bio 1.2.1 → 1.3.0

data/test/unit/bio/db/test_medline.rb

@@ -0,0 +1,127 @@
+#
+# test/unit/bio/db/test_medline.rb - Unit test for Bio::MEDLINE
+#
+# Copyright::  Copyright (C) 2008 Collaborative Drug Discovery, Inc. <github@collaborativedrug.com>
+# License::    The Ruby License
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio/db/medline'
+
+module Bio
+  class TestMEDLINE < Test::Unit::TestCase
+    def test_authors
+      assert_equal(["Kane, D. W.",
+                    "Hohman, M. M.",
+                    "Cerami, E. G.",
+                    "McCormick, M. W.",
+                    "Kuhlmann, K. F.",
+                    "Byrd, J. A."], Bio::MEDLINE.new(AGILE).authors)
+    end
+   
+    def test_authors_with_suffix
+      assert_equal(["Jenkins, F. A. Jr"], Bio::MEDLINE.new("AU  - Jenkins FA Jr").authors)
+    end
+    
+    def test_authors_with_last_name_all_caps
+      assert_equal(["GARTLER, S. M."], Bio::MEDLINE.new("AU  - GARTLER SM").authors)
+    end
+    
+    AGILE = <<-EOMED
+PMID- 16734914
+OWN - NLM
+STAT- MEDLINE
+DA  - 20060811
+DCOM- 20060928
+LR  - 20081120
+IS  - 1471-2105 (Electronic)
+VI  - 7
+DP  - 2006
+TI  - Agile methods in biomedical software development: a multi-site experience
+      report.
+PG  - 273
+AB  - BACKGROUND: Agile is an iterative approach to software development that
+      relies on strong collaboration and automation to keep pace with dynamic
+      environments. We have successfully used agile development approaches to
+      create and maintain biomedical software, including software for
+      bioinformatics. This paper reports on a qualitative study of our
+      experiences using these methods. RESULTS: We have found that agile methods
+      are well suited to the exploratory and iterative nature of scientific
+      inquiry. They provide a robust framework for reproducing scientific
+      results and for developing clinical support systems. The agile development
+      approach also provides a model for collaboration between software
+      engineers and researchers. We present our experience using agile
+      methodologies in projects at six different biomedical software development
+      organizations. The organizations include academic, commercial and
+      government development teams, and included both bioinformatics and
+      clinical support applications. We found that agile practices were a match
+      for the needs of our biomedical projects and contributed to the success of
+      our organizations. CONCLUSION: We found that the agile development
+      approach was a good fit for our organizations, and that these practices
+      should be applicable and valuable to other biomedical software development
+      efforts. Although we found differences in how agile methods were used, we
+      were also able to identify a set of core practices that were common to all
+      of the groups, and that could be a focus for others seeking to adopt these
+      methods.
+AD  - SRA International, 4300 Fair Lakes Court, Fairfax, VA 22033, USA.
+      david_kane@sra.com
+FAU - Kane, David W
+AU  - Kane DW
+FAU - Hohman, Moses M
+AU  - Hohman MM
+FAU - Cerami, Ethan G
+AU  - Cerami EG
+FAU - McCormick, Michael W
+AU  - McCormick MW
+FAU - Kuhlmann, Karl F
+AU  - Kuhlmann KF
+FAU - Byrd, Jeff A
+AU  - Byrd JA
+LA  - eng
+GR  - U01 MH061915-03/MH/NIMH NIH HHS/United States
+GR  - U01 MH061915-04/MH/NIMH NIH HHS/United States
+GR  - U01 MH61915/MH/NIMH NIH HHS/United States
+PT  - Journal Article
+PT  - Research Support, N.I.H., Extramural
+PT  - Research Support, Non-U.S. Gov't
+DEP - 20060530
+PL  - England
+TA  - BMC Bioinformatics
+JT  - BMC bioinformatics
+JID - 100965194
+SB  - IM
+MH  - Algorithms
+MH  - Automation
+MH  - Computational Biology/*methods
+MH  - Computers
+MH  - Database Management Systems
+MH  - Databases, Genetic
+MH  - Diffusion of Innovation
+MH  - Hospital Information Systems
+MH  - Hospitals
+MH  - Humans
+MH  - Medical Informatics
+MH  - Multicenter Studies as Topic
+MH  - Programming Languages
+MH  - Software
+MH  - *Software Design
+MH  - Systems Integration
+PMC - PMC1539031
+OID - NLM: PMC1539031
+EDAT- 2006/06/01 09:00
+MHDA- 2006/09/29 09:00
+CRDT- 2006/06/01 09:00
+PHST- 2005/11/17 [received]
+PHST- 2006/05/30 [accepted]
+PHST- 2006/05/30 [aheadofprint]
+AID - 1471-2105-7-273 [pii]
+AID - 10.1186/1471-2105-7-273 [doi]
+PST - epublish
+SO  - BMC Bioinformatics. 2006 May 30;7:273.
+EOMED
+  end
+end

