ssu-esl-mask(1)

NAME

ssu-esl-mask - mask sequence residues with X's (or other characters)

SYNOPSIS
ssu-esl-mask [options] seqfile maskfile

DESCRIPTION
ssu-esl-mask reads lines from maskfile that give start/end coordinates for regions in each sequence in seqfile, masks these residues (changes them to X's), and outputs the masked sequence. The maskfile is a space-delimited file. Blank lines and lines that start with '#' (comments) are ignored. Each data line contains at least three fields: seqname, start, and end. The seqname is the name of a sequence in the seqfile, and start and end are coordinates defining a region in that sequence. The coordinates are indexed <1..L> with respect to a sequence of length <L>. By default, the sequence names must appear in exactly the same order and number as the sequences in the seqfile. This is easy to enforce, because the format of maskfile is also legal as a list of names for ssu-esl-sfetch, so you can always fetch a temporary sequence file with ssu-esl-sfetch and pipe that to ssu-esl-mask. (Alternatively, see the -R option for fetching from an SSI-indexed seqfile.) The default is to mask the region indicated by <start>..<end>. Alternatively, everything but this region can be masked; see the -r reverse masking option. The default is to mask residues by converting them to X's. Any other masking character can be chosen (see -m option), or alternatively, masked residues can be lowercased (see -l option). The seqfile can be in any sequence file format that Easel reads, such as FASTA format. The format will be autodetected. Alternatively, for increased reliability, you can specify the input format; see the --informat option.

OPTIONS

-h  Print brief help; includes version number and summary of all options, including expert options.

-l  Lowercase; mask by converting masked characters to lower case and unmasked characters to upper case.

-m <c>
    Mask by converting masked residues to <c> instead of the default X.

-o <f>
    Send output to file <f> instead of stdout.

-r  Reverse mask; mask everything outside the region start..end, as opposed to the default of masking that region.

-R  Random access; fetch sequences from <seqfile> rather than requiring that sequence names in <maskfile> and <seqfile> come in exactly the same order and number. The <seqfile> must be SSI indexed (see ssu-esl-sfetch --index.)

-x <n>
    Extend all masked regions by up to <n> residues on each side. For normal masking, this means masking <start>-<n>..<end>+<n>. For reverse masking, this means masking 1..<start>-1+<n> and <end>+1-<n>..L in a srquence of length L.

--informat <s>
    Specify that the sequence file is in format <s>, rather than allowing the program to autodetect the file format.

AUTHOR
Easel and its documentation are Copyright (C) 2016 HHMI Janelia Farm Research Campus. Freely distributed under the BSD open source license.. See COPYING in the source code distribution for more details. The Easel home page is: http://bioeasel.org/