SLICE_MERCATOR_ALIGNMENT

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.