data/test/unit/bio/db/test_nexus.rb

@@ -5,13 +5,17 @@
 #
 # License::     The Ruby License
 #
-# $Id: test_nexus.rb,v 1.2 2007/04/05 23:35:43 trevor Exp $
+# $Id:$
 #
 # == Description
 #
 # This file contains unit tests for Bio::Nexus.
 #
 
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
 require 'test/unit'
 require 'bio/db/nexus'
 

data/test/unit/bio/db/test_prosite.rb

@@ -1233,7 +1233,7 @@ module Bio
  "P11616",
  "P23275",
  "Q01338"]
-      assert_equal(data, @obj.list_truepositive)
+      assert_equal(data.sort, @obj.list_truepositive.sort)
     end
 
     def test_list_falsenegative
@@ -1301,7 +1301,7 @@ module Bio
  "P77933",
  "P34529",
  "Q00126"]
-      assert_equal(data, @obj.list_falsenegative)
+      assert_equal(data.sort, @obj.list_falsenegative.sort)
     end
     
     def test_list_falsepositive
@@ -1353,7 +1353,7 @@ module Bio
  "Q95137",
  "Q62953",
  "Q95195"]
-      assert_equal(data, @obj.list_falsepositive)
+      assert_equal(data.sort, @obj.list_falsepositive.sort)
     end
 
     def test_list_potentialhit
@@ -1405,7 +1405,7 @@ module Bio
  "Q95137",
  "Q62953",
  "Q95195"]
-      assert_equal(data, @obj.list_potentialhit)
+      assert_equal(data.sort, @obj.list_potentialhit.sort)
     end
 
