Bio::Tools::Lucy(3pm)

NAME
Bio::Tools::Lucy - Object for analyzing the output from Lucy,
  a vector and quality trimming program from TIGR

SYNOPSIS
  # Create the Lucy object from an existing Lucy output file
  @params = ('seqfile' => 'lucy.seq', 'lucy_verbose' => 1);
  $lucyObj = Bio::Tools::Lucy->new(@params);

  # Get names of all sequences
  $names = $lucyObj->get_sequence_names();

  #  Print seq and qual values for sequences >400 bp in order to run CAP3
  foreach $name (@$names) {
      next unless $lucyObj->length_clear($name) > 400;
      print SEQ ">$name\n", $lucyObj->sequence($name), "\n";
      print QUAL ">$name\n", $lucyObj->quality($name), "\n";
  }

  # Get an array of Bio::PrimarySeq objects
  @seqObjs = $lucyObj->get_Seq_Objs();

DESCRIPTION
Bio::Tools::Lucy.pm provides methods for analyzing the sequence and quality values generated by Lucy program from TIGR.

Lucy will identify vector, poly-A/T tails, and poor quality regions in a sequence. (www.genomics.purdue.edu/gcg/other/lucy.pdf)

The input to Lucy can be the Phred sequence and quality files generated from running Phred on a set of chromatograms.

Lucy can be obtained (free of charge to academic users) from www.tigr.org/softlab

There are a few methods that will only be available if you make some minor changes to the source for Lucy and then recompile. The changes are in the 'lucy.c' file and there is a diff between the original and the modified file in the Appendix

Please contact the author of this module if you have any problems making these modifications.

You do not have to make these modifications to use this module.

  Creating a Lucy object
  @params = ('seqfile' => 'lucy.seq', 'adv_stderr' => 1,
             'fwd_desig' => '_F', 'rev_desig' => '_R');
  $lucyObj = Bio::Tools::Lucy->new(@params);

  Using a Lucy object
  You should get an array with the sequence names in order to use
  accessor methods.  Note: The Lucy binary program will fail unless
  the sequence names provided as input are unique.

  $names_ref = $lucyObj->get_sequence_names();

  This code snippet will produce a Fasta format file with sequence
  lengths and %GC in the description line.

  foreach $name (@$names) {
      print FILE ">$name\t",
                 $lucyObj->length_clear($name), "\t",
                 $lucyObj->per_GC($name), "\n",
                 $lucyObj->sequence($name), "\n";
  }

  Print seq and qual values for sequences >400 bp in order to assemble
  them with CAP3 (or other assembler).

  foreach $name (@$names) {
      next unless $lucyObj->length_clear($name) > 400;
      print SEQ ">$name\n", $lucyObj->sequence($name), "\n";
      print QUAL ">$name\n", $lucyObj->quality($name), "\n";
  }

  Get all the sequences as Bio::PrimarySeq objects (eg., for use with
  Bio::Tools::Run::StandaloneBlast to perform BLAST).

  @seqObjs = $lucyObj->get_Seq_Objs();

  Or use only those sequences that are full length and have a Poly-A
  tail.

  foreach $name (@$names) {
      next unless ($lucyObj->full_length($name) and $lucy->polyA($name));
      push @seqObjs, $lucyObj->get_Seq_Obj($name);
  }

  Get the names of those sequences that were rejected by Lucy.

  $rejects_ref = $lucyObj->get_rejects();

  Print the names of the rejects and 1 letter code for reason they
  were rejected.

  foreach $key (sort keys %$rejects_ref) {
      print "$key:  ", $rejects_ref->{$key};
  }

  There is a lot of other information available about the sequences
  analyzed by Lucy (see APPENDIX).  This module can be used with the
  DBI module to store this sequence information in a database.

