slice_mercator_alignment1

Extracts the corresponding subalignment from a mercator multiple alignment

Usage

slice_mercator_alignment [options] <genome> <chromosome> <start> <end> <strand>

Overview

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.