[Bioperl-guts-l] bioperl-live/doc/howto/txt SearchIO.txt,1.3,1.4

Brian Osborne bosborne at pub.open-bio.org
Mon Apr 25 21:47:42 EDT 2005


Update of /home/repository/bioperl/bioperl-live/doc/howto/txt
In directory pub.open-bio.org:/tmp/cvs-serv30182/doc/howto/txt

Modified Files:
	SearchIO.txt 
Log Message:
Add POD, move to scripts/


Index: SearchIO.txt
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/doc/howto/txt/SearchIO.txt,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** SearchIO.txt	2 Dec 2004 02:22:47 -0000	1.3
--- SearchIO.txt	26 Apr 2005 01:47:40 -0000	1.4
***************
*** 1,4 ****
  
!    BioPerl DocBook
  
  Bio::SearchIO HOWTO
--- 1,4 ----
  
!    Bioperl DocBook ([1]Bioperl)
  
  Bio::SearchIO HOWTO
***************
*** 6,12 ****
  Jason Stajich
  
!    [1]Duke University
!    [2]University Program in Genetics
!    [3]Center for Genome Technology
  
       Duke University Medical Center
--- 6,12 ----
  Jason Stajich
  
!    [2]Duke University
!    [3]University Program in Genetics
!    [4]Center for Genome Technology
  
       Duke University Medical Center
***************
*** 16,28 ****
       27710-3568
       USA
!      <[4]jason-at-bioperl.org>
  
  Brian Osborne
  
!    [5]Cognia Corporation
  
       NYC, NY 10022
       USA
!      <[6]brian-at-cognia.com>
  
     This document is copyright Jason Stajich, Brian Osborne, 2002-2004. It
--- 16,28 ----
       27710-3568
       USA
!      <[5]jason-at-bioperl.org>
  
  Brian Osborne
  
!    [6]Cognia Corporation
  
       NYC, NY 10022
       USA
!      <[7]brian-at-cognia.com>
  
     This document is copyright Jason Stajich, Brian Osborne, 2002-2004. It
***************
*** 44,51 ****
     Revision 0.6 2004-06-21 JES
     Made document redistributable under Perl Artistic.
  
     Abstract
  
!    This is a HOWTO written in DocBook (SGML) for the reasoning behind the
     creation of the Bio::SearchIO system, how to use it, and how one goes
     about writing new adaptors to different output formats. We will also
--- 44,53 ----
     Revision 0.6 2004-06-21 JES
     Made document redistributable under Perl Artistic.
+    Revision 0.7 2004-12-02 JES and BIO
+    Section on lightweight objects
  
     Abstract
  
!    This is a HOWTO written in DocBook (XML) for the reasoning behind the
     creation of the Bio::SearchIO system, how to use it, and how one goes
     about writing new adaptors to different output formats. We will also
***************
*** 56,68 ****
     Table of Contents
  
!    1. [7]Background
!    2. [8]Design
!    3. [9]Parsing with Bio::SearchIO
!    4. [10]Creating Reports for SearchIO
!    5. [11]Implementation
!    6. [12]Writing and formatting output
!    7. [13]Extending SearchIO
!    8. [14]Lightweight Objects
!    9. [15]Useful links
  
  1. Background
--- 58,70 ----
     Table of Contents
  
!    [8]1. Background
!    [9]2. Design
!    [10]3. Parsing with Bio::SearchIO
!    [11]4. Creating Reports for SearchIO
!    [12]5. Implementation
!    [13]6. Writing and formatting output
!    [14]7. Extending SearchIO
!    [15]8. Lightweight Objects
!    [16]9. Useful links
  
