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 Open-Source ultimaker ultimaker (Ultimaker) / debian-backup Project
A certifiably-awesome open-source package repository curated by Ultimaker, hosted by Cloudsmith.
Note: Packages in this repository are licensed as GNU General Public License v3.0 or later (dependencies may be licensed differently).

Debian logo python3-pyvcf  0.6.8+git20170215.476169c-1

One-liner (summary)

Variant Call Format (VCF) parser for Python 3

Description

The Variant Call Format (VCF) specifies the format of a text file used in bioinformatics for storing gene sequence variations. The format has been developed with the advent of large-scale genotyping and DNA sequencing projects, such as the 1000 Genomes Project.

The intent of this module is to mimic the ``csv`` module in the Python stdlib, as opposed to more flexible serialization formats like JSON or YAML. ``vcf`` will attempt to parse the content of each record based on the data types specified in the meta-information lines -- specifically the ##INFO and ##FORMAT lines. If these lines are missing or incomplete, it will check against the reserved types mentioned in the spec. Failing that, it will just return strings.

This package provides the Python 3 modules.

License

Unknown

Size

47.9 KB

Downloads

0

Status  Completed
Checksum (MD5) 212e70e958c11c76646b191338b49777
Checksum (SHA-1) 67b30ab6b47fc0e7e909ff15f383a4cf5f174677
Checksum (SHA-256) 81f8ff25ba151615f718f6d43e4db2d8c03b4826f2c6422dbeb2b7a4966a83a0
Checksum (SHA-512) 65e19c9079ec11e9112320099f953b380f8580f09c8633868350e3586e8e299989…
GPG Signature
GPG Fingerprint c0a114330029b468b1146f70c334efcb2c4f9be3
Distribution debian/buster - Debian - 10 (Buster)
Storage Region  Dublin, Ireland
Type  Binary (contains binaries and binary artifacts)
Uploaded At 3 months, 3 weeks ago
Uploaded By alex-borro
Slug Id python3-pyvcf_068git20170215476169c-1_armhfde-no1s
Unique Id HeojxPKMXvYJ
Version (Raw) 0.6.8+git20170215.476169c-1
Version (Parsed)
  • Major: 0
  • Minor: 6
  • Patch: 8
  • Type: SemVer (Strict)
  • Metadata: git20170215.476169c-1
  extended metadata
Homepage https://pypi.python.org/pypi/PyVCF
Installed Size 207.0 KB
Maintainer Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Priority optional
Section python
Source python-pyvcf

Dependencies

5

Checksum (md5)

d0d43a29f7e6c1a31d0fb9e59e8433fb

Depends
libc6 >=2.4
Depends
python3 >=3.6~
Depends
python3 <<3.8
Depends
python3-pkg-resources
Depends
python3:any

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These instructions assume you have setup the repository first (or read it).

To install/use python3-pyvcf @ version 0.6.8+git20170215.476169c-1 ...

To install packages, you can quickly setup the repository automatically (recommended):

curl -1sLf \
  'https://dl.cloudsmith.io/public/ultimaker/debian-backup/setup.deb.sh' \
  | sudo -E bash

If you need to force a specific distribution, release/version, architecture, or component (if supported), you can also do that (e.g. if your system is compatible but not identical):

curl -1sLf \
  'https://dl.cloudsmith.io/public/ultimaker/debian-backup/setup.deb.sh' \
  | sudo -E distro=debian codename=buster arch=ARCH component=COMPONENT bash

or ... you can manually configure it yourself before installing packages:

apt-get install -y debian-keyring  # debian only
apt-get install -y debian-archive-keyring  # debian only
apt-get install -y apt-transport-https
# For Debian Stretch, Ubuntu 16.04 and later
keyring_location=/usr/share/keyrings/ultimaker-debian-backup-archive-keyring.gpg
# For Debian Jessie, Ubuntu 15.10 and earlier
keyring_location=/etc/apt/trusted.gpg.d/ultimaker-debian-backup.gpg
curl -1sLf 'https://dl.cloudsmith.io/public/ultimaker/debian-backup/gpg.C334EFCB2C4F9BE3.key' |  gpg --dearmor >> ${keyring_location}
curl -1sLf 'https://dl.cloudsmith.io/public/ultimaker/debian-backup/config.deb.txt?distro=debian&codename=buster&component=main' > /etc/apt/sources.list.d/ultimaker-debian-backup.list
sudo chmod 644 ${keyring_location}
sudo chmod 644 /etc/apt/sources.list.d/ultimaker-debian-backup.list
apt-get update
sudo apt-get install python3-pyvcf=0.6.8+git20170215.476169c-1
Warning: Note that this package is for Debian 10 (Buster) / armhf and may only work for that configuration.
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