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2 Bioperl FAQ
3 -----------
4 v. 1.0.2
6 This FAQ maintained by:
7 * Jason Stajich <jason@bioperl.org>
8 * Brian Osborne <brian_osborne@cognia.com>
9 * Heikki Lehvaslaiho <heikki@ebi.ac.uk>
12 ---------------------------------------------------------------------------
14 Contents
16 ---------------------------------------------------------------------------
18 0. About this FAQ
20 Q0.1: What is this FAQ?
21 Q0.2: How is it maintained?
23 1. Bioperl in general
25 Q1.1: What is Bioperl?
26 Q1.2: Where do I go to get the latest release?
27 Q1.3: What is the difference between 0.9.x and 0.7.x? What do you mean
28 developer release?
29 Q1.4: Is it BioPerl, bioperl, bio.perl.org, Bioperl? What's the deal?
30 Q1.5: How do I figure out how to use a module?
31 Q1.6: I'm interested in the bleeding edge version of the code, where can
32 I get it?
33 Q1.7: Who uses this toolkit?
34 Q1.8: How should I cite Bioperl?
35 Q1.9: What are the license terms for Bioperl?
36 Q1.10: I want to help, where do I start?
37 Q1.11: I've got an idea for a module how do I contribute it?
39 2. Sequences
41 Q2.1: How do I parse a sequence file?
42 Q2.2: I can't get sequences with Bio::DB::GenBank any more, why not?
43 Q2.3: How can I get NT_ or NM_ or NP_ accessions from NCBI
44 (Reference Sequences)?
45 Q2.4: How can I use SeqIO to parse sequence data from a string?
47 3. Report parsing
49 Q3.1: I want to parse BLAST, how do I do this?
50 Q3.2: What's wrong with Bio::Tools::Blast?
51 Q3.3: I want to parse FastA or NCBI -m7 (XML) format, how do I do this?
52 Q3.4: Let's say I want to do pairwise alignments of 2 sequences how can
53 I do this?
54 Q3.5: I'm using BPLite.pm and its frame() to parse Blast but I'm seeing
55 0, 1, or 2 instead of the expected -3, -2, -1, +1, +2, +3. Why am
56 I seeing these different numbers and how do I get the frame
57 according to Blast?
59 4. Utilities
61 Q4.1: How do I find all the ORFs in a nucleotide sequence? Antigenic
62 sites in a protein? Calculate nucleotide melting temperature? Find
63 repeats?
64 Q4.2: How do I do motif searches with Bioperl? Can I do "find all
65 sequences that are 75% identical" to a given motif?
66 Q4.3: Can I query MEDLINE or other bibliographic repositories using
67 Bioperl?
69 5. Annotations and Features
71 Q5.1: I get the warning "(old style Annotation) on new style
72 Annotation::Collection". What is wrong?
73 Q5.2: How do I retrieve all the features from a Sequence? How about all
74 the features which are exons or have a /note field that contains a
75 certain gene name?
76 Q5.3: How do I parse the CDS join() statements in Genbank or EMBL files
77 so I can reconstruct the CDS sequence?
79 6. Running external programs
81 Q6.1: I want to run StandAloneBlast within bioperl - where did it go?
82 Q6.2: What does the future hold for running applications within Bioperl?
84 ---------------------------------------------------------------------------
86 0. About this FAQ
88 ---------------------------------------------------------------------------
92 Q0.1: What is this FAQ?
94 A: It is the list of Frequently Asked Questions about Bioperl.
97 Q0.2: How is it maintained?
99 A: This FAQ was generated using a Perl script and an XML file. All
100 the files are in the Bioperl distribution directory doc/faq. So do
101 not edit this file! Edit file faq.xml and run:
103 % faq.pl -text faq.xml
105 The XML structure was originally used by the Perl XML project.
106 Their website seems to have vanished, though. The XML and
107 modifying scripts were copied from Michael Rodriguez's web site
108 http://www.xmltwig.com/xmltwig/XML-Twig-FAQ.html and modified to
109 our needs.