     def test_list_unknown

data/test/unit/bio/io/flatfile/test_autodetection.rb

@@ -0,0 +1,375 @@
+#
+# = test/unit/bio/io/flatfile/test_autodetection.rb - unit test for Bio::FlatFile::AutoDetect
+#
+#   Copyright (C) 2006 Naohisa Goto <ng@bioruby.org>
+#
+# License:: The Ruby License
+#
+#  $Id: test_flatfile.rb,v 1.2 2007/04/05 23:35:43 trevor Exp $
+#
+
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 5, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+
+require 'test/unit'
+require 'bio'
+
+module Bio::TestFlatFile
+
+  # testing default AutoDetect's behavior
+  class TestDefaultAutoDetect < Test::Unit::TestCase
+    
+    bioruby_root = Pathname.new(File.join(File.dirname(__FILE__),
+                                          ['..'] * 5)).cleanpath.to_s
+    TestDataPath = Pathname.new(File.join(bioruby_root,
+                                          'test', 'data')).cleanpath.to_s
+
+    def setup
+      @ad = Bio::FlatFile::AutoDetect.default
+    end
+
+    def test_genbank
+      # modified from GenBank AB009803.1
+      # (E-mail and telephone/FAX numbers are removed from original entry)
+      text = <<__END_OF_TEXT__
+LOCUS       AB009803                  81 bp    DNA     linear   PRI 14-APR-2000
+DEFINITION  Homo sapiens gene for osteonidogen, intron 4.
+ACCESSION   AB009803
+VERSION     AB009803.1  GI:2749808
+KEYWORDS    osteonidogen.
+SOURCE      Homo sapiens (human)
+  ORGANISM  Homo sapiens
+            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
+            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
+            Catarrhini; Hominidae; Homo.
+REFERENCE   1
+  AUTHORS   Ohno,I., Okubo,K. and Matsubara,K.
+  TITLE     Human osteonidogen gene: intron-exon junctions and chromosomal
+            localization
+  JOURNAL   Published Only in Database (1998)
+REFERENCE   2  (bases 1 to 81)
+  AUTHORS   Ohno,I., Okubo,K. and Matsubara,K.
+  TITLE     Direct Submission
+  JOURNAL   Submitted (13-DEC-1997) Ikko Ohno, Institute for Molecular and
+            Cellular Biology, Osaka University, Molecular Genetics; 1-3
+            Yamada-oka, Suita, Osaka 565, Japan
+FEATURES             Location/Qualifiers
+     source          1..81
+                     /organism="Homo sapiens"
+                     /mol_type="genomic DNA"
+                     /db_xref="taxon:9606"
+                     /chromosome="14"
+                     /map="14q21-22"
+                     /clone_lib="Lambda FIX II STRATAGENE"
+     intron          1..81
+                     /number=4
+ORIGIN
+        1 gtaggatctc ccctccagat tctgatctgt cctccccctt gcatccaaca cctacttatt
+       61 ggccattcta tcctgaaaca g
+//
+__END_OF_TEXT__
+      assert_equal(Bio::GenBank, @ad.autodetect(text))
+    end
+
+    def test_genpept
+      # modified from: NCBI: P04637.2 GI:129369
+      # (to shorten data, many elements are omitted)
+      text = <<__END_OF_TEXT__
+LOCUS       P04637                   393 aa            linear   PRI 01-JUL-2008
+DEFINITION  Cellular tumor antigen p53 (Tumor suppressor p53) (Phosphoprotein
+            p53) (Antigen NY-CO-13).
+ACCESSION   P04637
+VERSION     P04637.2  GI:129369
+KEYWORDS    3D-structure; Acetylation; Activator; Alternative splicing;
+            Anti-oncogene; Apoptosis; Cell cycle; Covalent protein-RNA linkage;
+            Cytoplasm; Disease mutation; DNA-binding; Endoplasmic reticulum;
+            Glycoprotein; Host-virus interaction; Li-Fraumeni syndrome;
+            Metal-binding; Methylation; Nucleus; Phosphoprotein; Polymorphism;
+            Transcription; Transcription regulation; Ubl conjugation; Zinc.
+SOURCE      Homo sapiens (human)
