NAME

Bio::AGP::LowLevel - functions for dealing with AGP files

SYNOPSIS

 $lines_arrayref = agp_parse('my_agp_file.agp');

 agp_write( $lines => 'my_agp_file.agp');

DESCRIPTION

functions for working with AGP files.

FUNCTIONS

All functions below are EXPORT_OK.

str_in

  Usage: print "it's valid" if str_in($thingy,qw/foo bar baz/);
  Desc : return 1 if the first argument is string equal to at least one of the
         subsequent arguments
  Ret  : 1 or 0
  Args : string to search for, array of strings to search in
  Side Effects: none

  I kept writing this over and over in validation code and got sick of it.

is_filehandle

  Usage: print "it's a filehandle" if is_filehandle($my_thing);
  Desc : check whether the given thing is usable as a filehandle.
         I put this in a module cause a filehandle might be either
         a GLOB or isa IO::Handle or isa Apache::Upload
  Ret  : true if it is a filehandle, false otherwise
  Args : a single thing
  Side Effects: none

agp_parse

  Usage: my $lines = agp_parse('~/myagp.agp',validate_syntax => 1, validate_identifiers => 1);
  Desc : parse an agp file
  Args : filename or filehandle, hash-style list of options as 
                       validate_syntax => if true, error
                           if there are any syntax errors,
                       validate_identifiers => if true, error
                          if there are any identifiers that
                          CXGN::Tools::Identifiers doesn't recognize
                          IMPLIES validate_syntax
                       error_array => an arrayref.  if given, will push
                          error descriptions onto this array instead of
                          using warn to print them to stderr
  Ret  : undef if error, otherwise return an
         arrayref containing line records, each of which is like:
         { comment => 'text' } if a comment,
         or if a data line:
         {  objname  => the name of the object being assembled
                       (same for every record),
            ostart   => start coordinate for this component (object),
            oend     => end coordinate for this component   (object),
            partnum  => the part number appearing in the 4th column,
            linenum  => the line number in the file,
            type     => letter type present in the file (/[ADFGNOPUW]/),
            typedesc => description of the type, one of:
                         - (A) active_finishing
                         - (D) draft
                         - (F) finished
                         - (G) wgs_finishing
                         - (N) known_gap
                         - (O) other
                         - (P) predraft
                         - (U) unknown_gap
                         - (W) wgs_contig
            ident    => identifier of the component, if any,
            length   => length of the component,
            is_gap   => 1 if the line is some kind of gap, 0 if it
                        is covered by a component,
            gap_type => one of:
                 fragment: gap between two sequence contigs (also
                    called a "sequence gap"),
                 clone: a gap between two clones that do not overlap.
                 contig: a gap between clone contigs (also called a
                    "layout gap").
                 centromere: a gap inserted for the centromere.
                 short_arm: a gap inserted at the start of an
                    acrocentric chromosome.
                 heterochromatin: a gap inserted for an especially
                    large region of heterochromatic sequence (may also
                    include the centromere).
                 telomere: a gap inserted for the telomere.
                 repeat: an unresolvable repeat.
            cstart   => start coordinate relative to the component,
            cend     => end coordinate relative to the component,
            linkage  => 'yes' or 'no', only set for type of 'N',
            orient   => '+', '-', 0, or 'na'
                        orientation of the component
                        relative to the object,
         }

  Side Effects: unless error_array is given, will print error
                descriptions to STDERR with warn()
  Example:

agp_write

  Usage: agp_write($lines,$file);
  Desc : writes a properly formatted AGP file
  Args : arrayref of line records to write, with the line records being
             in the same format as those returned by agp_parse above,
         filename or filehandle to write to,
  Ret :  nothing meaningful

  Side Effects: dies on failure.  if you gave it a filehandle, does
                not close it
  Example:

agp_format_part( $record )

Format a single AGP part line (string terminated with a newline) from the given record hashref.

agp_contigs

  Usage: my @contigs = agp_contigs( agp_parse($agp_filename) );
  Desc : extract and number contigs from a parsed AGP file
  Args : arrayref of AGP lines, like those returned by agp_parse() above
  Ret  : list of contigs, in the same order as they occur in the
         file, formatted as:
            [ agp_line_hashref, agp_line_hashref, ... ],
            [ agp_line_hashref, agp_line_hashref, ... ],
            ...

AUTHOR(S)

Robert Buels

Sheena Scroggins