  1. Background
***************
*** 113,127 ****
     programming to separate the entity which process data from objects
     which will hold the information produced. In the same manner that the
!    [16]Bio::SeqIO module is used to parse different file formats and
!    produces objects which are [17]Bio::PrimarySeqI compliant, we have
!    written [18]Bio::SearchIO to produce the Bio::Search objects.
     Sequences are a little less complicated so there is only one primary
     object (Bio::PrimarySeqI) which Search results need three main
     components to represent the data processed in a file:
!    [19]Bio::Search::Result::ResultI (top level results),
!    [20]Bio::Search::Hit::HitI (hits) and [21]Bio::Search::HSP::HSPI
!    (HSPs). The [22]Bio::SearchIO object is then a factory which produces
!    [23]Bio::Search::Result::ResultI objects and the
!    [24]Bio::Search::Result::ResultI objects contain information about the
     query, the database searched, and the full collection of Hits found
     for the query.
--- 115,129 ----
     programming to separate the entity which process data from objects
     which will hold the information produced. In the same manner that the
!    [17]Bio::SeqIO module is used to parse different file formats and
!    produces objects which are [18]Bio::PrimarySeqI compliant, we have
!    written [19]Bio::SearchIO to produce the Bio::Search objects.
     Sequences are a little less complicated so there is only one primary
     object (Bio::PrimarySeqI) which Search results need three main
     components to represent the data processed in a file:
!    [20]Bio::Search::Result::ResultI (top level results),
!    [21]Bio::Search::Hit::HitI (hits) and [22]Bio::Search::HSP::HSPI
!    (HSPs). The [23]Bio::SearchIO object is then a factory which produces
!    [24]Bio::Search::Result::ResultI objects and the
!    [25]Bio::Search::Result::ResultI objects contain information about the
     query, the database searched, and the full collection of Hits found
     for the query.
***************
*** 287,291 ****
     used
     Result num_hits 1 number of hits
!    Result hits   Search::Hit::GenericHit object
     Hit name gb|443893|124775 hit name
     Hit length 331 Length of the Hit sequence
--- 289,293 ----
     used
     Result num_hits 1 number of hits
!    Result hits Search::Hit::GenericHit object
     Hit name gb|443893|124775 hit name
     Hit length 331 Length of the Hit sequence
***************
*** 296,300 ****
     Hit significance 2e-022 hit significance
     Hit bits 92.0 hit bits
!    Hit hsps   Search::HSP::GenericHSP object
     Hit num_hsps 1 number of HSPs in hit
     Hit locus 124775 locus name
--- 298,302 ----
     Hit significance 2e-022 hit significance
     Hit bits 92.0 hit bits
!    Hit hsps Search::HSP::GenericHSP object
     Hit num_hsps 1 number of HSPs in hit
     Hit locus 124775 locus name
***************
*** 341,348 ****
     HSP matches('query') (46,48) number of identical and conserved as
     array
!    HSP alignment   Bio::SimpleAlign object
!    HSP hsp_group   Group field from WU-BLAST reports run with -topcomboN
!    or -topcomboE specified
!    HSP links   Links field from WU-BLAST reports run with -links showing
     consistent HSP linking
  
--- 343,350 ----
     HSP matches('query') (46,48) number of identical and conserved as
     array
!    HSP alignment Bio::SimpleAlign object
!    HSP hsp_group Group field from WU-BLAST reports run with -topcomboN or
!    -topcomboE specified
!    HSP links Links field from WU-BLAST reports run with -links showing
     consistent HSP linking
  
***************
*** 353,357 ****
     be needed to get the data of interest. For example, if you wanted a
     printable alignment after you'd parsed BLAST output you could use the
!    get_aln() method, retrieve a [25]Bio::SimpleAlign object and use it
     like this:
          use Bio::AlignIO;
--- 355,359 ----
     be needed to get the data of interest. For example, if you wanted a
     printable alignment after you'd parsed BLAST output you could use the
!    get_aln() method, retrieve a [26]Bio::SimpleAlign object and use it
     like this:
          use Bio::AlignIO;
***************
*** 404,408 ****
     used by many Bioperl modules involved in gene annotation (for more on
     GFF see
!    [26]http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml).
  
     Specifically, the frame() method returns 0, 1, or 2 instead of the
--- 406,410 ----
     used by many Bioperl modules involved in gene annotation (for more on
     GFF see
!    [27]http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml).
  
     Specifically, the frame() method returns 0, 1, or 2 instead of the
***************
*** 416,420 ****
     Our simple table of methods does not show all available arguments or
     returned values for all the SearchIO methods. The best place to
!    explore any method in detail is [27]http://doc.bioperl.org which
     provides the HTML versions of the Perl POD (Plain Old Documentation)
     that is embedded in every well-written Perl module - there's also a
--- 418,422 ----
     Our simple table of methods does not show all available arguments or
     returned values for all the SearchIO methods. The best place to
!    explore any method in detail is [28]http://doc.bioperl.org which
     provides the HTML versions of the Perl POD (Plain Old Documentation)
     that is embedded in every well-written Perl module - there's also a
***************
*** 439,442 ****
--- 441,464 ----
     can't parse.
  