+  ORGANISM  Homo sapiens
+            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
+            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
+            Catarrhini; Hominidae; Homo.
+REFERENCE   1  (residues 1 to 393)
+  AUTHORS   Zakut-Houri,R., Bienz-Tadmor,B., Givol,D. and Oren,M.
+  TITLE     Human p53 cellular tumor antigen: cDNA sequence and expression in
+            COS cells
+  JOURNAL   EMBO J. 4 (5), 1251-1255 (1985)
+   PUBMED   4006916
+  REMARK    NUCLEOTIDE SEQUENCE [MRNA].
+FEATURES             Location/Qualifiers
+     source          1..393
+                     /organism="Homo sapiens"
+                     /db_xref="taxon:9606"
+     gene            1..393
+                     /gene="TP53"
+                     /note="synonym: P53"
+     Protein         1..393
+                     /gene="TP53"
+                     /product="Cellular tumor antigen p53"
+ORIGIN
+        1 meepqsdpsv epplsqetfs dlwkllpenn vlsplpsqam ddlmlspddi eqwftedpgp
+       61 deaprmpeaa ppvapapaap tpaapapaps wplsssvpsq ktyqgsygfr lgflhsgtak
+      121 svtctyspal nkmfcqlakt cpvqlwvdst pppgtrvram aiykqsqhmt evvrrcphhe
+      181 rcsdsdglap pqhlirvegn lrveylddrn tfrhsvvvpy eppevgsdct tihynymcns
+      241 scmggmnrrp iltiitleds sgnllgrnsf evrvcacpgr drrteeenlr kkgephhelp
+      301 pgstkralpn ntssspqpkk kpldgeyftl qirgrerfem frelnealel kdaqagkepg
+      361 gsrahsshlk skkgqstsrh kklmfktegp dsd
+//
+__END_OF_TEXT__
+
+      assert_equal(Bio::GenPept, @ad.autodetect(text))
+    end
+
+    def test_medline
+      # PMID: 13054692
+      text = <<__END_OF_TEXT__
+PMID- 13054692
+OWN - NLM
+STAT- MEDLINE
+DA  - 19531201
+DCOM- 20030501
+LR  - 20061115
+PUBM- Print
+IS  - 0028-0836 (Print)
+VI  - 171
+IP  - 4356
+DP  - 1953 Apr 25
+TI  - Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid.
+PG  - 737-8
+FAU - WATSON, J D
+AU  - WATSON JD
+FAU - CRICK, F H
+AU  - CRICK FH
+LA  - eng
+PT  - Journal Article
+PL  - Not Available
+TA  - Nature
+JT  - Nature
+JID - 0410462
+RN  - 0 (Nucleic Acids)
+SB  - OM
+MH  - *Nucleic Acids
+OID - CLML: 5324:25254:447
+OTO - NLM
+OT  - *NUCLEIC ACIDS
+EDAT- 1953/04/25
+MHDA- 1953/04/25 00:01
+PST - ppublish
+SO  - Nature. 1953 Apr 25;171(4356):737-8.
+__END_OF_TEXT__
+
+      assert_equal(Bio::MEDLINE, @ad.autodetect(text))
+    end
+
+    def test_embl_oldrelease
+      fn = File.join(TestDataPath, 'embl', 'AB090716.embl')
+      text = File.read(fn)
+      assert_equal(Bio::EMBL, @ad.autodetect(text))
+    end
+
+    def test_embl
+      fn = File.join(TestDataPath, 'embl', 'AB090716.embl.rel89')
+      text = File.read(fn)
+      assert_equal(Bio::EMBL, @ad.autodetect(text))
+    end
+
+    def test_sptr
+      fn = File.join(TestDataPath, 'uniprot', 'p53_human.uniprot')
+      text = File.read(fn)
+      assert_equal(Bio::SPTR, @ad.autodetect(text))
+    end
+
+    def test_prosite
+      fn = File.join(TestDataPath, 'prosite', 'prosite.dat')
+      text = File.read(fn)
+      assert_equal(Bio::PROSITE, @ad.autodetect(text))
+    end
+
+    def test_transfac
+      # Dummy data; Generated from random data
+      text = <<__END_OF_TEXT__
+AC  M99999
+XX
+ID  V$XXXX_99
+XX
+DT  13.01.98 (created); ewi.
+DT  31.12.99 (updated); ewi.
+XX
+NA  XXXX
+XX
+DE  example gene protein
+XX
+BF  T99998; XXXX; Species: human, Homo sapiens.
+BF  T99999; XXXX; Species: mouse, Mus musculus.
+XX
+P0      A      C      G      T
+01      1      2      2      2      N
+02      0      2      2      3      N
+03      1      1      5      0      G
+04      3      1      1      2      N
+05      7      0      0      0      A
+06      2      0      1      4      W
