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  • Committer: Package Import Robot
  • Author(s): Charles Plessy
  • Date: 2013-09-22 13:39:48 UTC
  • mfrom: (3.1.11 sid)
  • Revision ID: package-import@ubuntu.com-20130922133948-c6z62zegjyp7ztou
Tags: 1.6.922-1
http://bugs.debian.org/722910
* New upstream release.
* Replaces and Breaks grinder (<< 0.5.3-3~) because of overlaping contents.
  Closes: #722910
* Stop Replacing and Breaking bioperl ( << 1.6.9 ): not needed anymore. 

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MANIFEST
 
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.travis.yml
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AUTHORS
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Bio/Align/AlignI.pm
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Bio/Align/DNAStatistics.pm
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Bio/Assembly/ScaffoldI.pm
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Bio/Biblio/Book.pm
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Bio/Cluster/SequenceFamily.pm
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Bio/DB/Failover.pm
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Bio/DB/HIV/HIVAnnotProcessor.pm
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Bio/DB/HIV/HIVQueryHelper.pm
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Bio/DB/HIV/lanl-schema.xml
 
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Bio/DB/Universal.pm
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Bio/FeatureIO.pm
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Bio/FeatureIO/interpro.pm
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Bio/FeatureIO/vecscreen_simple.pm
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Bio/HandlerBaseI.pm
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Bio/IdCollectionI.pm
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Bio/IdentifiableI.pm
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Bio/Ontology/RelationshipI.pm
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Bio/Ontology/RelationshipType.pm
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Bio/Ontology/SimpleGOEngine/GraphAdaptor.pm
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Bio/Ontology/SimpleGOEngine/GraphAdaptor02.pm
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Bio/Ontology/SimpleOntologyEngine.pm
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Bio/Ontology/Term.pm
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Bio/Ontology/TermFactory.pm
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Bio/Root/RootI.pm
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Bio/Root/Storable.pm
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Bio/Root/Test.pm
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Bio/Root/Test/Warn.pm
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Bio/Root/Utilities.pm
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Bio/Root/Version.pm
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Bio/Search/BlastStatistics.pm
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Bio/Search/HSP/BlastPullHSP.pm
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Bio/Search/HSP/FastaHSP.pm
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Bio/Search/HSP/GenericHSP.pm
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Bio/Search/HSP/hmmer3HSP.pm
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Bio/Search/HSP/HMMERHSP.pm
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Bio/Search/HSP/HmmpfamHSP.pm
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Bio/Search/HSP/HSPFactory.pm
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Bio/Seq/SeqFastaSpeedFactory.pm
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Bio/Seq/SequenceTrace.pm
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Bio/Seq/SeqWithQuality.pm
 
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Bio/Seq/SimulatedRead.pm
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Bio/Seq/TraceI.pm
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Bio/SeqAnalysisParserI.pm
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Bio/SeqEvolution/DNAPoint.pm
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Bio/SeqEvolution/EvolutionI.pm
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Bio/SeqEvolution/Factory.pm
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Bio/SeqFeature/Annotated.pm
 
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Bio/SeqFeature/Amplicon.pm
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Bio/SeqFeature/AnnotationAdaptor.pm
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Bio/SeqFeature/Collection.pm
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Bio/SeqFeature/CollectionI.pm
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Bio/SeqFeature/SubSeq.pm
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Bio/SeqFeature/Tools/FeatureNamer.pm
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Bio/SeqFeature/Tools/IDHandler.pm
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Bio/SeqFeature/Tools/TypeMapper.pm
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Bio/Tools/AlignFactory.pm
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Bio/Tools/Alignment/Consed.pm
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Bio/Tools/Alignment/Trim.pm
 
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Bio/Tools/AmpliconSearch.pm
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Bio/Tools/Analysis/DNA/ESEfinder.pm
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Bio/Tools/Analysis/Protein/Domcut.pm
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Bio/Tools/Analysis/Protein/ELM.pm
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Bio/Tools/ERPIN.pm
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Bio/Tools/EUtilities/Link/LinkSet.pm
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Bio/Tools/EUtilities/Link/UrlLink.pm
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Bio/Tools/EUtilities/Query.pm
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Bio/Tools/EUtilities/Query/GlobalQuery.pm
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Bio/Tools/EUtilities/Summary.pm
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Bio/Tools/EUtilities/Summary/DocSum.pm
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Bio/Tools/EUtilities/Summary/Item.pm
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Bio/Tools/EUtilities/Summary/ItemContainerI.pm
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Bio/Tools/Fgenesh.pm
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Bio/Tools/FootPrinter.pm
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Bio/Tools/Gel.pm
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examples/align/align_on_codons.pl
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examples/align/aligntutorial.pl
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examples/align/clustalw.pl
 