FEEDBACK

  Mailing Lists
User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  Support
Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

  Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR
Andrew G. Walsh    paeruginosa@hotmail.com

APPENDIX
Methods available to Lucy objects are described below. Please note that any method beginning with an underscore is considered internal and should not be called directly.

  new
 Title   :  new
 Usage   :  $lucyObj = Bio::Tools::Lucy->new(seqfile => lucy.seq, rev_desig => '_R',
            fwd_desig => '_F')
 Function:  creates a Lucy object from Lucy analysis files
 Returns :  reference to Bio::Tools::Lucy object
 Args    :  seqfile     Fasta sequence file generated by Lucy
               qualfile Quality values file generated by Lucy
               infofile Info file created when Lucy is run with -debug
                     'infofile' option
               stderrfile       Standard error captured from Lucy when Lucy is run
                         with -info option and STDERR is directed to stderrfile
                         (ie. lucy ... 2> stderrfile).
                         Info in this file will include sequences dropped for low
                         quality. If you've modified Lucy source (see adv_stderr below),
                         it will also include info on which sequences were dropped because
                         they were vector, too short, had no insert, and whether a poly-A
                         tail was found (if Lucy was run with -cdna option).
               lucy_verbose verbosity level (0-1).
               fwd_desig        The string used to determine whether sequence is a
          forward read.
                         The parser will assume that this match will occus at the
                         end of the sequence name string.
               rev_desig        As above, for reverse reads.
               adv_stderr       Can be set to a true value (1).  Will only work if
          you have modified
                         the Lucy source code as outlined in DESCRIPTION and capture
                         the standard error from Lucy.

If you don't provide filenames for qualfile, infofile or stderrfile, the module will assume that .qual, .info, and .stderr are the file extensions and search in the same directory as the .seq file for these files.

For example, if you create a Lucy object with $lucyObj = Bio::Tools::Lucy->new(seqfile =>lucy.seq), the module will find lucy.qual, lucy.info and lucy.stderr.

You can omit any or all of the quality, info or stderr files, but you will not be able to use all of the object methods (see method documentation below).

  _parse
 Title   :  _parse
 Usage   :  n/a (internal function)
 Function:  called by new() to parse Lucy output files
 Returns :  nothing
 Args    :  none

  get_Seq_Objs
 Title   :  get_Seq_Objs
 Usage   :  $lucyObj->get_Seq_Objs()
 Function:  returns an array of references to Bio::PrimarySeq objects
            where -id = 'sequence name' and -seq = 'sequence'

 Returns :  array of Bio::PrimarySeq objects
 Args    :  none

  get_Seq_Obj
 Title   :  get_Seq_Obj
 Usage   :  $lucyObj->get_Seq_Obj($seqname)
 Function:  returns reference to a Bio::PrimarySeq object where -id = 'sequence name'
            and -seq = 'sequence'
 Returns :  reference to Bio::PrimarySeq object
 Args    :  name of a sequence

  get_sequence_names
 Title   :  get_sequence_names
 Usage   :  $lucyObj->get_sequence_names
 Function:  returns reference to an array of names of the sequences analyzed by Lucy.
            These names are required for most of the accessor methods.
            Note: The Lucy binary will fail unless sequence names are unique.
 Returns :  array reference
 Args    :  none

  sequence
 Title   :  sequence
 Usage   :  $lucyObj->sequence($seqname)
 Function:  returns the DNA sequence of one of the sequences analyzed by Lucy.
 Returns :  string
 Args    :  name of a sequence

  quality
 Title   :  quality
 Usage   :  $lucyObj->quality($seqname)
 Function:  returns the quality values of one of the sequences analyzed by Lucy.
            This method depends on the user having provided a quality file.
 Returns :  string
 Args    :  name of a sequence

  avg_quality
 Title   :  avg_quality
 Usage   :  $lucyObj->avg_quality($seqname)
 Function:  returns the average quality value for one of the sequences analyzed by Lucy.
 Returns :  float
 Args    :  name of a sequence

  direction
 Title   :  direction
 Usage   :  $lucyObj->direction($seqname)
 Function:  returns the direction for one of the sequences analyzed by Lucy
            providing that 'fwd_desig' or 'rev_desig' were set when the
            Lucy object was created.
            Strings returned are: 'F' for forward, 'R' for reverse.
 Returns :  string
 Args    :  name of a sequence

  length_raw
 Title   :  length_raw
 Usage   :  $lucyObj->length_raw($seqname)
 Function:  returns the length of a DNA sequence prior to quality/ vector
            trimming by Lucy.
 Returns :  integer
 Args    :  name of a sequence

  length_clear
 Title   :  length_clear
 Usage   :  $lucyObj->length_clear($seqname)
 Function:  returns the length of a DNA sequence following quality/ vector
            trimming by Lucy.
 Returns :  integer
 Args    :  name of a sequence

  start_clear
 Title   :  start_clear
 Usage   :  $lucyObj->start_clear($seqname)
 Function:  returns the beginning position of good quality, vector free DNA sequence
            determined by Lucy.
 Returns :  integer
 Args    :  name of a sequence

