[med-svn] [obitools] 08/09: Update upstream source from tag 'upstream/1.2.11'
Andreas Tille
tille at debian.org
Wed Dec 13 18:18:17 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository obitools.
commit 9efa0bb54307b66221d0ab6c5af7315c710f9965
Merge: 96022b9 207ebbe
Author: Andreas Tille <tille at debian.org>
Date: Wed Dec 13 19:17:14 2017 +0100
Update upstream source from tag 'upstream/1.2.11'
Update to upstream version '1.2.11'
with Debian dir e0c1000ee3bfdeac95bfcf1bcc1b4a57f30aaa2f
MANIFEST.in | 10 +
PKG-INFO | 19 +
README.txt | 0
distutils.ext/obidistutils/__init__.py | 0
distutils.ext/obidistutils/command/__init__.py | 7 +
distutils.ext/obidistutils/command/build.py | 47 +
distutils.ext/obidistutils/command/build_cexe.py | 72 +
distutils.ext/obidistutils/command/build_ctools.py | 60 +
distutils.ext/obidistutils/command/build_exe.py | 213 +++
distutils.ext/obidistutils/command/build_ext.py | 114 ++
distutils.ext/obidistutils/command/build_files.py | 58 +
.../obidistutils/command/build_filters.py | 10 +
.../obidistutils/command/build_scripts.py | 102 ++
distutils.ext/obidistutils/command/build_sphinx.py | 38 +
distutils.ext/obidistutils/command/install.py | 25 +
.../obidistutils/command/install_scripts.py | 79 +
.../obidistutils/command/install_sphinx.py | 46 +
distutils.ext/obidistutils/command/littlebigman.py | 62 +
distutils.ext/obidistutils/command/pidname.py | 53 +
distutils.ext/obidistutils/command/sdist.py | 46 +
distutils.ext/obidistutils/core.py | 205 +++
distutils.ext/obidistutils/dist.py | 48 +
distutils.ext/obidistutils/serenity/__init__.py | 117 ++
.../obidistutils/serenity/checkpackage.py | 184 +++
distutils.ext/obidistutils/serenity/checkpip.py | 82 +
distutils.ext/obidistutils/serenity/checkpython.py | 170 +++
distutils.ext/obidistutils/serenity/checksystem.py | 19 +
distutils.ext/obidistutils/serenity/getcython.py | 72 +
distutils.ext/obidistutils/serenity/globals.py | 15 +
distutils.ext/obidistutils/serenity/rerun.py | 60 +
distutils.ext/obidistutils/serenity/snake.py | 35 +
distutils.ext/obidistutils/serenity/util.py | 27 +
distutils.ext/obidistutils/serenity/virtual.py | 133 ++
distutils.ext/src/littlebigman.c | 24 +
distutils.ext/src/pidname.c | 24 +
doc/sphinx/Makefile | 100 ++
doc/sphinx/make.bat | 113 ++
doc/sphinx/source/annotations.rst | 11 +
doc/sphinx/source/attributes.rst | 128 ++
doc/sphinx/source/attributes/ali_dir.rst | 9 +
doc/sphinx/source/attributes/ali_length.rst | 9 +
doc/sphinx/source/attributes/avg_quality.rst | 18 +
doc/sphinx/source/attributes/best_identity.rst | 11 +
doc/sphinx/source/attributes/best_match.rst | 11 +
doc/sphinx/source/attributes/class.rst | 11 +
doc/sphinx/source/attributes/cluster.rst | 8 +
doc/sphinx/source/attributes/complemented.rst | 9 +
doc/sphinx/source/attributes/count.rst | 16 +
doc/sphinx/source/attributes/cut.rst | 11 +
doc/sphinx/source/attributes/direction.rst | 8 +
doc/sphinx/source/attributes/distance.rst | 11 +
doc/sphinx/source/attributes/error.rst | 11 +
doc/sphinx/source/attributes/experiment.rst | 9 +
doc/sphinx/source/attributes/family.rst | 30 +