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examples/align/FastAlign.pl
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examples/align/simplealign.pl
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examples/biblio/biblio-eutils-example.pl
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examples/Bio-DB-GFF/load_ucsc.pl
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examples/bioperl.pl
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examples/cluster/dbsnp.pl
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models/population_proposal.txt
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models/README
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README
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scripts/biblio/biblio.PLS
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scripts/biblio/TAG
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scripts/Bio-DB-EUtilities/einfo.PLS
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scripts/Bio-DB-GFF/bulk_load_gff.PLS
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scripts/Bio-DB-GFF/fast_load_gff.PLS
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scripts/Bio-DB-GFF/genbank2gff.PLS
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scripts/Bio-DB-GFF/genbank2gff3.PLS
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scripts/Bio-DB-GFF/generate_histogram.PLS
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scripts/Bio-DB-GFF/load_gff.PLS
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scripts/Bio-DB-GFF/meta_gff.PLS
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scripts/Bio-DB-GFF/process_gadfly.PLS
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scripts/Bio-DB-GFF/process_sgd.PLS
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scripts/Bio-DB-GFF/process_wormbase.PLS
 
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scripts/DB-HIV/hivq.PLS
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scripts/DB/biofetch_genbank_proxy.PLS
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scripts/DB/bioflat_index.PLS
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scripts/DB/biogetseq.PLS
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t/data/frac_problems2.blast
1442
1365
t/data/frac_problems3.blast
1470
1393
t/data/hmmpfam.out
1471
1394
t/data/hmmpfam_cs.out
1472
1395
t/data/hmmpfam_fake.out
 
1396
t/data/hmmpfam_HSPdashline.txt
 
1397
t/data/hmmpfam_multiresult.out
1473
1398
t/data/hmmscan.out
1474
1399
t/data/hmmscan_multi_domain.out
1475
1400
t/data/hmmscan_sec_struct.out
1490
1415
t/data/HUMBETGLOA.tblastx
1491
1416
t/data/humor.maf
1492
1417
t/data/humts1.pal
1493
 
t/data/hybrid1.gff3
1494
1418
t/data/hybrid2.gff3
1495
1419
t/data/in.fasta
1496
1420
t/data/insulin.water
1501
1425
t/data/interpro_short.xml
1502
1426
t/data/intrablock-comment.nex
1503
1427
t/data/Kingdoms_DNA.nex
1504
 
t/data/knownGene.gff3
1505
1428
t/data/L77119.hmmer
1506
1429
t/data/little.largemultifasta
1507
1430
t/data/LittleChrY.dbsnp.xml
1609
1532
t/data/MmCT
1610
1533
t/data/mpath.ontology.test
1611
1534
t/data/MSGEFTUA.gb
 
1535
t/data/msout/bad_msout_infile1
 
1536
t/data/msout/bad_msout_infile2
1612
1537
t/data/msout/msout_infile1
1613
1538
t/data/msout/msout_infile2
1614
1539
t/data/msout/msout_infile3
1622
1547
t/data/multifa.seq
1623
1548
t/data/multifa.seq.qual
1624
1549
t/data/multiline-intrablock-comment.nex
 
1550
t/data/multiresult_blastn+.bls
1625
1551
t/data/multiseq.bls
1626
1552
t/data/multiseq_tags.phd
1627
1553
t/data/mus.bls.xml
1630
1556
t/data/mutations.old.xml
1631
1557
t/data/mutations.xml
1632
1558
t/data/myco_sites.gff
 
1559
t/data/NC_000007-ribosomal-slippage.gb
1633
1560
t/data/NC_001284.gbk
 
1561
t/data/NC_002058_multDBLINK_bug3375.gb
1634
1562
t/data/NC_006346.gb
1635
1563
t/data/NC_006511-short.gbk
1636
1564
t/data/NC_008536.gb
1642
1570
t/data/nexml/characters.nexml.xml
1643
1571
t/data/nexml/trees.nexml.8.xml
1644
1572
t/data/nexml/trees.nexml.xml
 
1573
t/data/nhmmer-3.1.out
1645
1574
t/data/nhx-bacteria.nhx
1646
1575
t/data/NM_002254.gb
1647
1576
t/data/no-genes.genscan
1662
1591
t/data/PAM250
1663
1592
t/data/pep-266.aln
1664
1593
t/data/pfam_tests.stk
 
1594
t/data/pfamOutput-bug3376.out
1665
1595
t/data/phi.out
1666
1596
t/data/phipsi.out
1667
1597
t/data/phylipdist-36.out
1717
1647
t/data/roa1.swiss
1718
1648
t/data/roa1_v2.dat
1719
1649
t/data/rpsblast.bls
 
