Bio::Tools::Lucy.3pm

Langue: en

Version: 2010-04-29 (fedora - 01/12/10)

Section: 3 (Bibliothèques de fonctions)

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:
   http://bugzilla.open-bio.org/
 
 

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);