doc/sphinx/source/attributes/family_name.rst | 29 +
doc/sphinx/source/attributes/forward_error.rst | 13 +
doc/sphinx/source/attributes/forward_match.rst | 15 +
doc/sphinx/source/attributes/forward_primer.rst | 12 +
doc/sphinx/source/attributes/forward_score.rst | 11 +
doc/sphinx/source/attributes/forward_tag.rst | 14 +
doc/sphinx/source/attributes/forward_tm.rst | 13 +
doc/sphinx/source/attributes/genus.rst | 33 +
doc/sphinx/source/attributes/genus_name.rst | 29 +
doc/sphinx/source/attributes/head_quality.rst | 18 +
doc/sphinx/source/attributes/id_status.rst | 8 +
doc/sphinx/source/attributes/merged.rst | 9 +
doc/sphinx/source/attributes/merged_star.rst | 14 +
doc/sphinx/source/attributes/mid_quality.rst | 19 +
doc/sphinx/source/attributes/mode.rst | 11 +
doc/sphinx/source/attributes/obiclean_cluster.rst | 11 +
doc/sphinx/source/attributes/obiclean_count.rst | 13 +
doc/sphinx/source/attributes/obiclean_head.rst | 12 +
.../source/attributes/obiclean_headcount.rst | 14 +
.../source/attributes/obiclean_internalcount.rst | 14 +
.../source/attributes/obiclean_samplecount.rst | 13 +
.../source/attributes/obiclean_singletoncount.rst | 14 +
doc/sphinx/source/attributes/obiclean_status.rst | 14 +
doc/sphinx/source/attributes/occurrence.rst | 9 +
doc/sphinx/source/attributes/order.rst | 30 +
doc/sphinx/source/attributes/order_name.rst | 29 +
doc/sphinx/source/attributes/pairend_limit.rst | 13 +
doc/sphinx/source/attributes/partial.rst | 11 +
doc/sphinx/source/attributes/rank.rst | 15 +
doc/sphinx/source/attributes/reverse_error.rst | 13 +
doc/sphinx/source/attributes/reverse_match.rst | 15 +
doc/sphinx/source/attributes/reverse_primer.rst | 13 +
doc/sphinx/source/attributes/reverse_score.rst | 11 +
doc/sphinx/source/attributes/reverse_tag.rst | 13 +
doc/sphinx/source/attributes/reverse_tm.rst | 13 +
doc/sphinx/source/attributes/sample.rst | 10 +
doc/sphinx/source/attributes/scientific_name.rst | 28 +
doc/sphinx/source/attributes/score.rst | 8 +
doc/sphinx/source/attributes/score_norm.rst | 8 +
doc/sphinx/source/attributes/select.rst | 11 +
doc/sphinx/source/attributes/seq_a_deletion.rst | 8 +
doc/sphinx/source/attributes/seq_a_insertion.rst | 8 +
doc/sphinx/source/attributes/seq_a_mismatch.rst | 8 +
doc/sphinx/source/attributes/seq_a_single.rst | 9 +
doc/sphinx/source/attributes/seq_ab_match.rst | 7 +
doc/sphinx/source/attributes/seq_b_deletion.rst | 8 +
doc/sphinx/source/attributes/seq_b_insertion.rst | 8 +
doc/sphinx/source/attributes/seq_b_mismatch.rst | 8 +
doc/sphinx/source/attributes/seq_b_single.rst | 9 +
doc/sphinx/source/attributes/seq_length.rst | 10 +
doc/sphinx/source/attributes/seq_length_ori.rst | 9 +
doc/sphinx/source/attributes/seq_rank.rst | 9 +
doc/sphinx/source/attributes/sminL.rst | 8 +
doc/sphinx/source/attributes/sminR.rst | 8 +
doc/sphinx/source/attributes/species.rst | 32 +
doc/sphinx/source/attributes/species_list.rst | 12 +
doc/sphinx/source/attributes/species_name.rst | 31 +
doc/sphinx/source/attributes/status.rst | 10 +
doc/sphinx/source/attributes/strand.rst | 10 +