1650
t/data/rpsblast_no_hits.bls
1720
1651
t/data/sample_dataset.tigr
1721
1652
t/data/sbay_c127.fas
1722
1653
t/data/sbay_c545-yeast.BLASTZ.PSL
1741
1672
t/data/sim4.for.rev
1742
1673
t/data/sim4.rev
1743
1674
t/data/singleNSsite.mlc
 
1675
t/data/singlescore.gbk
1744
1676
t/data/singlet_w_CT.ace
1745
1677
t/data/so.obo
1746
1678
t/data/sofa.ontology
1747
1679
t/data/sp_subset.obo
 
1680
t/data/spaced_fasta.fa
1748
1681
t/data/spaces.nex
1749
1682
t/data/SPAN_Family4nl.nex
1750
1683
t/data/SPAN_Family7n.nex
1754
1687
t/data/spidey.test1
1755
1688
t/data/sprintf.rnamotif
1756
1689
t/data/ssp160.embl.1
1757
 
t/data/stress_test_medline.xml
1758
 
t/data/stress_test_pubmed.xml
1759
1690
t/data/sv40_small.xml
1760
1691
t/data/swiss.dat
1761
1692
t/data/swisspfam.data
1770
1701
t/data/targetp.out
1771
1702
t/data/taxdump/names.dmp
1772
1703
t/data/taxdump/nodes.dmp
 
1704
t/data/taxonomy/greengenes_taxonomy_16S_candiv_gg_2011_1.txt
 
1705
t/data/taxonomy/silva_SSURef_108_tax_silva_trunc.fasta
1773
1706
t/data/tblastn.out
1774
1707
't/data/test 2.txt'
 
1708
t/data/test-3.0-1.meme
 
1709
t/data/test-3.0-2.meme
 
1710
t/data/test-4.9.meme
1775
1711
t/data/test.abi
1776
1712
t/data/test.ace
1777
1713
t/data/test.bam
1796
1732
t/data/test.locuslink
1797
1733
t/data/test.maq
1798
1734
t/data/test.mase
1799
 
t/data/test.meme
1800
 
t/data/test.meme2
1801
1735
t/data/test.metafasta
1802
1736
t/data/test.nh
1803
1737
t/data/test.nhx
1805
1739
t/data/test.phd
1806
1740
t/data/test.pir
1807
1741
t/data/test.pln
1808
 
t/data/test.ptt
1809
1742
t/data/test.raw
1810
1743
t/data/test.ref.fas
1811
1744
t/data/test.swiss
1850
1783
t/data/testdbaccnums.out
1851
1784
t/data/testfile.erpin
1852
1785
t/data/testfuzzy.genbank
 
1786
t/data/tiny.stk
1853
1787
t/data/tmhmm.out
1854
1788
t/data/tmp.fst
1855
1789
t/data/tol-2010-02-18.nhx
1876
1810
t/data/UnaSmithHIV-both.nex
1877
1811
t/data/unigene.data
1878
1812
t/data/urease.tre.nexus
1879
 
t/data/vecscreen_simple.test_output
1880
1813
t/data/version2.scf
1881
1814
t/data/version3.scf
1882
1815
t/data/wellcome_tol.nhx
1885
1818
t/data/X98338_Adh-mRNA.gb
1886
1819
t/data/yeast.tRNAscanSE
1887
1820
t/data/yn00.mlc
 
1821
t/data/yn00_45.mlc
1888
1822
t/data/ZABJ4EA7014.CH878695.1.blast.txt
1889
1823
t/Draw/Pictogram.t
1890
 
t/lib/Array/Compare.pm
1891
1824
t/lib/Error.pm
1892
 
t/lib/Sub/Uplevel.pm
1893
 
t/lib/Test/Builder.pm
1894
 
t/lib/Test/Builder/Module.pm
1895
 
t/lib/Test/Builder/Tester.pm
1896
 
t/lib/Test/Builder/Tester/Color.pm
1897
 
t/lib/Test/Exception.pm
1898
 
t/lib/Test/Harness.pm
1899
 
t/lib/Test/Harness/Assert.pm
1900
 
t/lib/Test/Harness/Iterator.pm
1901
 
t/lib/Test/Harness/Point.pm
1902
 
t/lib/Test/Harness/Results.pm
1903
 
t/lib/Test/Harness/Straps.pm
1904
 
t/lib/Test/Harness/TAP.pod
1905
 
t/lib/Test/Harness/Util.pm
1906
 
t/lib/Test/More.pm
1907
 
t/lib/Test/Simple.pm
1908
 
t/lib/Test/Tutorial.pod
1909
 
t/lib/Test/Warn.pm
1910
 
t/lib/Tree/DAG_Node.pm
1911
1825
t/LiveSeq/Chain.t
1912
1826
t/LiveSeq/LiveSeq.t
1913
1827
t/LiveSeq/Mutation.t
1914
1828
t/LiveSeq/Mutator.t
1915
1829
t/LocalDB/BioDBGFF.t
1916
 
t/LocalDB/DBFasta.t
1917
 
t/LocalDB/DBQual.t
 
1830
t/LocalDB/Fasta.t
1918
1831
t/LocalDB/Flat.t
1919
1832
t/LocalDB/Index/Blast.t
1920
1833
t/LocalDB/Index/BlastTable.t
1921
1834
t/LocalDB/Index/Index.t
 
