The command line script is available in the Galaxy distribution under galaxy_root/tools/maf/interval_maf_to_merged_fasta.py.

Dan

Hi,

On the Galaxy website there is a facility in the 'Fetch Alignments' section to 'Stitch MAF blocks given a set of genomic intervals'. I have all the Galaxy scripts also set up and would like to do the above with a command line python script but I cant find any in the python/bx-python-trunk/scripts folder that relate to stitching maf blocks together. At the moment all I can use is maf_extract_ranges_indexed.py but this doesn't stitch the blocks. Is this python script available and if so which script is it?

Many thanks

Adam

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