doc/sphinx/source/attributes/tail_quality.rst | 18 +
doc/sphinx/source/attributes/taxid.rst | 30 +
doc/sphinx/source/barcodes.rst | 11 +
doc/sphinx/source/conf.py | 262 ++++
doc/sphinx/source/conversions.rst | 11 +
doc/sphinx/source/embl.rst | 2 +
doc/sphinx/source/fasta.rst | 47 +
doc/sphinx/source/fastq.rst | 163 ++
doc/sphinx/source/filtering.rst | 14 +
doc/sphinx/source/formats.rst | 59 +
doc/sphinx/source/genbank.rst | 2 +
doc/sphinx/source/index.rst | 23 +
doc/sphinx/source/introduction.rst | 8 +
doc/sphinx/source/iupac.rst | 63 +
doc/sphinx/source/manipulations.rst | 15 +
doc/sphinx/source/obitaxonomy.rst | 26 +
doc/sphinx/source/optionsSet/defaultoptions.txt | 13 +
doc/sphinx/source/optionsSet/inputformat.txt | 79 +
doc/sphinx/source/optionsSet/outputformat.txt | 30 +
doc/sphinx/source/optionsSet/sequenceEdit.txt | 83 +
doc/sphinx/source/optionsSet/sequenceFilter.txt | 174 +++
doc/sphinx/source/optionsSet/taxonomyDB.txt | 13 +
doc/sphinx/source/optionsSet/taxonomyFilter.txt | 14 +
doc/sphinx/source/scripts.rst | 13 +
doc/sphinx/source/scripts/ecoPCR.rst | 193 +++
doc/sphinx/source/scripts/ecoPrimers.rst | 253 ++++
doc/sphinx/source/scripts/ecodbtaxstat.rst | 49 +
doc/sphinx/source/scripts/ecofind.rst | 85 ++
doc/sphinx/source/scripts/ecotag.rst | 91 ++
doc/sphinx/source/scripts/ecotaxspecificity.rst | 31 +
doc/sphinx/source/scripts/ecotaxstat.rst | 21 +
doc/sphinx/source/scripts/illuminapairedend.rst | 61 +
doc/sphinx/source/scripts/ngsfilter.rst | 54 +
doc/sphinx/source/scripts/obiaddtaxids.rst | 57 +
doc/sphinx/source/scripts/obiannotate.rst | 36 +
doc/sphinx/source/scripts/obiclean.rst | 63 +
doc/sphinx/source/scripts/obicomplement.rst | 7 +
doc/sphinx/source/scripts/obiconvert.rst | 21 +
doc/sphinx/source/scripts/obicount.rst | 42 +
doc/sphinx/source/scripts/obicut.rst | 21 +
doc/sphinx/source/scripts/obidistribute.rst | 20 +
doc/sphinx/source/scripts/obiextract.rst | 61 +
doc/sphinx/source/scripts/obigrep.rst | 11 +
doc/sphinx/source/scripts/obihead.rst | 14 +
doc/sphinx/source/scripts/obijoinpairedend.rst | 15 +
doc/sphinx/source/scripts/obipr2.rst | 22 +
doc/sphinx/source/scripts/obisample.rst | 67 +
doc/sphinx/source/scripts/obiselect.rst | 126 ++
doc/sphinx/source/scripts/obisilva.rst | 71 +
doc/sphinx/source/scripts/obisort.rst | 35 +
doc/sphinx/source/scripts/obisplit.rst | 21 +
doc/sphinx/source/scripts/obistat.rst | 95 ++
doc/sphinx/source/scripts/obisubset.rst | 81 +
doc/sphinx/source/scripts/obitab.rst | 48 +
doc/sphinx/source/scripts/obitail.rst | 14 +
doc/sphinx/source/scripts/obitaxonomy.rst | 160 ++
doc/sphinx/source/scripts/obiuniq.rst | 79 +
doc/sphinx/source/scripts/oligotag.rst | 134 ++
doc/sphinx/source/statistics.rst | 9 +
doc/sphinx/source/taxdump.rst | 2 +
doc/sphinx/source/tutorials.rst | 12 +
doc/sphinx/source/utilities.rst | 13 +
doc/sphinx/source/welcome.rst | 405 +++++
doc/sphinx/source/wolves.rst | 648 ++++++++
doc/sphinx/sphinxext/apigen.py | 427 ++++++
doc/sphinx/sphinxext/docscrape.py | 497 ++++++
doc/sphinx/sphinxext/docscrape_sphinx.py | 136 ++
.../sphinxext/ipython_console_highlighting.py | 114 ++