1835
t/LocalDB/Qual.t
1922
1836
t/LocalDB/Registry.t
1923
1837
t/LocalDB/SeqFeature.t
 
1838
t/LocalDB/Taxonomy/greengenes.t
 
1839
t/LocalDB/Taxonomy/silva.t
1924
1840
t/LocalDB/transfac_pro.t
1925
1841
t/Map/Cyto.t
1926
1842
t/Map/Linkage.t
1967
1883
t/RemoteDB/CUTG.t
1968
1884
t/RemoteDB/EMBL.t
1969
1885
t/RemoteDB/EntrezGene.t
1970
 
t/RemoteDB/EUtilities.t
1971
1886
t/RemoteDB/GenBank.t
1972
1887
t/RemoteDB/GenPept.t
1973
1888
t/RemoteDB/HIV/HIV.t
2033
1948
t/Seq/PrimedSeq.t
2034
1949
t/Seq/Quality.t
2035
1950
t/Seq/Seq.t
 
1951
t/Seq/SimulatedRead.t
2036
1952
t/Seq/WithQuality.t
2037
1953
t/SeqEvolution.t
 
1954
t/SeqFeature/Amplicon.t
2038
1955
t/SeqFeature/Clone.t
2039
 
t/SeqFeature/FeatureIO.t
 
1956
t/SeqFeature/Collection.t
 
1957
t/SeqFeature/Computation.t
 
1958
t/SeqFeature/FeaturePair.t
 
1959
t/SeqFeature/Gene.t
 
1960
t/SeqFeature/Generic.t
2040
1961
t/SeqFeature/Location.t
2041
1962
t/SeqFeature/LocationFactory.t
2042
1963
t/SeqFeature/Primer.t
2043
1964
t/SeqFeature/Range.t
2044
1965
t/SeqFeature/RangeI.t
2045
1966
t/SeqFeature/SeqAnalysisParser.t
2046
 
t/SeqFeature/SeqFeatAnnotated.t
2047
 
t/SeqFeature/SeqFeatCollection.t
2048
 
t/SeqFeature/SeqFeature.t
2049
 
t/SeqFeature/SeqFeaturePrimer.t
 
1967
t/SeqFeature/SubSeq.t
2050
1968
t/SeqFeature/Unflattener.t
2051
1969
t/SeqFeature/Unflattener2.t
2052
1970
t/SeqIO/abi.t
2116
2034
t/Symbol.t
2117
2035
t/TaxonTree.t
2118
2036
t/Tools/Alignment/Consed.t
 
2037
t/Tools/AmpliconSearch.t
2119
2038
t/Tools/Analysis/DNA/ESEfinder.t
2120
2039
t/Tools/Analysis/Protein/Domcut.t
2121
2040
t/Tools/Analysis/Protein/ELM.t
2128
2047
t/Tools/EMBOSS/Palindrome.t
2129
2048
t/Tools/ePCR.t
2130
2049
t/Tools/Est2Genome.t
2131
 
t/Tools/EUtilities/egquery.t
2132
 
t/Tools/EUtilities/einfo.t
2133
 
t/Tools/EUtilities/elink_acheck.t
2134
 
t/Tools/EUtilities/elink_lcheck.t
2135
 
t/Tools/EUtilities/elink_llinks.t
2136
 
t/Tools/EUtilities/elink_ncheck.t
2137
 
t/Tools/EUtilities/elink_neighbor.t
2138
 
t/Tools/EUtilities/elink_neighbor_history.t
2139
 
t/Tools/EUtilities/elink_scores.t
2140
 
t/Tools/EUtilities/epost.t
2141
 
t/Tools/EUtilities/esearch.t
2142
 
t/Tools/EUtilities/espell.t
2143
 
t/Tools/EUtilities/esummary.t
2144
 
t/Tools/EUtilities/EUtilParameters.t
2145
2050
t/Tools/FootPrinter.t
2146
2051
t/Tools/Geneid.t
2147
2052
t/Tools/Genewise.t
2211
2116
t/Variation/SeqDiff.t
2212
2117
t/Variation/SNP.t
2213
2118
t/Variation/Variation_IO.t
 
2119
travis_scripts/dependency_installs
2214
2120
META.yml
2215
2121
META.json