112 ---------------------------------------------------------------------------
114 1. Bioperl in general
116 ---------------------------------------------------------------------------
120 Q1.1: What is Bioperl?
122 A: Bioperl is a tookit of perl modules useful in building
123 bioinformatics solutions in perl. It is built in an
124 object-oriented manner so that many modules depend on each other
125 to achieve a task. The collection of modules in the bioperl-live
126 repository consist of the core of the functionality of bioperl.
127 Additionally auxiliary modules for creating graphical interfaces
128 (bioperl-gui), persistent storage in RDMBS (bioperl-db), and CORBA
129 bridges to the BioCORBA (http://www.biocorba.org) specification
130 (bioperl-corba-server and bioperl-corba-client) are all available
131 as CVS modules in our repository.
134 Q1.2: Where do I go to get the latest release?
136 A: You can always get our releases from ftp://bioperl.org/pub/DIST.
137 Official releases will be noted on the website http://bioperl.org.
140 Q1.3: What is the difference between 0.9.x and 0.7.x? What do you mean
141 developer release?
143 A: 0.7.X series (0.7.0, 0.7.2) were all released in 2001 and were
144 stable releases on 0.7 branch. This means they had a set of
145 functionality that is maintained throughout (no experimental
146 modules) and were guaranteed to have all tests and subsequent bug
147 fix releases with the 0.7 designation would not have any API
148 changes.
150 The 0.9.X series was our first attempt at releasing so called
151 developer releases. These are snapshots of the actively developed
152 code that at a minimum pass all our tests.
154 But really, you should be using version 1.*!
157 Q1.4: Is it BioPerl, bioperl, bio.perl.org, Bioperl? What's the deal?
159 A: Well, the perl.org guys granted us use of bio.perl.org. We prefer
160 to be called Bioperl or BioPerl (unlike our Biopython friends).
161 We're part of the Open Bioinformatics Foundation (OBF) and so as
162 part of the Bio{*} toolkits we prefer the Bioperl spelling. But
163 we're not really all that picky so no worries.
166 Q1.5: How do I figure out how to use a module?
168 A: Read the embedded perl documentation (Plain Old Documentation -
169 POD) that is part of every modules. Do:
171 % perldoc MODULE
173 (careful - spelling and case counts!).
175 The bioperl tutorial - bptutorial.pl - provided in the root
176 directory of the bioperl release will also provide a good
177 introduction. There are links to tutorials off the bioperl
178 website that may provide some additional help.
180 There are also many scripts in the examples/ and scripts/
181 directories that could be useful - see bioperl.pod for a brief
182 description of all of them.
184 Additionally we have written many tests for our modules, you can
185 see test data and example usage of the modules in these tests -
186 look in the test dir (called 't').
189 Q1.6: I'm interested in the bleeding edge version of the code, where can
190 I get it?
192 A: Go to http://cvs.bioperl.org and you'll see instructions on how to
193 get the CVS code.
195 Basically:
197 % cvs -d :pserver:cvs@cvs.bioperl.org:/home/repository/bioperl
198 login
200 enter 'cvs' for the password
203 % cvs -d :pserver:cvs@cvs.bioperl.org:/home/repository/bioperl
204 co bioperl_all
207 Q1.7: Who uses this toolkit?
209 A: Lots of people. Sanger Centre, EBI, many large and small academic
210 laboratories, large and small pharmaceutical companies. All the
211 developers on the bioperl list use the toolkit in some capacity on
212 a regular basis.
214 The Genquire annotation system
215 (http://www.bioinformatics.org/Genquire/) and Ensembl
216 (http://www.ensembl.org/) use bioperl as the basis for their
217 implementation.