doc/sphinx/sphinxext/numpydoc.py | 116 ++
requirements.txt | 6 +
setup.cfg | 5 +
setup.py | 70 +
src/OBITools.egg-info/PKG-INFO | 19 +
src/OBITools.egg-info/SOURCES.txt | 591 ++++++++
src/OBITools.egg-info/dependency_links.txt | 1 +
src/OBITools.egg-info/not-zip-safe | 1 +
src/OBITools.egg-info/requires.txt | 5 +
src/OBITools.egg-info/top_level.txt | 1 +
src/ali2consensus.py | 111 ++
src/ecodbtaxstat.py | 76 +
src/ecotag.py | 460 ++++++
src/ecotaxspecificity.py | 239 +++
src/ecotaxstat.py | 109 ++
src/extractreads.py | 243 +++
src/extractreads2.py | 119 ++
src/illuminapairedend.py | 280 ++++
src/ngsfilter.py | 458 ++++++
src/obiaddtaxids.py | 424 ++++++
src/obiannotate.py | 85 ++
src/obiclean.py | 416 +++++
src/obicomplement.py | 62 +
src/obiconvert.py | 54 +
src/obicount.py | 59 +
src/obicut.py | 53 +
src/obidistribute.py | 140 ++
src/obiextract.py | 81 +
src/obigrep.py | 45 +
src/obihead.py | 57 +
src/obijoinpairedend.py | 134 ++
src/obipr2.py | 302 ++++
src/obisample.py | 119 ++
src/obiselect.py | 281 ++++
src/obisilva.py | 355 +++++
src/obisort.py | 61 +
src/obisplit.py | 135 ++
src/obistat.py | 221 +++
src/obisubset.py | 116 ++
src/obitab.py | 178 +++
src/obitail.py | 54 +
src/obitaxonomy.py | 350 +++++
src/obitools/SVGdraw.py | 1054 +++++++++++++
src/obitools/__init__.py | 57 +
src/obitools/_obitools.h | 25 +
src/obitools/_obitools.pxd | 109 ++
src/obitools/_obitools.pyx | 800 ++++++++++
src/obitools/align/__init__.py | 15 +
src/obitools/align/_assemble.pxd | 10 +
src/obitools/align/_assemble.pyx | 169 +++
src/obitools/align/_codonnws.pxd | 15 +
src/obitools/align/_codonnws.pyx | 1589 ++++++++++++++++++++
src/obitools/align/_dynamic.pxd | 90 ++
src/obitools/align/_dynamic.pyx | 365 +++++
src/obitools/align/_freeendgap.pxd | 9 +
src/obitools/align/_freeendgap.pyx | 161 ++
src/obitools/align/_freeendgapfm.pxd | 5 +
src/obitools/align/_freeendgapfm.pyx | 19 +
src/obitools/align/_gprofilenws.pxd | 8 +
src/obitools/align/_gprofilenws.pyx | 167 ++
src/obitools/align/_lcs.cfiles | 1 +
src/obitools/align/_lcs.ext.1.c | 168 +++
src/obitools/align/_lcs.ext.2.c | 34 +
src/obitools/align/_lcs.ext.3.c | 34 +
src/obitools/align/_lcs.ext.4.c | 225 +++
src/obitools/align/_lcs.h | 29 +
src/obitools/align/_lcs.pxd | 9 +
src/obitools/align/_lcs.pyx | 206 +++
src/obitools/align/_lcs_fast.h | 597 ++++++++
src/obitools/align/_nws.pxd | 10 +
src/obitools/align/_nws.pyx | 162 ++
src/obitools/align/_nwsdnabyprot.pxd | 36 +
src/obitools/align/_nwsdnabyprot.pyx | 516 +++++++
src/obitools/align/_profilenws.pxd | 23 +
src/obitools/align/_profilenws.pyx | 211 +++
src/obitools/align/_qsassemble.pyx | 89 ++
src/obitools/align/_qsrassemble.pyx | 88 ++
src/obitools/align/_rassemble.pxd | 10 +
src/obitools/align/_rassemble.pyx | 157 ++
src/obitools/align/_sse.h | 929 ++++++++++++
src/obitools/align/_upperbond.cfiles | 1 +
src/obitools/align/_upperbond.ext.1.c | 225 +++
src/obitools/align/_upperbond.h | 7 +
src/obitools/align/_upperbond.pxd | 16 +
src/obitools/align/_upperbond.pyx | 90 ++
src/obitools/align/homopolymere.py | 56 +
src/obitools/align/ssearch.py | 46 +
