python-pbcore_1.2.7+dfsg-1_all.deb


Advertisement

Description

python-pbcore - Python library for processing PacBio data files

Distribution: Ubuntu 16.04 LTS (Xenial Xerus)
Repository: Ubuntu Universe amd64
Package name: python-pbcore
Package version: 1.2.7+dfsg
Package release: 1
Package architecture: all
Package type: deb
Installed size: 16.51 KB
Download size: 8.66 MB
Official Mirror: archive.ubuntu.com
The pbcore package provides Python modules for processing Pacific Biosciences data files and building PacBio bioinformatics applications. These modules include tools to read/write PacBio data formats, sample data files for testing and debugging, base classes, and utilities for building bioinformatics applications. This package is part of the SMRTAnalysis suite.

Alternatives

    Download

    Source package: python-pbcore

    Install Howto

    1. Update the package index:
      # sudo apt-get update
    2. Install python-pbcore deb package:
      # sudo apt-get install python-pbcore

    Files

    • /usr/bin/pbdataset
    • /usr/bin/pbopen
    • /usr/lib/python2.7/dist-packages/pbcore/__init__.py
    • /usr/lib/python2.7/dist-packages/pbcore/sequence.py
    • /usr/lib/python2.7/dist-packages/pbcore-1.2.7.egg-info/PKG-INFO
    • /usr/lib/python2.7/dist-packages/pbcore-1.2.7.egg-info/dependency_links.txt
    • /usr/lib/python2.7/dist-packages/pbcore-1.2.7.egg-info/entry_points.txt
    • /usr/lib/python2.7/dist-packages/pbcore-1.2.7.egg-info/not-zip-safe
    • /usr/lib/python2.7/dist-packages/pbcore-1.2.7.egg-info/requires.txt
    • /usr/lib/python2.7/dist-packages/pbcore-1.2.7.egg-info/top_level.txt
    • /usr/lib/python2.7/dist-packages/pbcore/chemistry/__init__.py
    • /usr/lib/python2.7/dist-packages/pbcore/chemistry/chemistry.py
    • /usr/lib/python2.7/dist-packages/pbcore/chemistry/resources/mapping.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/1.4_bas_files.fofn
    • /usr/lib/python2.7/dist-packages/pbcore/data/2.0_bax_files.fofn
    • /usr/lib/python2.7/dist-packages/pbcore/data/2.1_bax_files.fofn
    • /usr/lib/python2.7/dist-packages/pbcore/data/2.1_ccs_files.fofn
    • /usr/lib/python2.7/dist-packages/pbcore/data/2.3_bax_files.fofn
    • /usr/lib/python2.7/dist-packages/pbcore/data/Fluidigm_human_amplicons.fasta
    • /usr/lib/python2.7/dist-packages/pbcore/data/Fluidigm_human_amplicons.fasta.fai
    • /usr/lib/python2.7/dist-packages/pbcore/data/Fluidigm_human_amplicons_tiny.fasta
    • /usr/lib/python2.7/dist-packages/pbcore/data/__init__.py
    • /usr/lib/python2.7/dist-packages/pbcore/data/aligned_reads_1.cmp.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/barcodes-ed65-450.fasta
    • /usr/lib/python2.7/dist-packages/pbcore/data/barcodes-ed65-450.fasta.fai
    • /usr/lib/python2.7/dist-packages/pbcore/data/bc_files.fofn
    • /usr/lib/python2.7/dist-packages/pbcore/data/blasr-output.m4
    • /usr/lib/python2.7/dist-packages/pbcore/data/blasr-output.m5
    • /usr/lib/python2.7/dist-packages/pbcore/data/empty.ccs.bam
    • /usr/lib/python2.7/dist-packages/pbcore/data/empty.ccs.bam.pbi
    • /usr/lib/python2.7/dist-packages/pbcore/data/lambdaNEB.fa
    • /usr/lib/python2.7/dist-packages/pbcore/data/lambdaNEB.fa.fai
    • /usr/lib/python2.7/dist-packages/pbcore/data/m110818_075520_42141_c100129202555500000315043109121112_s1_p0.bas.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m110818_075520_42141_c100129202555500000315043109121112_s2_p0.bas.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m130522_092457_42208_c100497142550000001823078008081323_s1_p0.1.bax.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m130522_092457_42208_c100497142550000001823078008081323_s1_p0.2.bax.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m130522_092457_42208_c100497142550000001823078008081323_s1_p0.3.bax.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m130522_092457_42208_c100497142550000001823078008081323_s1_p0.bas.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.1.ccs.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam
    • /usr/lib/python2.7/dist-packages/pbcore/data/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.bai
    • /usr/lib/python2.7/dist-packages/pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.1.bax.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.1.rgn.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.2.bax.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.2.rgn.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.3.bax.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.3.rgn.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m130731_192718_42129_c100564662550000001823085912221321_s1_p0.bas.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m140307_221913_42203_c100626172550000001823119008061414_s1_p0.1.bc.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m140307_221913_42203_c100626172550000001823119008061414_s1_p0.2.bc.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m140307_221913_42203_c100626172550000001823119008061414_s1_p0.3.bc.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.1.bax.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam
    • /usr/lib/python2.7/dist-packages/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.bai
    • /usr/lib/python2.7/dist-packages/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.bam.pbi
    • /usr/lib/python2.7/dist-packages/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.aligned_subreads.cmp.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam
    • /usr/lib/python2.7/dist-packages/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.scraps.bam.pbi
    • /usr/lib/python2.7/dist-packages/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam
    • /usr/lib/python2.7/dist-packages/pbcore/data/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.bam.pbi
    • /usr/lib/python2.7/dist-packages/pbcore/data/m140912_020930_00114_c100702482550000001823141103261590_s1_p0.1.bax.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m140912_020930_00114_c100702482550000001823141103261590_s1_p0.2.bax.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m140912_020930_00114_c100702482550000001823141103261590_s1_p0.3.bax.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/m140912_020930_00114_c100702482550000001823141103261590_s1_p0.bas.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/variants.gff
