slice_mercator_alignment(1) 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.