NAME
slice_mercator_alignment - Extracts the corresponding subalignment from a Mercator multiple alignment
SYNOPSIS
slice_mercator_alignment [options] <genome> <chromosome> <start> <end> <strand>
DESCRIPTION
slice_mercator_alignment from FSA 1.15.9
Extracts the corresponding subalignment from a Mercator multiple alignment.
OPTIONS
- -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.
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.