220 Q1.8: How should I cite Bioperl?
222 A: Please cite it as.
223 Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA,
224 Dagdigian C, Fuellen G, Gilbert JGR, Korf I, Lapp H,
225 Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI,
226 Pocock MR, Schattner P, Senger M, Stein LD, Stupka ED,
227 Wilkinson M, Birney E.
228 The Bioperl Toolkit: Perl modules for the life sciences.
229 Genome Research. 2002 Oct;12(10):1161-8.
232 Q1.9: What are the license terms for Bioperl?
234 A: Bioperl is licensed under the same terms as Perl itself which is
235 the Perl Artistic License. You can see more information on that
236 license at http://www.perl.com/pub/a/language/misc/Artistic.html
237 and http://www.opensource.org/licenses/artistic-license.html.
240 Q1.10: I want to help, where do I start?
242 A: Bioperl is a pretty diverse collection of modules which has grown
243 from the direct needs of the developers participating in the
244 project. So if you don't have a need for a specific module in the
245 toolkit it becomes hard to just describe ways it needs to be
246 expanded or adapted. One area, however is the development of
247 stand alone scripts which use bioperl components for common tasks.
248 Some starting points for script: find out what people in your
249 institution do routinely that a shortcut can be developed for.
250 Identify modules in bioperl that need easy intefaces and write
251 that wrapper - you'll learn how to use the module inside and out.
252 We always need people to help fix bugs - read the jitterbug bug
253 tracking system (webpage linked from bioperl website sidebar
254 under "Bugs").
257 Q1.11: I've got an idea for a module how do I contribute it?
259 A: We suggest the following. Post your idea to the bioperl list,
260 bioperl-l@bioperl.org. If it is a really new idea consider taking
261 us through your thought process. We'll help you tease out the
262 necessary information such as what methods you'll want and how it
263 can interact with other bioperl modules. If it is a port of
264 something you've already worked on, give us a summary of the
265 current methods. Make sure there is an interface to the module,
266 not just an implementation (see the biodesign.pod for more info)
267 and make sure there will be a set of tests that will be in the t/
268 directory to insure that your module is tested.
271 ---------------------------------------------------------------------------
273 2. Sequences
275 ---------------------------------------------------------------------------
279 Q2.1: How do I parse a sequence file?
281 A: Use the Bio::SeqIO system. This will create Bio::Seq objects for
282 you. See the tutorial bptutorial.pl for more information or the
283 documentation for Bio::SeqIO (e.g. 'perldoc SeqIO.pm').
286 Q2.2: I can't get sequences with Bio::DB::GenBank any more, why not?
288 A: NCBI changed the web CGI script that provided this access. You
289 must be using bioperl <= 0.7.2. The developer release 0.9.3
290 contains this fix as does the 1.0 release.
293 Q2.3: How can I get NT_ or NM_ or NP_ accessions from NCBI
294 (Reference Sequences)?
296 A: Use Bio::DB::RefSeq not Bio::DB::GenBank or Bio::DB::GenPept when
297 you are retrieving these accessions. This is still an area of
298 active development because the data providers have not provided
299 the best interface for us to query. EBI has provided a mirror
300 with their dbfetch system which is accessible through the
301 Bio::DB::RefSeq object however, there are cases where NT_
302 accessions will not be retrievable.
305 Q2.4: How can I use SeqIO to parse sequence data from a string?
307 A:
308 use IO::String;
309 use Bio::SeqIO;
310 my $stringfh = new IO::String($string);
312 my $seqio = new Bio::SeqIO(-fh => $stringfh,
313 -format => 'fasta');
314 while( my $seq = $seqio->next_seq ) { # process each seq
315 }
318 ---------------------------------------------------------------------------
320 3. Report parsing
322 ---------------------------------------------------------------------------
326 Q3.1: I want to parse BLAST, how do I do this?
328 A: Well you might notice that there are a lot of choices. Sorry
329 about that. We've been evolving towards a single solution.
331 Currently the best way to parse a report is to use the SearchIO
332 system. This supports blast and fasta report parsing. The
333 bptutorial provides an example of how to use this system as well
334 as the documentation in the Bio::SearchIO system.