+    You might also find it useful not to have to create reports as files.
+    SearchIO, like [29]SeqIO, is aware of STDIN so you can pipe output
+    from the search application directly to it (on operating systems that
+    allow such things). It could look something like this:
+ 
+ use strict;
+ use Bio::SearchIO;
+ 
+ my $fh;
+ my $fasta   = "/usr/local/bin/fasta34";
+ my $library = "hs.seq";
+ my $query   = "deserts.seq";
+ my $options = "-E 0.01 -m 0 -d 10 -Q";
+ my $command = "$fasta $options $query $library";
+ 
+ open $fh,"$command |";
+ 
+ my $searchio  = Bio::SearchIO->new(-format => 'fasta',
+                                    -fh => $fh);
+ 
  5. Implementation
  
***************
*** 490,494 ****
     and end events and the existing framework will do the work of creating
     the objects for you. Here's how we've implemented event-based parsing
!    for [28]Bio::SearchIO. The Bio::SearchIO is just the front-end to this
     process, in fact the processing of these reports is done by different
     modules in the Bio/SearchIO directory. So if you look at your bioperl
--- 512,516 ----
     and end events and the existing framework will do the work of creating
     the objects for you. Here's how we've implemented event-based parsing
!    for [30]Bio::SearchIO. The Bio::SearchIO is just the front-end to this
     process, in fact the processing of these reports is done by different
     modules in the Bio/SearchIO directory. So if you look at your bioperl
***************
*** 499,503 ****
     also a SearchWriterI.pm and Writer directory in there but we'll save
     that for later. If you don't have the distribution handy you can
!    navigate this at the bioperl [29]CVS web page.
  
     Let's use the blast.pm module as an example to describe the
--- 521,525 ----
     also a SearchWriterI.pm and Writer directory in there but we'll save
     that for later. If you don't have the distribution handy you can
!    navigate this at the bioperl [31]CVS web page.
  
     Let's use the blast.pm module as an example to describe the
***************
*** 522,527 ****
     list of events and know which ones are related to Hits and which ones
     are related to HSPs. The listener in our architecture is the
!    [30]Bio::SearchIO::SearchResultEventBuilder. This object is attached
!    as a listener through the [31]Bio::SearchIO method add_EventListener.
     In fact you could have multiple event listeners and they could do
     different things. In our case we want to create Bio::Search objects,
--- 544,549 ----
     list of events and know which ones are related to Hits and which ones
     are related to HSPs. The listener in our architecture is the
!    [32]Bio::SearchIO::SearchResultEventBuilder. This object is attached
!    as a listener through the [33]Bio::SearchIO method add_EventListener.
     In fact you could have multiple event listeners and they could do
     different things. In our case we want to create Bio::Search objects,
***************
*** 542,548 ****
     Often people want to write back out a BLAST report for users who are
     most comfortable with that output or if you want to visualize the
!    context of a weakly aligned region to use human intuition to score the
!    confidence of a putative homologue. The Bio::SearchIO::Writer modules
!    are for creating output using the information.
  
     Bio::SearchIO::Writer currently creates output in a few different
--- 564,570 ----
     Often people want to write back out a BLAST report for users who are
     most comfortable with that output or if you want to visualize the
!    context of a weakly aligned region and use human intuition to score
!    the confidence of a putative homologue. The Bio::SearchIO::Writer
!    modules are for creating output using the information.
  
     Bio::SearchIO::Writer currently creates output in a few different
***************
*** 555,560 ****
     my $writerhtml = new Bio::SearchIO::Writer::HTMLResultWriter();
     my $outhtml = new Bio::SearchIO(-writer => $writerhtml,
!                                                        -file   => ">searchio.ht
! ml");
     # get a result from Bio::SearchIO parsing or build it up in memory
     $outhtml->write_result($result);
--- 577,581 ----
     my $writerhtml = new Bio::SearchIO::Writer::HTMLResultWriter();
     my $outhtml = new Bio::SearchIO(-writer => $writerhtml,
!                         -file   => ">searchio.html");
     # get a result from Bio::SearchIO parsing or build it up in memory
     $outhtml->write_result($result);
***************
*** 583,587 ****
  7. Extending SearchIO
  
!    The framework for [32]Bio::SearchIO is just a starting point for
     parsing these reports and creating objects which represent the
     information. If you would like to create your own set of objects which
--- 604,608 ----
  7. Extending SearchIO
  
