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.
Thank you very much, your comments have been a huge help to me and has saved me a lot of time