src/obitools/alignment/__init__.py | 175 +++
src/obitools/alignment/ace.py | 47 +
src/obitools/barcodecoverage/__init__.py | 7 +
src/obitools/barcodecoverage/calcBc.py | 62 +
src/obitools/barcodecoverage/drawBcTree.py | 108 ++
src/obitools/barcodecoverage/findErrors.py | 56 +
src/obitools/barcodecoverage/readFiles.py | 69 +
src/obitools/barcodecoverage/writeBcTree.py | 42 +
src/obitools/blast/__init__.py | 207 +++
src/obitools/carto/__init__.py | 376 +++++
src/obitools/collections.py | 190 +++
src/obitools/decorator.py | 0
src/obitools/distances/__init__.py | 29 +
src/obitools/distances/observed.py | 77 +
src/obitools/distances/phylip.py | 35 +
src/obitools/distances/r.py | 25 +
src/obitools/dnahash/__init__.py | 100 ++
src/obitools/ecobarcode/__init__.py | 0
src/obitools/ecobarcode/databases.py | 32 +
src/obitools/ecobarcode/ecotag.py | 50 +
src/obitools/ecobarcode/options.py | 64 +
src/obitools/ecobarcode/rawdata.py | 38 +
src/obitools/ecobarcode/taxonomy.py | 120 ++
src/obitools/ecopcr/__init__.py | 69 +
src/obitools/ecopcr/annotation.py | 104 ++
src/obitools/ecopcr/options.py | 140 ++
src/obitools/ecopcr/sequence.py | 183 +++
src/obitools/ecopcr/taxonomy.py | 704 +++++++++
src/obitools/ecotag/__init__.py | 2 +
src/obitools/ecotag/parser.py | 150 ++
src/obitools/eutils/__init__.py | 54 +
src/obitools/fast.py | 56 +
src/obitools/fasta/__init__.py | 13 +
src/obitools/fasta/_fasta.pxd | 13 +
src/obitools/fasta/_fasta.pyx | 515 +++++++
src/obitools/fastq/__init__.py | 19 +
src/obitools/fastq/_fastq.pyx | 530 +++++++
src/obitools/fnaqual/__init__.py | 2 +
src/obitools/fnaqual/fasta.py | 8 +
src/obitools/fnaqual/quality.py | 137 ++
src/obitools/format/__init__.py | 28 +
src/obitools/format/_format.pyx | 19 +
src/obitools/format/genericparser/__init__.py | 219 +++
.../format/genericparser/_genericparser.pyx | 232 +++
src/obitools/format/ontology/__init__.py | 0
src/obitools/format/ontology/go_obo.py | 274 ++++
src/obitools/format/options.py | 375 +++++
src/obitools/format/sequence/__init__.py | 69 +
src/obitools/format/sequence/embl.py | 2 +
src/obitools/format/sequence/fasta.py | 4 +
src/obitools/format/sequence/fastq.py | 16 +
src/obitools/format/sequence/fnaqual.py | 8 +
src/obitools/format/sequence/genbank.py | 4 +
src/obitools/format/sequence/tagmatcher.py | 5 +
src/obitools/goa/__init__.py | 0
src/obitools/goa/parser.py | 33 +
src/obitools/graph/__init__.py | 1016 +++++++++++++
src/obitools/graph/algorithms/__init__.py | 0
src/obitools/graph/algorithms/clique.py | 134 ++
src/obitools/graph/algorithms/compact.py | 8 +
src/obitools/graph/algorithms/component.py | 82 +
src/obitools/graph/dag.py | 99 ++
src/obitools/graph/layout/__init__.py | 0
src/obitools/graph/layout/radialtree.py | 0
src/obitools/graph/rootedtree.py | 115 ++
src/obitools/graph/tree.py | 37 +
src/obitools/gzip.py | 504 +++++++
src/obitools/interactive/__init__.py | 30 +
src/obitools/location/__init__.py | 547 +++++++
src/obitools/location/feature.py | 177 +++
src/obitools/metabarcoding/__init__.py | 301 ++++
src/obitools/metabarcoding/options.py | 34 +