!    The framework for [34]Bio::SearchIO is just a starting point for
     parsing these reports and creating objects which represent the
     information. If you would like to create your own set of objects which
***************
*** 605,611 ****
  
     So, you're going to write your new special module, you do need to make
!    sure it inherits from the base [33]Bio::Search::HSP::HSPI object.
     Additionally unless you want to reimplement all the initialization
!    state in the current [34]Bio::Search::HSP::GenericHSP you should just
     plan to extend that object. You need to follow the chained constructor
     system that we have set up so that the arguments are properly
--- 626,632 ----
  
     So, you're going to write your new special module, you do need to make
!    sure it inherits from the base [35]Bio::Search::HSP::HSPI object.
     Additionally unless you want to reimplement all the initialization
!    state in the current [36]Bio::Search::HSP::GenericHSP you should just
     plan to extend that object. You need to follow the chained constructor
     system that we have set up so that the arguments are properly
***************
*** 678,682 ****
     each of the components of a report. When you have 2000 hits in a
     BLASTX result there will be quite a few objects built, and a lot of
!    memory consumed. It may be that you will need to use an approach
     that's less memory-intensive if your result sets are large. One option
     is to use the tabular output from BLAST when dealing with large
--- 699,703 ----
     each of the components of a report. When you have 2000 hits in a
     BLASTX result there will be quite a few objects built, and a lot of
!    memory consumed. It's possible that you'll want to use an approach
     that's less memory-intensive if your result sets are large. One option
     is to use the tabular output from BLAST when dealing with large
***************
*** 686,696 ****
     We designed SearchIO to be a modular system which separates parsing
     the data from instantiating objects by throwing events (like SAX) and
!    having a listener build objects from these events. One can instantiate
!    a different listener which builds simpler objects and throws away the
!    data you don't want.
  
!    Here is an example of how you can use an existing, lightweight
!    listener - FastHitEventBuilder - which just throws away the HSPs and
!    only builds Result and Hit objects.
  
                    use Bio::SearchIO;
--- 707,717 ----
     We designed SearchIO to be a modular system which separates parsing
     the data from instantiating objects by throwing events (like SAX) and
!    having a listener build objects from these events. So one can
!    instantiate a different listener which builds simpler objects and
!    throws away the data you don't want.
  
!    Here is an example of such a lightweight listener -
!    FastHitEventBuilder - it just throws away the HSPs and only builds
!    Result and Hit objects.
  
                    use Bio::SearchIO;
***************
*** 727,881 ****
  
     SearchIO Modules
!    [35]SearchIO.pm
!    [36]SearchIO/axt.pm
!    [37]SearchIO/blast.pm
!    [38]SearchIO/blasttable.pm
!    [39]SearchIO/blastxml.pm
!    [40]SearchIO/EventHandlerI.pm
!    [41]SearchIO/exonerate.pm
!    [42]SearchIO/fasta.pm
!    [43]SearchIO/FastHitEventBuilder.pm
!    [44]SearchIO/hmmer.pm
!    [45]SearchIO/IteratedSearchResultEventBuilder.pm
!    [46]SearchIO/megablast.pm
!    [47]SearchIO/psl.pm
!    [48]SearchIO/SearchResultEventBuilder.pm
!    [49]SearchIO/SearchWriterI.pm
!    [50]SearchIO/sim4.pm
!    [51]SearchIO/waba.pm
!    [52]SearchIO/wise.pm
!    [53]SearchIO/Writer/BSMLResultWriter.pm
!    [54]SearchIO/Writer/GbrowseGFF.pm
!    [55]SearchIO/Writer/HitTableWriter.pm
!    [56]SearchIO/Writer/HSPTableWriter.pm
!    [57]SearchIO/Writer/HTMLResultWriter.pm
!    [58]SearchIO/Writer/ResultTableWriter.pm
!    [59]SearchIO/Writer/TextResultWriter.pm
!    [60]Search/BlastUtils.pm
!    [61]Search/DatabaseI.pm
!    [62]Search/GenericDatabase.pm
!    [63]Search/Hit/BlastHit.pm
!    [64]Search/Hit/Fasta.pm
!    [65]Search/Hit/GenericHit.html">Search/Hit/GenericHit.pm
!    [66]Search/Hit/HitFactory.pm
!    [67]Search/Hit/HitI.pm
!    [68]Search/Hit/HMMERHit.pm
!    [69]Search/Hit/PsiBlastHit.pm
!    [70]Search/HSP/BlastHSP.pm
!    [71]Search/HSP/FastaHSP.pm
!    [72]Search/HSP/GenericHSP.pm
!    [73]Search/HSP/HMMERHSP.pm
!    [74]Search/HSP/HSPFactory.pm
!    [75]Search/HSP/HSPI.pm
!    [76]Search/HSP/PsiBlastHSP.pm
!    [77]Search/HSP/PSLHSP.pm
!    [78]Search/HSP/WABAHSP.pm
!    [79]Search/Iteration/GenericIteration.pm
!    [80]Search/Iteration/IterationI
!    [81]Search/Processor.pm
!    [82]Search/Result/BlastResult.pm
!    [83]Search/Result/GenericResult.pm
!    [84]Search/Result/HMMERResult.pm
!    [85]Search/Result/ResultFactory.pm
!    [86]Search/Result/ResultI.pm
!    [87]Search/Result/WABAResult.pm
!    [88]Search/SearchUtils.pm
!    [89]Search/BlastStatistics.pm
!    [90]Search/GenericStatistics.pm
!    [91]Search/StatisticsI.pm
  
