Provided by: phast_1.4+dfsg-1_amd64 
NAME
maf_parse - Reads a MAF file and perform various operations on it.
DESCRIPTION
Reads a MAF file and perform various operations on it. Performs parsing operations block-by-block
whenever possible, rather than storing entire alignment in memory. Can extract a sub-alignment from an
alignment (by row or by column). Can extract features given GFF, BED, or genepred file. Can also
extract sub-features such as CDS1,2,3 or 4d sites. Can perform various functions such as gap stripping
or re-ordering of sequences. Capable of reading and
writing in a few common formats, but will not load input or output alignments into memory if
output format is MAF.
OPTIONS
Output format
--out-format, -o MAF|PHYLIP|FASTA|MPM|SS (Default MAF). Output file format. SS format is only available
un-ordered. Note that some options, which involve reversing alignments based on strand, or
stripping gaps, cannot be output in MAF format and use FASTA by default. Also note that when
output format is not MAF, the entire output must be loaded into memory.
--pretty, -p
Pretty-print alignment (use '.' when character matches corresponding character in first sequence).
Ignored if --out-format SS is selected.
Obtaining sub-alignments and re-ordering rows
--start, -s <start_col> Start index of sub-alignment (indexing starts with 1). Coordinates are in terms
of the reference sequence unless the --no-refseq option is used, in which case they are in terms
of alignment columns. Default is 1.
--end, -e <end_col> End index of sub-alignment. Default is length of alignment.
Coordinates defined as in --start option, above.
--seqs, -l <seq_list>
Comma-separated list of sequences to include (default) exclude (if --exclude). Indicate by
sequence number or name (numbering starts with 1 and is evaluated *after* --order is applied).
--exclude, -x Exclude rather than include specified sequences.
--order, -O <name_list>
Change order of rows in alignment to match sequence names specified in name_list. The first name
in the alignment becomes the reference sequence.
--no-refseq, -n Do not assume first sequence in MAF is refseq. Instead, use coordinates given by
absolute position in alignment (starting from 1).
Splitting into multiple MAFs by length
--split, -S length
Split MAF into pieces by length, and puts output in outRootX.maf, where X=1,2,...,numPieces.
outRoot can be modified with --out-root, and the minimum number of digits in X can be modified
with --out-root-digits. Splits between blocks, so that each output file does not exceed specified
length. By default, length is counted by distance spanned in alignment by refseq, unless
--no-refseq is specified.
--out-root, -r <name>
Filename root for output files produced by --split (default "maf_parse").
--out-root-digits, -d <numdigits> (for use with --split). The minimum number of digits used to
index each output file produced by split.
Extracting features from MAF
--features, -g <fname> Annotations file. May be GFF, BED, or genepred format.
Coordinates assumed to be in frame of first sequence of alignment (reference sequence). By
default, outputs subset of MAF which are labeled in annotations file. But can be used with
--by-category, --by-group, and/or --do-cats to split MAF by annotation type. Or if used with
--mask-features, is only used to determine regions to mask. Implies --strip-i-lines,
--strip-e-lines
--by-category, -L
(Requires --features).
Split by category, as defined by annotations file and (optionally) category map (see --catmap).
--do-cats, -C <cat_list> (For use with --by-category) Output sub-alignments for only the specified
categories.
--catmap, -c <fname>|<string>
(Optionally use with --by-category) Mapping of feature types to category numbers. Can either give
a filename or an "inline" description of a simple category map, e.g.,
--catmap "NCATS = 3 ; CDS 1-3" or
--catmap "NCATS = 1; UTR 1".
--by-group, -P <tag> (Requires --features). Split by groups in annotation file, as defined by specified
tag.
Masking by quality score
--mask-bases, -b <qscore> Mask all bases with quality score <= n. Note that n is in the same units as
displayed in the MAF (ranging from 0-9), and represents min(9, floor(PHRED_score/5)). Bases
without any quality score will not be masked.
--masked-file, -m <filename> (For use with --mask-bases). Write a file containing all the regions masked
for low quality. The file will be in 0-based coordinates relative to the refseq, with an
additional column giving the name of the species masked. Note that low-quality bases masked at
alignment columns with a gap in the reference sequence may not be represented in the output file.
--mask-features -M <spec> (Requires --features). Mask all bases annotated in features in the given
species (can be a comma-delimited list of species). Note that
coordinates are always in terms of refseq, even if a different species is being masked.
Other
--strip-i-lines, -I
Remove lines in MAF starting with i.
--strip-e-lines, -E Remove lines in MAF starting with e.
--help, -h
Print this help message.