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isect_mercator_alignment_gff - Extracts subalignments from a Mercator multiple alignment for the features in the GFF file


isect_mercator_alignment_gff [options] <genome> <GFF file>


isect_mercator_alignment_gff from FSA 1.15.9

Extracts subalignments from a Mercator multiple alignment for the features in the GFF file.


show this message
show version information
only look at features of particular type
path to map, genome and alignment files
path to map and genome files
path to alignment files
warn, rather than die, if the subalignment can't be obtained
truncate unmappable sequence (rather than skipping) and show truncated subalignment
use and display Stockholm-format alignments with conservation statistics (default is multi-FASTA)
report progress

PLEASE NOTE: While this program is reasonably fast if the GFF is properly ordered by chromosome and the start and end coordinates of features, it will be *very slow* if the GFF is not sorted. Assumes that the "seqid" or "name" field (the first field) of the GFF entries holds the chromosome name.

Note that the GFF specification defines coordinates to be 1-based and fully-closed, therefore representing the interval [start, end]. Conformance to this specification is assumed internally.

If requested, unmappable sequence will be truncated to the mappable portion; note that the truncation will favor the beginning of the requested sequence.

If a GFF feature 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.

December 2015 isect_mercator_alignment_gff 1.15.9