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/__init__.py
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/alignment.dataset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/barcode.dataset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/ccsaligned.dataset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/ccsread.dataset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/contig.dataset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/fofn.fofn
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/hdfsubread_dataset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/lambda.alignmentset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/lambda.referenceset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.bai
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/m140905_042212_sidney_c100564852550000001823085912221377_s1_X0.subreads.fake_bc.bam.pbi
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/m150430_142051_Mon_p1_b25.sts.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/m150616_053259_ethan_c100710482550000001823136404221563_s1_p0.sts.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim.alignmentset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim.hdfsubreadset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim0.alignmentset.chunk0contigs.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim0.alignmentset.chunk1contigs.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim0.alignmentset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim0.bas.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim0.hdfsubreadset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim0.pbalign.bam
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim0.pbalign.bam.bai
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim0.pbalign.bam.pbi
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim0.reference.fasta
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim0.reference.fasta.fai
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim0.referenceset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim0.subreads.bam
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim0.subreads.bam.bai
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim0.subreads.bam.pbi
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim0.subreadset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim1.alignmentset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim1.bas.h5
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim1.hdfsubreadset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim1.pbalign.bam
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim1.pbalign.bam.bai
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim1.pbalign.bam.pbi
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim1.subreads.bam
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim1.subreads.bam.bai
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim1.subreads.bam.pbi
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/pbalchemysim1.subreadset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/reference.dataset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/subread.dataset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/subreadSetWithStats.xml
    • /usr/lib/python2.7/dist-packages/pbcore/data/datasets/transformed_rs_subread.dataset.xml
    • /usr/lib/python2.7/dist-packages/pbcore/io/BarcodeH5Reader.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/BasH5IO.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/FastaIO.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/FastqIO.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/FofnIO.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/GffIO.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/__init__.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/_utils.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/base.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/opener.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/rangeQueries.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/align/BamAlignment.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/align/BamIO.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/align/BlasrIO.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/align/CmpH5IO.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/align/PacBioBamIndex.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/align/_AlignmentMixin.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/align/_BamSupport.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/align/__init__.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/align/_bgzf.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetIO.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetMembers.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetReader.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetValidator.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetWriter.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetXsd.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/dataset/EntryPoints.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/dataset/__init__.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/dataset/_pbbase.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/dataset/_pbmeta.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/dataset/_pbrk.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/dataset/_pbsample.py
    • /usr/lib/python2.7/dist-packages/pbcore/io/dataset/utils.py
    • /usr/lib/python2.7/dist-packages/pbcore/model/__init__.py
    • /usr/lib/python2.7/dist-packages/pbcore/util/Process.py
    • /usr/lib/python2.7/dist-packages/pbcore/util/ToolRunner.py
    • /usr/lib/python2.7/dist-packages/pbcore/util/__init__.py
    • /usr/lib/python2.7/dist-packages/pbcore/util/decorators.py
    • /usr/share/doc/python-pbcore/README.Debian
    • /usr/share/doc/python-pbcore/README.md
    • /usr/share/doc/python-pbcore/changelog.Debian.gz
    • /usr/share/doc/python-pbcore/copyright
    • /usr/share/man/man1/pbdataset.1.gz
    • /usr/share/man/man1/pbopen.1.gz

