Provided by: fsa_1.15.9+dfsg-4_amd64
slice_mercator_alignment - Extracts the corresponding subalignment from a Mercator multiple alignment
slice_mercator_alignment [options] <genome> <chromosome> <start> <end> <strand>
slice_mercator_alignment from FSA 1.15.9 Extracts the corresponding subalignment from a Mercator multiple alignment.
-h, --help show this message -D, --data <directory> path to map, genome and alignment files -M, --map <directory> path to map and genome files -A, --align <directory> path to alignment files -L, --lazy warn, rather than die, if the subalignment can't be obtained -U, --truncate truncate unmappable sequence (rather than skipping) and show truncated subalignment -s, --stockholm use and display Stockholm-format alignments with conservation statistics (default is multi-FASTA) -0, --zerobased coordinates are 0-based (default is 1-based) -o, --halfopen end coordinate is open, i.e., [start, end) Assumes that coordinates are 1-based and fully-closed, therefore representing the interval [start, end]. If requested, unmappable sequence will be truncated to the mappable portion; note that the truncation will favor the beginning of the requested sequence. If the requested sequence is on the - strand, then the corresponding subalignment will be reverse-complemented.
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.