python-pbcore_1.2.11+dfsg-1ubuntu1_all.deb


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Description

python-pbcore - Python library for processing PacBio data files

Property Value
Distribution Ubuntu 17.10 (Artful Aardvark)
Repository Ubuntu Universe i386
Package name python-pbcore
Package version 1.2.11+dfsg
Package release 1ubuntu1
Package architecture all
Package type deb
Installed size 16.58 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

Package Version Architecture Repository
python-pbcore_1.2.11+dfsg-1ubuntu1_all.deb 1.2.11+dfsg all Ubuntu Universe
python-pbcore - - -

Requires

Name Value
python-h5py -
python-numpy -
python-pkg-resources -
python-pysam -
python:any >= 2.7.5-5~
python:any << 2.8

Download

Type URL
Binary Package python-pbcore_1.2.11+dfsg-1ubuntu1_all.deb
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

Path
/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-1.2.11.egg-info/PKG-INFO
/usr/lib/python2.7/dist-packages/pbcore-1.2.11.egg-info/dependency_links.txt
/usr/lib/python2.7/dist-packages/pbcore-1.2.11.egg-info/entry_points.txt
/usr/lib/python2.7/dist-packages/pbcore-1.2.11.egg-info/not-zip-safe
/usr/lib/python2.7/dist-packages/pbcore-1.2.11.egg-info/requires.txt
/usr/lib/python2.7/dist-packages/pbcore-1.2.11.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.aligned_subreads.bam
/usr/lib/python2.7/dist-packages/pbcore/data/empty.aligned_subreads.bam.pbi
/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/m130727_114215_42211_c100569412550000001823090301191423_s1_p0.ccs.bam.pbi
/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/empty_lambda.aligned.bam
/usr/lib/python2.7/dist-packages/pbcore/data/datasets/empty_lambda.aligned.bam.bai
/usr/lib/python2.7/dist-packages/pbcore/data/datasets/empty_lambda.aligned.bam.pbi
/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/DataSetErrors.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/DataSetMetaTypes.py
/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetReader.py
/usr/lib/python2.7/dist-packages/pbcore/io/dataset/DataSetUtils.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/__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/model/baseRegions.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/NEWS.Debian.gz
/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/pbopen.1.gz

Changelog

2017-04-12 - Graham Inggs <ginggs@ubuntu.com>
python-pbcore (1.2.11+dfsg-1ubuntu1) zesty; urgency=medium
* Suppress numpy warnings which cause false test failures in
kineticstools with h5py 2.7.0 on ppc64el
2017-01-26 - Afif Elghraoui <afif@debian.org>
python-pbcore (1.2.11+dfsg-1) unstable; urgency=medium
* New upstream release (git 32b6883 from 2016-09-19)
* Update patches
2016-10-09 - Afif Elghraoui <afif@debian.org>
python-pbcore (1.2.10+dfsg-1) unstable; urgency=medium
* Imported Upstream version 1.2.10+dfsg
* Drop patch applied upstream
* Don't raise exception if pyxb version does not exactly match
(Closes: #839346)
* Bump Standards-Version to 3.9.8
2016-04-11 - Afif Elghraoui <afif@debian.org>
python-pbcore (1.2.9+dfsg-1) unstable; urgency=medium
* Imported Upstream version 1.2.9+dfsg
* Refresh patches
* Remove handling for pbdataset script
* Add new tests dependency on python-pyxb
* Add NEWS file to warn users about the missing pbdataset script
* Make corrections to the pbopen manpage
2016-03-10 - Afif Elghraoui <afif@debian.org>
python-pbcore (1.2.7+dfsg-2) unstable; urgency=medium
* Fix compatibility with pysam 0.9.0
* Bump standards version
* Use https for VCS URLs
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

See Also

Package Description
python-pbgenomicconsensus_2.1.0-1_all.deb Pacific Biosciences variant and consensus caller (Python 2)
python-pbh5tools-doc_0.8.0+dfsg-5build1_all.deb tools for manipulating HDF5 files produced by Pacific Biosciences (doc)
python-pbkdf2_1.3+20110613.git2a0fb15~ds0-3_all.deb Python RSA PKCS#5 v2.0 module (Python 2)
python-pbsuite-utils_15.8.24+dfsg-2_all.deb software for Pacific Biosciences sequencing data -- Python utilities
python-pcapy_0.10.8-1build1_i386.deb Python interface to the libpcap packet capture library
python-pcl-msgs_0.2.0-6_all.deb Python code for PCL-related Robot OS Messages
python-pcp_3.12.1_i386.deb Performance Co-Pilot Python PMAPI module
python-pcs_0.6+debian-0ubuntu3_i386.deb Packet Construction Set for Python
python-pdal_1.5.0+ds-2_i386.deb Point Data Abstraction Library - Python 2 extension
python-pdfkit_0.5.0-1_all.deb Python wrapper for wkhtmltopdf to convert HTML to PDF (Python 2)
python-pdfminer_20140328+dfsg-1_all.deb PDF parser and analyser
python-pdfrw-doc_0.2-3_all.deb PDF file manipulation library (documentation)
python-pdfrw_0.2-3_all.deb PDF file manipulation library (Python 2)
python-pdftools_0.37-4_all.deb PDF document reading classes
python-peak.rules_0.5a1+r2713-1_all.deb generic functions support for Python
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