337 Q3.2: What's wrong with Bio::Tools::Blast?
339 A: Nothing is really wrong with it, it has just been outgrown by a
340 more generic approach to reports. This generic approach allows us
341 to just write pluggable modules for fasta and Blast parsing while
342 using the same framework. This is completely analogous to the
343 Bio::SeqIO system of parsing sequence files. However, the objects
344 produced are of the Bio::Search rather than Bio::Seq variety.
347 Q3.3: I want to parse FastA or NCBI -m7 (XML) format, how do I do this?
349 A: It is as simple as parsing text BLAST results - you simply need to
350 specify the format as "fasta" or "blastxml" and the parser will
351 load the appropriate module for you. You can use the exact logic
352 and code for all of these formats as we have generalized the
353 modules for sequence database searching.
356 Q3.4: Let's say I want to do pairwise alignments of 2 sequences how can
357 I do this?
359 A: Look at Bio::Factory::EMBOSS to see how to use the 'water' and
360 'needle' alignment programs that are part of the EMBOSS suite.
362 Additionally you can use the pSW module that is part of the
363 bioperl-ext package (distributed separated at
364 ftp://bioperl.org/pub/DIST). However note this only does protein
365 alignments and is no longer a supported module. Instead the
366 EMBOSS implementation is the the best path ahead unless someone
367 else wants to provide an Inline::C implementation.
370 Q3.5: I'm using BPLite.pm and its frame() to parse Blast but I'm seeing
371 0, 1, or 2 instead of the expected -3, -2, -1, +1, +2, +3. Why am
372 I seeing these different numbers and how do I get the frame
373 according to Blast?
375 A: These are GFF frames - so +1 is 0 in GFF, -3 will be encoded with
376 a frame of 2 with the strand being set to -1 (for more on GFF see
377 http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml).
379 Frames are relative to the hit or query sequence so you need to
380 query it based on sequence you are interested in:
382 $hsp->hit->strand();
383 $hsp->hit->frame();
385 or
387 $hsp->query->strand();
388 $hsp->query->frame();
390 So the value according to a blast report of -3 can be constructed
391 as:
393 my $blastvalue = ($hsp->query->frame + 1) * $hsp->query->strand;
396 ---------------------------------------------------------------------------
398 4. Utilities
400 ---------------------------------------------------------------------------
404 Q4.1: How do I find all the ORFs in a nucleotide sequence? Antigenic
405 sites in a protein? Calculate nucleotide melting temperature? Find
406 repeats?
408 A: In fact, none of these functions are built into Bioperl but they
409 are all available in the EMBOSS package (http://www.emboss.org/),
410 as well as many others. The Bioperl developers created a simple
411 interface to EMBOSS such that any and all EMBOSS programs can be
412 run from within Bioperl. See Bio::Factory::EMBOSS for more
413 information.
415 If you can't find the functionality you want in Bioperl then make
416 sure to look for it in EMBOSS, these packages integrate quite
417 gracefully with Bioperl. Of course, you will have to install
418 EMBOSS to get this access.
420 In addition, Bioperl after version 1.0.1 contains the Pise/Bioperl
421 modules. The Pise package
422 (http://www-alt.pasteur.fr/~letondal/Pise) was designed to provide
423 a uniform interface to bioinformatics applications, and currently
424 provides wrappers to greater than 250 such applications! Included
425 amongst these wrapped apps are HMMER, Phylip, BLAST, GENSCAN, even
426 the EMBOSS suite. Use of the Pise/Bioperl modules does not require
427 installation of the Pise package.
430 Q4.2: How do I do motif searches with Bioperl? Can I do "find all
431 sequences that are 75% identical" to a given motif?
433 A: There are a number of approaches. Within Bioperl take a look at
434 Bio::Tools::SeqPattern. Or, take a look at the TFBS package, at
435 http://forkhead.cgb.ki.se/TFBS(Transcription Factor Binding Site).
436 This Bioperl-compliant package specializes in pattern searching of
437 nucleotide sequence using matrices.
