[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
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RCS file: /home/repository/bioperl/bioperl-live/doc/howto/txt/SearchIO.txt,v
retrieving revision 1.3
retrieving revision 1.4
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*** SearchIO.txt 2 Dec 2004 02:22:47 -0000 1.3
--- SearchIO.txt 26 Apr 2005 01:47:40 -0000 1.4
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*** 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
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*** 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
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*** 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;
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*** 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
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*** 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
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*** 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
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*** 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
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*** 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,
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*** 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
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*** 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);
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*** 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
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*** 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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