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pyranges_0.0.79+ds-1_amd64.changes (click to toggle)
Format:1.8
Date:Sun, 21 Jun 2020 20:13:10 +0530
Source:pyranges
Binary:python3-pyranges
Architecture:source all
Version:0.0.79+ds-1
Distribution:unstable
Urgency:medium
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Changed-By:Nilesh Patra <npatra974@gmail.com>
Description:
python3-pyranges - 2D representation of genomic intervals and their annotations
Closes:963015
Changes:
pyranges (0.0.79+ds-1) unstable; urgency=medium

  [ Steffen Moeller, Nilesh Patra ]
  * Initial release (Closes: #963015)
Files:
81de28ac0e5fd641e58cdf829e62804d 2226 python optional pyranges_0.0.79+ds-1.dsc
6f7ec0818180aa167872f343b6c47a78 3281824 python optional pyranges_0.0.79+ds.orig.tar.xz
fa6aad34efe17b3dd9b477594f4f05c5 79660 python optional pyranges_0.0.79+ds-1.debian.tar.xz
0581d7a5dc6d2d01a940c8bf6aab9825 8393 python optional pyranges_0.0.79+ds-1_amd64.buildinfo
3600ba14549d61a1413c138724fdf5aa 434996 python optional python3-pyranges_0.0.79+ds-1_all.deb
pyranges_0.0.79+ds-1.dsc (click to toggle)
Format:3.0 (quilt)
Source:pyranges
Binary:python3-pyranges
Architecture:all
Version:0.0.79+ds-1
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Uploaders:Steffen Moeller <moeller@debian.org>, Nilesh Patra <npatra974@gmail.com>
Homepage:https://github.com/biocore-ntnu/pyranges
Standards-Version:4.5.0
Vcs-Browser:https://salsa.debian.org/med-team/pyranges
Vcs-Git:https://salsa.debian.org/med-team/pyranges.git
Testsuite:autopkgtest-pkg-python
Build-Depends:debhelper-compat (=13), dh-python, python3-setuptools, python3-all, python3-ncls<!nocheck>, python3-pyrle<!nocheck>, python3-pytest<!nocheck>, python3-sorted-nearest, python3-hypothesis, bedtools, samtools
Package-List:python3-pyranges deb python optional arch=all
Files:
6f7ec0818180aa167872f343b6c47a78 3281824 pyranges_0.0.79+ds.orig.tar.xz
fa6aad34efe17b3dd9b477594f4f05c5 79660 pyranges_0.0.79+ds-1.debian.tar.xz
lintian 2.79.0~bpo10+1 check for pyranges_0.0.79+ds-1.dsc (click to toggle)
README.source for pyranges_0.0.79+ds-1.dsc (click to toggle)
Upstream provides binary files without sources for:

* tests/test_data/test_sorted.bam.bai 
* tests/test_data/test_sorted.bam
* pyranges/example_data/control.bam.bai
* pyranges/example_data/control.bam

These have been converted to corresponding text (.sam) files with the commands:
* samtools view -h -o test_sorted.sam test_sorted.bam
* samtools view -h -o control.sam control.bam

And the corresponding *.sam files are added to: debian/missing-sources

They can be generated back with the following commands:

* cat debian/missing-sources/test_sorted.sam| samtools view -Sb - > tests/test_data/test_sorted.bam
* cat debian/missing-sources/control.sam| samtools view -Sb - > pyranges/example_data/control.bam
* samtools index tests/test_data/test_sorted.bam tests/test_data/test_sorted.bam.bai
* samtools index pyranges/example_data/control.bam pyranges/example_data/control.bam.bai

These commands are also being run in debian/rules since these binaries are needed for testing.

