MAF_PARSE

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.