    Changelog

    2015-12-13 - Afif Elghraoui <afif@ghraoui.name> python-pbcore (1.2.7+dfsg-1) unstable; urgency=medium * Revert "Set watch file to point to pypi rather than github" * Imported Upstream version 1.2.7+dfsg * Drop patch applied upstream * Refresh patches

    2015-11-27 - Afif Elghraoui <afif@ghraoui.name> python-pbcore (1.2.6+dfsg-1) unstable; urgency=medium * Set watch file to point to pypi rather than github * Imported Upstream version 1.2.6+dfsg * Refresh patches * Fix compatibility with pysam 0.8.4 (Closes: #805687) * Add license statement for a file added in-between releases

    2015-10-26 - Afif Elghraoui <afif@ghraoui.name> python-pbcore (1.2.4+dfsg-1) unstable; urgency=medium * Fix watch file after dropping the dfsg counting. * Imported Upstream version 1.2.4+dfsg * Drop patch to skip integration tests at build time (applied upstream) * Drop rename-dataset.py patch in favor of build-time substitution

    2015-09-20 - Afif Elghraoui <afif@ghraoui.name> python-pbcore (1.2.3+dfsg-1) unstable; urgency=medium * Imported Upstream version 1.2.3+dfsg * Add patch to skip tests if the necessary scripts can't be found * Install scripts to /usr/bin, but give them sensible names * Add dependency on python-pkg-resources for python-pbcore * Add manpage stubs directing users to richer documentation sources

    2015-08-03 - Afif Elghraoui <afif@ghraoui.name> python-pbcore (1.2.2+dfsg1-1) unstable; urgency=medium * Imported Upstream version 1.2.1+dfsg1 * Install upstream-provided convenience scripts * Refresh patches * Install upstream changelog and readme in main package (not doc package) * Enable build-time testing * Configure autopkgtests * Drop nonfunctional Python3 package and merge data package with main one

    2015-06-06 - Afif Elghraoui <afif@ghraoui.name> python-pbcore (1.0.0-1) experimental; urgency=low * Initial release (Closes: #787981) * Add material for autopkgtest * Use packaged javascript libraries for HTML documentation where available * Use dh pybuild rather than the upstream-provided Makefile * Use default documentation theme rather than upstream's with corporate logo * Provide python3 package * Prepare python-pbcore-data package * Prepare documentation package * Add autopkgtest for python3 package * Update uscan calls to append suffix to package name for next release

    Advertisement
    Advertisement