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Bio::Tools::Lucy(3)   User Contributed Perl Documentation  Bio::Tools::Lucy(3)

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);

perl v5.32.1			  2019-12-07		   Bio::Tools::Lucy(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR | APPENDIX

Want to link to this manual page? Use this URL:
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