!    BioPerl DocBook
  
  References
  
!    1. http://www.duke.edu/
!    2. http://upg.duke.edu/
!    3. http://cgt.genetics.duke.edu/
!    4. mailto:jason-at-bioperl.org
!    5. http://www.cognia.com/
!    6. mailto:brian-at-cognia.com
!    7. file://localhost/cygdrive/c/docbook/deploy/SearchIO/SearchIO.html#background
!    8. file://localhost/cygdrive/c/docbook/deploy/SearchIO/SearchIO.html#design
!    9. file://localhost/cygdrive/c/docbook/deploy/SearchIO/SearchIO.html#use
!   10. file://localhost/cygdrive/c/docbook/deploy/SearchIO/SearchIO.html#creating-reports
!   11. file://localhost/cygdrive/c/docbook/deploy/SearchIO/SearchIO.html#implementation
!   12. file://localhost/cygdrive/c/docbook/deploy/SearchIO/SearchIO.html#outputting
!   13. file://localhost/cygdrive/c/docbook/deploy/SearchIO/SearchIO.html#extending
!   14. file://localhost/cygdrive/c/docbook/deploy/SearchIO/SearchIO.html#lightweight
!   15. file://localhost/cygdrive/c/docbook/deploy/SearchIO/SearchIO.html#links
!   16. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SeqIO.html
!   17. http://doc.bioperl.org/releases/bioperl-1.4/Bio/PrimarySeq.html
!   18. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO.html
!   19. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Result/ResultI.html
!   20. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Hit/HitI.html
!   21. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/HSPI.html
!   22. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO.html
!   23. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Result/ResultI.html
    24. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Result/ResultI.html
!   25. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SimpleAlign.html
!   26. http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml
!   27. http://doc.bioperl.org/
!   28. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO.html
!   29. http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/SearchIO/?cvsroot=bioperl
!   30. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/SearchResultEventBuilder.html
!   31. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO.html
!   32. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO.html
!   33. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/HSPI.html
!   34. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/GenericHSP.html
!   35. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO.html
!   36. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/axt.html
!   37. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/blast.html
!   38. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/blasttable.html
!   39. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/blastxml.html
!   40. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/EventHandlerI.html
!   41. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/exonerate.html
!   42. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/fasta.html
!   43. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/FastHitEventBuilder.html
!   44. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/hmmer.html
!   45. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/IteratedSearchResultEventBuilder.html
!   46. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/megablast.html
!   47. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/psl.html
!   48. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/SearchResultEventBuilder.html
!   49. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/SearchWriterI.html
!   50. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/sim4.html
!   51. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/waba.html
!   52. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/wise.html
!   53. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/Writer/BSMLResultWriter.html
!   54. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/Writer/GbrowseGFF.html
!   55. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/Writer/HitTableWriter.html
!   56. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/Writer/HSPTableWriter.html
!   57. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/Writer/HTMLResultWriter.html
!   58. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/Writer/ResultTableWriter.html
!   59. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/Writer/TextResultWriter.html
!   60. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/BlastUtils.html
!   61. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/DatabaseI.html
!   62. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/GenericDatabase.html
!   63. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Hit/BlastHit.html
!   64. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Hit/Fasta.html
!   65. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Hit/GenericHit.html
!   66. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Hit/HitFactory.html
!   67. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Hit/HitI.html
!   68. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Hit/HMMERHit.html
!   69. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Hit/PsiBlastHit.html
!   70. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/BlastHSP.html
!   71. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/FastaHSP.html
!   72. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/GenericHSP.html
!   73. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/HMMERHSP.html
!   74. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/HSPFactory.html
!   75. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/HSPI.html
!   76. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/PsiBlastHSP.html
!   77. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/PSLHSP.html
!   78. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/WABAHSP.html
!   79. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Iteration/GenericIteration.html
!   80. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Iteration/IterationI.html
!   81. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Processor.html
!   82. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Result/BlastResult.html
!   83. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Result/GenericResult.html
!   84. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Result/HMMERResult.html
!   85. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Result/ResultFactory.html
!   86. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Result/ResultI.html
!   87. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Result/WABAResult.html
!   88. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/SearchUtils.html
!   89. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/BlastStatistics.html
!   90. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/GenericStatistics.html
!   91. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/StatisticsI.html
--- 748,905 ----
  
