recipe pysam

Pysam is a python module for reading and manipulating Samfiles. It is a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.

Homepage

https://github.com/pysam-developers/pysam

License

MIT

Recipe

/pysam/meta.yaml

Links

biotools: pysam, doi: 10.1093/bioinformatics/btp352

package pysam

Versions

0.15.3-3, 0.15.3-1, 0.15.3-0, 0.15.2-3, 0.15.2-2, 0.15.2-1, 0.15.2-0, 0.15.1-0, 0.15.0.1-1, 0.15.0.1-0, 0.15.0-0, 0.14.1-1, 0.14.1-0, 0.14.0-2, 0.14.0-1, 0.14.0-0, 0.13.0-0, 0.12.0.1-2, 0.12.0.1-1, 0.12.0.1-0, 0.11.2.2-2, 0.11.2.2-1, 0.11.2.2-0, 0.11.2.1-0, 0.11.1-0, 0.11.0-0, 0.10.0-9, 0.10.0-8, 0.10.0-7, 0.10.0-6, 0.10.0-5, 0.10.0-4, 0.10.0-3, 0.10.0-1, 0.9.1.4-1, 0.9.1.4-0, 0.9.1-7, 0.9.1-6, 0.9.1-5, 0.9.1-4, 0.9.1-3, 0.9.1-2, 0.9.1-1, 0.9.1-0, 0.9.0-2, 0.9.0-1, 0.9.0-0, 0.8.4-0, 0.8.4pre0-0, 0.8.3-6, 0.8.3-5, 0.8.3-4, 0.8.3-3, 0.8.3-2, 0.8.3-1, 0.8.3-0, 0.7.7-3, 0.7.7-2, 0.7.7-1, 0.7.7-0

Depends

• bzip2 >=1.0.8,<2.0a0

• curl

• libdeflate >=1.3,<1.4.0a0

• libgcc-ng >=7.3.0

• python >=2.7,<2.8.0a0

• xz >=5.2.4,<5.3.0a0

• zlib >=1.2.11,<1.3.0a0

Required By

• rpkmforgenes

• quasitools

• compare-reads

• telescope

• monovar

• pydnase

• simlord

• aquila_umap

• umi_tools

• snaptools

• fings

• nanocomp

• probamconvert

• genomelake

• tetyper

• trnanalysis

• rmats2sashimiplot

• pb-falcon

• sqt

• whatshap

• misopy

• refinem

• tiddit

• relocate2

• recycler

• cnvkit

• seqcluster

• atropos

• besst

• iclipro

• nucleoatac

• optimir

• svviz

• phenix

• bs-seeker2

• rmetl

• clair

• sixgill

• paragraph

• umitools

• edd

• dr-disco

• python-bioext

• hap.py

• circexplorer2

• mqc

• moca

• tetoolkit

• xyalign

• rna-cd

• vamb

• flaimapper

• mirtop

• cgat-apps

• cgat-daisy

• mavis

• metaseq

• ribotish

• blobtools

• counterr

• cooler

• crossmap

• pyloh

• samplot

• clsify

• svim

• prophyle

• plastid

• gretel

• nanoget

• bcbio-nextgen-vm

• pbalign

• spliceai-wrapper

• spanki

• outrigger

• biofluff

• clinvar-tsv

• ngsutils

• pybedtools

• discasm

• icount

• tepid

• nanosv

• kipoi_veff

• wub

• ariba

• comparative-annotation-toolkit

• ctat-mutations

• checkm-genome

• circexplorer

• pomoxis

• wisecondorx

• pepr

• mvp

• pysamstats

• pneumocat

• rop

• emirge

• ribocode

• segmentation-fold

• pygenometracks

• anvio-minimal

• confindr

• reparation_blast

• qcat

• spliceai

• afplot

• hifive

• ribotricer

• samsift

• rseqc

• knock-knock

• transposcope

• sv2

• atactk

• microhapulator

• pynnotator

• lumpy-sv

• pbcoretools

• genomicassertions

• mark-nonconverted-reads

• gemini

• optitype

• wisestork

• phyluce

• smcounter2

• scanindel

• sequana

• nanosim

• midas

• tobias

• seroba

• umis

• deeptools

• slamdunk

• fast5seek

• cpat

• ebfilter

• imfusion

• tigmint

• connor

• advntr

• tapestry

• vcfpy

• peakachu

• vqsr_cnn

• igv-reports

• pyseer

• rnftools

• methylpy

• sccaller

• daisysuite

• riboseed

• aquila

• blockclust

• bam2fasta

• insilicoseq

• guidescan

• cutesv

• strainest

• metasv

• riboraptor

• rgt

• rilseq

• mapdamage2

• flair

• medaka

• aquila_stlfr

• bamread

• epic2

• hits

• metaphlan2

• athena_meta

• bactopia

• uropa

• wg-blimp

• pbcore

• targqc

• mockinbird

• bioconvert

• circle-map

• hapcut2

• circlator

• desman

• eagle

• iva

• somaticseq

• svtyper

• guessmylt

• popera

• hicexplorer

• nanoplot

• gimmemotifs

• riboseq-rust

• tophat-recondition

• mgkit

• smallgenomeutilities

• ipyrad

• bcbio-nextgen

• breakseq2

• dkfz-bias-filter

• dupre

• htseq

• patholive

• cgat-scripts

• starseqr

• riboplot

• oncotator

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install pysam

and update with:

conda update pysam

or use the docker container:

docker pull quay.io/biocontainers/pysam:<tag>

(see pysam/tags for valid values for <tag>)

Link to this page

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/pysam/README.html)