439 It's also conceivable that the combination of Bioperl and Perl's
440 regular expressions could do the trick. You might also consider
441 the CPAN module String::Approx (this module addresses the percent
442 match query), but experienced users question whether its distance
443 estimates are correct, the Unix agrep command is thought to be
444 faster and more accurate. Finally, you could use EMBOSS, as
445 discussed in the previous question (or you could use Pise to run
446 EMBOSS applications). The relevant programs would be fuzzpro or
447 fuzznuc.
450 Q4.3: Can I query MEDLINE or other bibliographic repositories using
451 Bioperl?
453 A: Yes! The solution lies in Bio::Biblio*, a set of modules that
454 provide access to MEDLINE and OpenBQS-compliant servers using
455 SOAP. See Bio/Biblio.pm or examples/biblio.pl for details and
456 example code.
459 ---------------------------------------------------------------------------
461 5. Annotations and Features
463 ---------------------------------------------------------------------------
467 Q5.1: I get the warning "(old style Annotation) on new style
468 Annotation::Collection". What is wrong?
470 A: This is because we have transitioned from the
471 add_Comment/each_Comment, add_Reference/each_Reference style to
472 add_Annotation('comment', $ann)/get_Annotations('comment). Please
473 update your code in order to avoid seeing these warning messages.
475 This is because we have changed (starting with 1.0) the annotation
476 collection implementation from the Bio::Annotation object to the
477 Bio::Annotation::Collection object which is a more general and
478 extensible system. In the future the Reference objects will
479 likely be implemented by the Bio::Biblio system but we hope to
480 maintain a compatible API for these.
483 Q5.2: How do I retrieve all the features from a Sequence? How about all
484 the features which are exons or have a /note field that contains a
485 certain gene name?
487 A: To get all the features:
489 my @features = $seq->all_SeqFeatures();
491 To get all the features filtering on only those which have the
492 primary tag 'exon'.
494 my @genes = grep { $_->primary_tag eq 'exon'}
495 $seq->all_SeqFeatures();
497 To get all the features filtering on this which have the tag
498 'note' and within the note field contain the requested string
499 $noteval.
501 my @f_with_note = grep {
502 my @a = $_->has_tag('note') ?
503 $_->each_tag_value('note') : ();
504 grep { /$noteval/ } @a;
505 } $seq->all_SeqFeatures();
508 Q5.3: How do I parse the CDS join() statements in Genbank or EMBL files
509 so I can reconstruct the CDS sequence?
511 A: You need to use a Location::SplitLocationI object to get the
512 coordinates and primary_tag() to find the CDS features:
514 if ( $feature->location->isa('Bio::Location::SplitLocationI')
515 && $feature->primary_tag eq 'CDS' ) {
516 foreach $location ( $feature->location->sub_Location ) {
517 print $location->start . ".." . $location->end . "\n";
518 }
519 }
522 ---------------------------------------------------------------------------
524 6. Running external programs
526 ---------------------------------------------------------------------------
530 Q6.1: I want to run StandAloneBlast within bioperl - where did it go?
532 A: The Bio::Tools::Run directory was moved to a new package to help
533 make the size of the core code smaller and separate out the more
534 specialized nature of application running from the rest of
535 Bioperl. You can get these modules by installing the bioperl-run
536 package. This is either available from CVS under the same name or
537 available in the http://bioperl.org/DIST directory and on CPAN.
538 This changeover began in the bioperl 1.1 developer release.
541 Q6.2: What does the future hold for running applications within Bioperl?
542 A: We are trying to build a standard starting point for analysis
543 application which will probably look like
544 Bio::Tools::Run::AnalysisFactory which will allow the user to
545 request which type of remote or local server they want to use to
546 run their analyses. This will connect to the Pasteur's PISE
547 server, the EBI's Novella server, as well as be aware of wrappers
548 to run applications locally.
550 Additionally we suggest investigating the BioPipe
551 project(http://www.biopipe.org) which is making it easier to chain
552 together various sets of analyses and build rules for peforming
553 these computes.
555 ---------------------------------------------------------------------------
556 Copyright (c)2002 Open Bioinformatics Foundation. You may distribute this
557 FAQ under the same terms as perl itself.