 -- Nilesh Patra <npatra974@gmail.com>  Sun, 21 Jun 2020 20:13:10 +0530
control file for python3-pyranges_0.0.79+ds-1_all.deb (click to toggle)
Package:python3-pyranges
Source:pyranges
Version:0.0.79+ds-1
Architecture:all
Maintainer:Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Installed-Size:1479
Depends:cython3, python3-natsort, python3-ncls, python3-pandas, python3-pyrle, python3-sorted-nearest, python3-tabulate, python3:any
Suggests:python-pyranges-doc
Section:python
Priority:optional
Homepage:https://github.com/biocore-ntnu/pyranges
Description:
2D representation of genomic intervals and their annotations
 A PyRanges object must have the columns Chromosome, Start and
 End. These describe the genomic position and function as implicit row
 labels. A Strand column is optional and adds strand information to the
 intervals. Any other columns are allowed and are considered metadata.
 .
 The structure can be filled from .bed, .bam or .gff files, also from
 tabular or textual representations.
lintian 2.79.0~bpo10+1 check for python3-pyranges_0.0.79+ds-1_all.deb (click to toggle)
contents of python3-pyranges_0.0.79+ds-1_all.deb (click to toggle)
drwxr-xr-x root/root         0 2020-06-21 14:43 ./
drwxr-xr-x root/root         0 2020-06-21 14:43 ./usr/
drwxr-xr-x root/root         0 2020-06-21 14:43 ./usr/lib/
drwxr-xr-x root/root         0 2020-06-21 14:43 ./usr/lib/python3/
drwxr-xr-x root/root         0 2020-06-21 14:43 ./usr/lib/python3/dist-packages/
drwxr-xr-x root/root         0 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/
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-rw-r--r-- root/root     23055 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/data.py
drwxr-xr-x root/root         0 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/example_data/
-rw-r--r-- root/root       327 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/example_data/aorta.bed
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-rw-r--r-- root/root     64417 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/example_data/exons.bed
-rw-r--r-- root/root        69 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/example_data/f1.bed
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-rw-r--r-- root/root     81253 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/example_data/gencode_human.gtf.gz
-rw-r--r-- root/root     55608 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/example_data/lamina.bed
-rw-r--r-- root/root     62540 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/example_data/ucsc_human.bed.gz
-rw-r--r-- root/root     31704 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/genomicfeatures.py
-rw-r--r-- root/root      2447 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/get_fasta.py
drwxr-xr-x root/root         0 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/
-rw-r--r-- root/root         0 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/__init__.py
-rw-r--r-- root/root      1799 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/attr.py
-rw-r--r-- root/root      1227 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/call.py
-rw-r--r-- root/root      1431 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/cluster.py
-rw-r--r-- root/root      1405 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/concat.py
-rw-r--r-- root/root      2032 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/coverage.py
-rw-r--r-- root/root      2132 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/drop.py
-rw-r--r-- root/root       241 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/drop_duplicates.py
-rw-r--r-- root/root      1130 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/getitem.py
-rw-r--r-- root/root      6530 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/init.py
-rw-r--r-- root/root       992 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/insert.py
-rw-r--r-- root/root      3447 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/intersection.py
-rw-r--r-- root/root         0 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/itergrs.py
-rw-r--r-- root/root      4077 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/join.py
-rw-r--r-- root/root      5386 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/k_nearest.py
-rw-r--r-- root/root      4970 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/k_nearest_old.py
-rw-r--r-- root/root      2555 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/merge.py
-rw-r--r-- root/root      4757 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/nearest.py
-rw-r--r-- root/root      1452 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/new_position.py
-rw-r--r-- root/root       576 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/sort.py
-rw-r--r-- root/root       751 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/methods/split.py
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-rw-r--r-- root/root      7832 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/out.py
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-rw-r--r-- root/root     19432 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges/readers.py
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-rw-r--r-- root/root       724 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges-0.0.79.egg-info/PKG-INFO
-rw-r--r-- root/root         1 2020-06-21 14:43 ./usr/lib/python3/dist-packages/pyranges-0.0.79.egg-info/dependency_links.txt
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drwxr-xr-x root/root         0 2020-06-21 14:43 ./usr/share/
drwxr-xr-x root/root         0 2020-06-21 14:43 ./usr/share/doc/
drwxr-xr-x root/root         0 2020-06-21 14:43 ./usr/share/doc/python3-pyranges/
-rw-r--r-- root/root       182 2020-06-21 14:43 ./usr/share/doc/python3-pyranges/changelog.Debian.gz
-rw-r--r-- root/root      5345 2020-06-21 14:43 ./usr/share/doc/python3-pyranges/changelog.gz
-rw-r--r-- root/root      1510 2020-06-21 14:43 ./usr/share/doc/python3-pyranges/copyright

Timestamp: 21.06.2020 / 18:01:09 (UTC)