of chr1.maf:
python /pub1/lvyl2012/software/lyl/galaxy/tools/maf/interval_maf_to_merged_fasta.py \
/pub1/lvyl2012/ExtractMultipleAlignment/mulAlign/chr1.maf \
-d hg17 \
-t cached \
-c 1 \
-s 2 \
-e 3 \
-S 6 \
-p hg17 \
-m /pub1/lvyl2012/ExtractMultipleAlignment/mulAlign/ \
-z /pub1/lvyl2012/software/lyl/galaxy/tool-data/ \
-i /pub1/lvyl2012/ExtractMultipleAlignment/aa.bed \
-o /pub1/lvyl2012/ExtractMultipleAlignment/results.fa
It gives the error mssage:
The MAF source specified (/pub1/lvyl2012/ExtractMultipleAlignment/mulAlign/) appears to be invalid
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.
•
written
by
johnfromgyh •
1 answer
I have found following command-line works. hope it helps for others
First, I use maf_build_index.py to create indexes of maf files
Then,
python interval_maf_to_merged_fasta.py \
-d hg17 \
-p hg17,mm5,rn3 \
-m chr1.maf \
-i /pub1/lvyl2012/software/lyl/galaxy/test-data/1.bed \
-o gyh.fa \
-t user \
-z /pub1/lvyl2012/software/lyl/galaxy/tool-data/ \
-c 0 \
-s 1 \
-e 2 \
-S 5 \
-I ./
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