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


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Description

python-pbcore - Python library for processing PacBio data files

Property Value
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

Package Version Architecture Repository
python-pbcore_1.2.7+dfsg-1_all.deb 1.2.7+dfsg all Ubuntu Universe
python-pbcore - - -

Requires

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

Download

Type URL
Binary Package python-pbcore_1.2.7+dfsg-1_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/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

See Also

Package Description
python-pbgenomicconsensus_2.0.0+20151210-1_all.deb Pacific Biosciences variant and consensus caller (Python 2)
python-pbh5tools-doc_0.8.0+dfsg-4_all.deb tools for manipulating HDF5 files produced by Pacific Biosciences (doc)
python-pbh5tools_0.8.0+dfsg-4_amd64.deb tools for manipulating Pacific Biosciences HDF5 files -- Python 2 library
python-pbkdf2_1.3+20110613.git2a0fb15~ds0-3_all.deb Python RSA PKCS#5 v2.0 module (Python 2)
python-pcapy_0.10.8-1build1_amd64.deb Python interface to the libpcap packet capture library
python-pcl-msgs_0.2.0-2_all.deb Python code for PCL-related Robot OS Messages
python-pcp_3.10.8build1_amd64.deb Performance Co-Pilot Python PMAPI module
python-pcs_0.6+debian-0ubuntu3_amd64.deb Packet Construction Set for Python
python-pdfminer_20140328+dfsg-1_all.deb PDF parser and analyser
python-pdfrw-doc_0.2-2_all.deb PDF file manipulation library (documentation)
python-pdfrw_0.2-2_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
python-peak.util.decorators_1.8-3_all.deb version-agnostic decorators support for Python
python-peak.util_20160204-1_all.deb utilities from the Python Enterprise Application Kit
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