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.