+07      0      1      6      0      G
+08      0      3      0      4      Y
+09      6      1      0      0      A
+10      1      1      0      5      T
+XX
+BA  7 functional elements in 3 genes
+XX
+CC  compiled sequences
+XX
+RN  [1]
+RA  Anonymou S., Whoam I.
+RT  Example article title for XXXX
+RL  J. Example. 99:990-999 (1999).
+__END_OF_TEXT__
+
+      assert_equal(Bio::TRANSFAC, @ad.autodetect(text))
+    end
+
+    def test_aaindex1
+      fn = File.join(TestDataPath, 'aaindex', 'PRAM900102')
+      text = File.read(fn)
+      assert_equal(Bio::AAindex1, @ad.autodetect(text))
+    end
+
+    def test_aaindex2
+      fn = File.join(TestDataPath, 'aaindex', 'DAYM780301')
+      text = File.read(fn)
+      assert_equal(Bio::AAindex2, @ad.autodetect(text))
+    end
+
+#    def test_litdb
+#    end
+
+#    def test_brite
+#    end
+
+#    def test_orthology
+#    end
+
+#    def test_drug
+#    end
+
+#    def test_glycan
+#    end
+
+#    def test_enzyme
+#    end
+
+#    def test_compound
+#    end
+
+#    def test_reaction
+#    end
+
+#    def test_genes
+#    end
+
+#    def test_genome
+#    end
+
+    def test_maxml_cluster
+      # dummy empty data
+      text = <<__END_OF_TEXT__
+<?xml version="1.0"?>
+<!DOCTYPE maxml-clusters SYSTEM "http://fantom.gsc.riken.go.jp/maxml/maxml.dtd"><maxml-clusters>
+</maxml-clusters>
+__END_OF_TEXT__
+      assert_equal(Bio::FANTOM::MaXML::Cluster, @ad.autodetect(text))
+    end
+
+    def test_maxml_sequence
+      # dummy empty data
+      text = <<__END_OF_TEXT__
+<?xml version="1.0"?>
+<!DOCTYPE maxml-sequences SYSTEM "http://fantom.gsc.riken.go.jp/maxml/maxml.dtd">
+<maxml-sequences>
+</maxml-sequences>
+__END_OF_TEXT__
+      assert_equal(Bio::FANTOM::MaXML::Sequence, @ad.autodetect(text))
+    end
+
+#    def test_pdb
+#    end
+
+#    def test_chemicalcomponent
+#    end
+
+#    def test_clustal
+#    end
+
+#    def test_gcg_msf
+#    end
+
+#    def test_gcg_seq
+#    end
+
+    def test_blastxml
+      fn = File.join(TestDataPath, 'blast', '2.2.15.blastp.m7')
+      text = File.read(fn)
+      assert_equal(Bio::Blast::Report, @ad.autodetect(text))
+    end
+
+#    def test_wublast
+#    end
+
+#    def test_wutblast
+#    end
+
+    def test_blast
+      fn = File.join(TestDataPath, 'blast', 'b0002.faa.m0')
+      text = File.read(fn)
+      assert_equal(Bio::Blast::Default::Report, @ad.autodetect(text))
+    end
+
+#    def test_tblast
+#    end
+
+#    def test_blat
+#    end
+
+#    def test_spidey
+#    end
+
+    def test_hmmer
+      fn = File.join(TestDataPath, 'HMMER', 'hmmpfam.out')
+      text = File.read(fn)
+      assert_equal(Bio::HMMER::Report, @ad.autodetect(text))
+
+      fn = File.join(TestDataPath, 'HMMER', 'hmmsearch.out')
+      text = File.read(fn)
+      assert_equal(Bio::HMMER::Report, @ad.autodetect(text))
+    end
+
+#    def test_sim4
+#    end
+
+    def test_fastaformat
+      fn = File.join(TestDataPath, 'fasta', 'example1.txt')
+      text = File.read(fn)
+      assert_equal(Bio::FastaFormat, @ad.autodetect(text))
+
+      fn = File.join(TestDataPath, 'fasta', 'example2.txt')
+      text = File.read(fn)
+      assert_equal(Bio::FastaFormat, @ad.autodetect(text))
+    end
+
+    def test_fastanumericformat
+      text = <<__END_OF_TEXT__
+>sample
+30 21 16 11 8 6 3 34 28 34 28 28 35 28 28 37 33 15 27 28 28 
+27 37 33 17 27 27 28 28 33 26 33 26 28 27 37 33 15 27 26 27 
+28 37 33 16 34 26 27 33 26 28 33 25 28 28 38 34 23 13 2
+__END_OF_TEXT__
+
+      assert_equal(Bio::FastaNumericFormat, @ad.autodetect(text))
+    end
+
+  end #class TestDefaultAutoDetect
+
+end #module Bio::TestFlatFile
+