     SearchIO Modules
!    [37]SearchIO.pm
!    [38]SearchIO/axt.pm
!    [39]SearchIO/blast.pm
!    [40]SearchIO/blasttable.pm
!    [41]SearchIO/blastxml.pm
!    [42]SearchIO/EventHandlerI.pm
!    [43]SearchIO/exonerate.pm
!    [44]SearchIO/fasta.pm
!    [45]SearchIO/FastHitEventBuilder.pm
!    [46]SearchIO/hmmer.pm
!    [47]SearchIO/IteratedSearchResultEventBuilder.pm
!    [48]SearchIO/megablast.pm
!    [49]SearchIO/psl.pm
!    [50]SearchIO/SearchResultEventBuilder.pm
!    [51]SearchIO/SearchWriterI.pm
!    [52]SearchIO/sim4.pm
!    [53]SearchIO/waba.pm
!    [54]SearchIO/wise.pm
!    [55]SearchIO/Writer/BSMLResultWriter.pm
!    [56]SearchIO/Writer/GbrowseGFF.pm
!    [57]SearchIO/Writer/HitTableWriter.pm
!    [58]SearchIO/Writer/HSPTableWriter.pm
!    [59]SearchIO/Writer/HTMLResultWriter.pm
!    [60]SearchIO/Writer/ResultTableWriter.pm
!    [61]SearchIO/Writer/TextResultWriter.pm
!    [62]Search/BlastUtils.pm
!    [63]Search/DatabaseI.pm
!    [64]Search/GenericDatabase.pm
!    [65]Search/Hit/BlastHit.pm
!    [66]Search/Hit/Fasta.pm
!    [67]Search/Hit/GenericHit.html">Search/Hit/GenericHit.pm
!    [68]Search/Hit/HitFactory.pm
!    [69]Search/Hit/HitI.pm
!    [70]Search/Hit/HMMERHit.pm
!    [71]Search/Hit/PsiBlastHit.pm
!    [72]Search/HSP/BlastHSP.pm
!    [73]Search/HSP/FastaHSP.pm
!    [74]Search/HSP/GenericHSP.pm
!    [75]Search/HSP/HMMERHSP.pm
!    [76]Search/HSP/HSPFactory.pm
!    [77]Search/HSP/HSPI.pm
!    [78]Search/HSP/PsiBlastHSP.pm
!    [79]Search/HSP/PSLHSP.pm
!    [80]Search/HSP/WABAHSP.pm
!    [81]Search/Iteration/GenericIteration.pm
!    [82]Search/Iteration/IterationI
!    [83]Search/Processor.pm
!    [84]Search/Result/BlastResult.pm
!    [85]Search/Result/GenericResult.pm
!    [86]Search/Result/HMMERResult.pm
!    [87]Search/Result/ResultFactory.pm
!    [88]Search/Result/ResultI.pm
!    [89]Search/Result/WABAResult.pm
!    [90]Search/SearchUtils.pm
!    [91]Search/BlastStatistics.pm
!    [92]Search/GenericStatistics.pm
!    [93]Search/StatisticsI.pm
  
!    Bioperl DocBook ([94]Bioperl)
  