  end_clear
 Title   :  end_clear
 Usage   :  $lucyObj->end_clear($seqname)
 Function:  returns the ending position of good quality, vector free DNA sequence
            determined by Lucy.
 Returns :  integer
 Args    :  name of a sequence

  per_GC
 Title   :  per_GC
 Usage   :  $lucyObj->per_GC($seqname)
 Function:  returns the percente of the good quality, vector free DNA sequence
            determined by Lucy.
 Returns :  float
 Args    :  name of a sequence

  full_length
 Title   :  full_length
 Usage   :  $lucyObj->full_length($seqname)
 Function:  returns the truth value for whether or not the sequence read was
            full length (ie. vector present on both ends of read).  This method
            depends on the user having provided the 'info' file (Lucy must be
            run with the -debug 'info_filename' option to get this file).
 Returns :  boolean
 Args    :  name of a sequence

  polyA
 Title   :  polyA
 Usage   :  $lucyObj->polyA($seqname)
 Function:  returns the truth value for whether or not a poly-A tail was detected
            and clipped by Lucy.  This method depends on the user having modified
            the source for Lucy as outlined in DESCRIPTION and invoking Lucy with
            the -cdna option and saving the standard error.
            Note, the final sequence will not show the poly-A/T region.
 Returns :  boolean
 Args    :  name of a sequence

  get_rejects
 Title   :  get_rejects
 Usage   :  $lucyObj->get_rejects()
 Function:  returns a hash containing names of rejects and a 1 letter code for the
            reason Lucy rejected the sequence.
            Q- rejected because of low quality values
            S- sequence was short
            V- sequence was vector
            E- sequence was empty
            P- poly-A/T trimming caused sequence to be too short
            In order to get the rejects, you must provide a file with the standard
            error from Lucy.  You will only get the quality category rejects unless
            you have modified the source and recompiled Lucy as outlined in DESCRIPTION.
 Returns :  hash reference
 Args    :  none

  Diff for Lucy source code
  352a353,354
  >       /* AGW added next line */
  >       fprintf(stderr, "Empty: %s\n", seqs[i].name);
  639a642,643
  >         /* AGW added next line */
  >         fprintf(stderr, "Short/ no insert: %s\n", seqs[i].name);
  678c682,686
  <     if (left) seqs[i].left+=left;
  ---
  >     if (left) {
  >       seqs[i].left+=left;
  >       /*  AGW added next line */
  >       fprintf(stderr, "%s has PolyA (left).\n", seqs[i].name);
  >     }
  681c689,693
  <     if (right) seqs[i].right-=right;
  ---
  >     if (right) {
  >       seqs[i].right-=right;
  >       /* AGW added next line */
  >       fprintf(stderr, "%s has PolyA (right).\n", seqs[i].name);
  >     }
  682a695,696
  >       /* AGW added next line */
  >       fprintf(stderr, "Dropped PolyA: %s\n", seqs[i].name);
  734a749,750
  >       /* AGW added next line */
  >       fprintf(stderr, "Vector: %s\n", seqs[i].name);

  This patch is to be applied to lucy.c from the lucy-1.19p release
 277a278,279
 >       /* AGW added next line */
 >       fprintf(stderr, "Short/ no insert: %s\n", seqs[i].name);
 588c590,592
 <     if ((seqs[i].len=bases)<=0)
 ---
 >     if ((seqs[i].len=bases)<=0) {
 >       /* AGW added next line */
 >       fprintf(stderr, "Empty: %s\n", seqs[i].name);
 589a594
 >     }
 893c898,902
 <       if (left) seqs[i].left+=left;
 ---
 >       if (left) {
 >         seqs[i].left+=left;
 >         /*  AGW added next line */
 >         fprintf(stderr, "%s has PolyA (left).\n", seqs[i].name);
 >       }
 896c905,909
 <       if (right) seqs[i].right-=right;
 ---
 >       if (right) {
 >         seqs[i].right-=right;
 >         /*  AGW added next line */
 >         fprintf(stderr, "%s has PolyA (right).\n", seqs[i].name);
 >         }
 898a912,913
 >         /* AGW added next line */
 >         fprintf(stderr, "Dropped PolyA: %s\n", seqs[i].name);
 949a965,966
 >         /* AGW added next line */
 >           fprintf(stderr, "Vector: %s\n", seqs[i].name);