src/obitools/obischemas/__init__.py | 28 +
src/obitools/obischemas/kb/__init__.py | 55 +
src/obitools/obischemas/kb/extern.py | 78 +
src/obitools/obischemas/options.py | 31 +
src/obitools/obo/__init__.py | 0
src/obitools/obo/go/__init__.py | 0
src/obitools/obo/go/parser.py | 53 +
src/obitools/obo/parser.py | 707 +++++++++
src/obitools/options/__init__.py | 101 ++
src/obitools/options/_bioseqfilter.pyx | 82 +
src/obitools/options/_options.pyx | 124 ++
src/obitools/options/bioseqcutter.py | 87 ++
src/obitools/options/bioseqedittag.py | 317 ++++
src/obitools/options/bioseqfilter.py | 121 ++
src/obitools/options/taxonomyfilter.py | 6 +
src/obitools/parallel/__init__.py | 99 ++
src/obitools/parallel/jobqueue.py | 183 +++
src/obitools/phylogeny/__init__.py | 119 ++
src/obitools/phylogeny/newick.py | 123 ++
src/obitools/profile/__init__.py | 0
src/obitools/profile/_profile.pxd | 72 +
src/obitools/profile/_profile.pyx | 289 ++++
src/obitools/sample.py | 87 ++
src/obitools/seqdb/__init__.py | 88 ++
src/obitools/seqdb/blastdb/__init__.py | 0
src/obitools/seqdb/dnaparser.py | 16 +
src/obitools/seqdb/embl/__init__.py | 13 +
src/obitools/seqdb/embl/parser.py | 52 +
src/obitools/seqdb/genbank/__init__.py | 84 ++
src/obitools/seqdb/genbank/ncbi.py | 79 +
src/obitools/seqdb/genbank/parser.py | 53 +
src/obitools/sequenceencoder/__init__.py | 73 +
src/obitools/solexa/__init__.py | 45 +
src/obitools/solexaPairEnd.py | 103 ++
src/obitools/statistics/__init__.py | 0
src/obitools/statistics/hypergeometric.py | 166 ++
src/obitools/statistics/noncentralhypergeo.py | 208 +++
src/obitools/svg.py | 120 ++
src/obitools/table/__init__.py | 633 ++++++++
src/obitools/table/csv.py | 52 +
src/obitools/tagmatcher/__init__.py | 35 +
src/obitools/tagmatcher/options.py | 14 +
src/obitools/tagmatcher/parser.py | 89 ++
src/obitools/thermo/__init__.py | 597 ++++++++
src/obitools/tools/__init__.py | 0
src/obitools/tools/_solexapairend.pyx | 187 +++
src/obitools/tools/solexapairend.py | 51 +
src/obitools/tree/__init__.py | 116 ++
src/obitools/tree/dot.py | 18 +
src/obitools/tree/layout.py | 103 ++
src/obitools/tree/newick.py | 117 ++
src/obitools/tree/svg.py | 70 +
src/obitools/tree/unrooted.py | 33 +
src/obitools/unit/__init__.py | 8 +
src/obitools/unit/obitools/__init__.py | 91 ++
src/obitools/utils/__init__.py | 319 ++++
src/obitools/utils/_utils.pxd | 42 +
src/obitools/utils/_utils.pyx | 160 ++
src/obitools/utils/bioseq.py | 234 +++
src/obitools/utils/crc64.py | 53 +
src/obitools/utils/iterator.py | 8 +
src/obitools/version.py | 5 +
src/obitools/word/__init__.py | 135 ++
src/obitools/word/_binary.pyx | 269 ++++
src/obitools/word/_readindex.cfiles | 1 +
src/obitools/word/_readindex.ext.1.c | 202 +++
src/obitools/word/_readindex.h | 94 ++
src/obitools/word/_readindex.pyx | 805 ++++++++++
src/obitools/word/options.py | 117 ++
src/obitools/word/predicate.py | 41 +
src/obitools/zipfile.py | 1282 ++++++++++++++++
src/obiuniq.py | 107 ++
src/oligotag.py | 106 ++
413 files changed, 43590 insertions(+)
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