  References
  
!    1. http://bioperl.org/
!    2. http://www.duke.edu/
!    3. http://upg.duke.edu/
!    4. http://cgt.genetics.duke.edu/
!    5. mailto:jason-at-bioperl.org
!    6. http://www.cognia.com/
!    7. mailto:brian-at-cognia.com
!    8. file://localhost/cygdrive/c/docbook/deploy/SearchIO/SearchIO.html#background
!    9. file://localhost/cygdrive/c/docbook/deploy/SearchIO/SearchIO.html#design
!   10. file://localhost/cygdrive/c/docbook/deploy/SearchIO/SearchIO.html#use
!   11. file://localhost/cygdrive/c/docbook/deploy/SearchIO/SearchIO.html#creating-reports
!   12. file://localhost/cygdrive/c/docbook/deploy/SearchIO/SearchIO.html#implementation
!   13. file://localhost/cygdrive/c/docbook/deploy/SearchIO/SearchIO.html#outputting
!   14. file://localhost/cygdrive/c/docbook/deploy/SearchIO/SearchIO.html#extending
!   15. file://localhost/cygdrive/c/docbook/deploy/SearchIO/SearchIO.html#lightweight
!   16. file://localhost/cygdrive/c/docbook/deploy/SearchIO/SearchIO.html#links
!   17. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SeqIO.html
!   18. http://doc.bioperl.org/releases/bioperl-1.4/Bio/PrimarySeq.html
!   19. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO.html
!   20. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Result/ResultI.html
!   21. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Hit/HitI.html
!   22. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/HSPI.html
!   23. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO.html
    24. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Result/ResultI.html
!   25. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Result/ResultI.html
!   26. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SimpleAlign.html
!   27. http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml
!   28. http://doc.bioperl.org/
!   29. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SeqIO.html
!   30. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO.html
!   31. http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/Bio/SearchIO/?cvsroot=bioperl
!   32. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/SearchResultEventBuilder.html
!   33. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO.html
!   34. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO.html
!   35. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/HSPI.html
!   36. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/GenericHSP.html
!   37. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO.html
!   38. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/axt.html
!   39. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/blast.html
!   40. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/blasttable.html
!   41. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/blastxml.html
!   42. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/EventHandlerI.html
!   43. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/exonerate.html
!   44. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/fasta.html
!   45. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/FastHitEventBuilder.html
!   46. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/hmmer.html
!   47. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/IteratedSearchResultEventBuilder.html
!   48. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/megablast.html
!   49. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/psl.html
!   50. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/SearchResultEventBuilder.html
!   51. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/SearchWriterI.html
!   52. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/sim4.html
!   53. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/waba.html
!   54. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/wise.html
!   55. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/Writer/BSMLResultWriter.html
!   56. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/Writer/GbrowseGFF.html
!   57. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/Writer/HitTableWriter.html
!   58. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/Writer/HSPTableWriter.html
!   59. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/Writer/HTMLResultWriter.html
!   60. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/Writer/ResultTableWriter.html
!   61. http://doc.bioperl.org/releases/bioperl-1.4/Bio/SearchIO/Writer/TextResultWriter.html
!   62. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/BlastUtils.html
!   63. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/DatabaseI.html
!   64. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/GenericDatabase.html
!   65. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Hit/BlastHit.html
!   66. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Hit/Fasta.html
!   67. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Hit/GenericHit.html
!   68. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Hit/HitFactory.html
!   69. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Hit/HitI.html
!   70. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Hit/HMMERHit.html
!   71. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Hit/PsiBlastHit.html
!   72. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/BlastHSP.html
!   73. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/FastaHSP.html
!   74. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/GenericHSP.html
!   75. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/HMMERHSP.html
!   76. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/HSPFactory.html
!   77. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/HSPI.html
!   78. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/PsiBlastHSP.html
!   79. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/PSLHSP.html
!   80. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/HSP/WABAHSP.html
!   81. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Iteration/GenericIteration.html
!   82. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Iteration/IterationI.html
!   83. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Processor.html
!   84. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Result/BlastResult.html
!   85. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Result/GenericResult.html
!   86. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Result/HMMERResult.html
!   87. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Result/ResultFactory.html
!   88. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Result/ResultI.html
!   89. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/Result/WABAResult.html
!   90. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/SearchUtils.html
!   91. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/BlastStatistics.html
!   92. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/GenericStatistics.html
!   93. http://doc.bioperl.org/releases/bioperl-1.4/Bio/Search/StatisticsI.html
!   94. http://bioperl.org/



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