Python library and utility scripts for working with genetic sequence data.

Navigation

Verified details

These details have been verified by PyPI
Maintainers
Avatar for bamueh from gravatar.com bamueh Avatar for imlew from gravatar.com imlew Avatar for LeonieMei from gravatar.com LeonieMei Avatar for terrycojones from gravatar.com terrycojones Avatar for UdoGi from gravatar.com UdoGi

Unverified details

These details have not been verified by PyPI
Project links
Meta
Classifiers
Report project as malware

Project description

PyPI Python Version Downloads License: MIT Build Status

Dark matter

A collection of Python tools for filtering and visualizing Next Generation Sequencing reads.

Installation

On Linux (at least) you will need to first:

sudo apt install zlib1g-dev libbz2-dev liblzma-dev

Then you should be able to install via

$ pip install dark-matter

Some additional information is available for Linux, OS X, and Windows.

Optional dependencies

Not all of the following are mandatory. It depends which part of the dark-matter code you try to use.

Picard

run-bowtie2.py can use Picard to mark duplicates.

GATK

run-bowtie2.py uses gatk if you call it with --markDuplicatesGATK or --callHaplotypesGATK. If you want to do this you'll need to download the gatk zip file, unzip it, and either put the directory where you unzip it into your shell's path or else move the contents of the zip file into a directory already in your path.

bcftools

You'll need bcftools if you want to make consensuses using the make-consensus.py script. Either follow the installation instructions or, if you use brew (or Linux brew), brew install bcftools.

samtools

The run-bowtie2.py and run-bwa.py scripts both make use of samtools.

EMBOSS

The compare-sequences.py script (if called with --align) requires the needle and (possibly) stretcher from EMBOSS.

iPython Notebook

If you are using dark matter in an iPython Notebook, you should install the requirements in requirements-ipynb.txt.

DIAMOND

If you want to use the DIAMOND functionality of dark-matter you will need DIAMOND version 2.1.16 or newer installed.

Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for bamueh from gravatar.com bamueh Avatar for imlew from gravatar.com imlew Avatar for LeonieMei from gravatar.com LeonieMei Avatar for terrycojones from gravatar.com terrycojones Avatar for UdoGi from gravatar.com UdoGi

Unverified details

These details have not been verified by PyPI
Project links
Meta
Classifiers

Release history Release notifications | RSS feed

7.2.5

This version

7.2.4

7.2.3

7.2.2

7.2.1

7.2.0

7.1.20

7.1.19

7.1.18

7.1.14

7.1.13

7.1.12

7.1.11

7.1.10

7.1.9

7.1.8

7.1.7

7.1.6

7.1.5

7.1.4

7.1.3

7.1.2

7.1.1

7.1.0

7.0.12

7.0.11

7.0.10

7.0.9

7.0.8

7.0.7

7.0.6

7.0.5

7.0.4

7.0.3

7.0.2

7.0.1

7.0.0

6.0.1

6.0.0

5.1.2

5.1.1

5.1.0

5.0.46

5.0.45

5.0.44

5.0.43

5.0.42

5.0.41

5.0.40

5.0.39

5.0.38

5.0.37

5.0.36

5.0.34

5.0.33

5.0.32

5.0.31

5.0.30

5.0.29

5.0.28

5.0.27

5.0.26

5.0.25

5.0.24

5.0.23

5.0.22

5.0.21

5.0.20

5.0.19

5.0.18

5.0.17

5.0.16

5.0.15

5.0.14

5.0.11

5.0.10

5.0.8

5.0.7

5.0.6

5.0.5

5.0.4

5.0.3

5.0.2

4.0.89

4.0.88

4.0.87

4.0.86

4.0.85

4.0.84

4.0.83

4.0.82

4.0.81

4.0.80

4.0.79

4.0.77

4.0.73

4.0.72

4.0.71

4.0.70

4.0.69

4.0.68

4.0.67

4.0.66

4.0.65

4.0.64

4.0.63

4.0.62

4.0.61

4.0.60

4.0.59

4.0.58

4.0.57

4.0.56

4.0.55

4.0.54

4.0.53

4.0.52

4.0.51

4.0.50

4.0.49

4.0.48

4.0.47

4.0.46

4.0.45

4.0.44

4.0.43

4.0.42

4.0.41

4.0.40

4.0.39

4.0.38

4.0.37

4.0.36

4.0.35

4.0.34

4.0.33

4.0.32

4.0.31

4.0.30

4.0.29

4.0.28

4.0.27

4.0.26

4.0.25

4.0.24

4.0.23

4.0.22

4.0.21

4.0.20

4.0.19

4.0.18

4.0.17

4.0.16

4.0.13

4.0.12

4.0.11

4.0.9

4.0.8

4.0.7

4.0.6

4.0.5

4.0.3

4.0.2

4.0.1

3.2.6

3.2.5

3.2.4

3.2.3

3.2.2

3.1.88

3.1.87

3.1.86

3.1.85

3.1.84

3.1.82

3.1.81

3.1.79

3.1.76

3.1.75

3.1.74

3.1.73

3.1.72

3.1.71

3.1.70

3.1.69

3.1.68

3.1.67

3.1.66

3.1.65

3.1.64

3.1.63

3.1.62

3.1.61

3.1.60

3.1.59

3.1.58

3.1.57

3.1.56

3.1.55

3.1.54

3.1.53

3.1.52

3.1.51

3.1.50

3.1.49

3.1.48

3.1.46

3.1.45

3.1.44

3.1.43

3.1.42

3.1.41

3.1.40

3.1.39

3.1.38

3.1.37

3.1.36

3.1.35

3.1.34

3.1.33

3.1.32

3.1.31

3.1.28

3.1.27

3.1.26

3.1.25

3.1.24

3.1.22

3.1.21

3.1.20

3.1.19

3.1.18

3.1.17

3.1.16

3.1.15

3.1.14

3.1.13

3.1.12

3.1.11

3.1.10

3.1.9

3.1.8

3.1.6

3.1.5

3.1.4

3.1.3

3.1.2

3.1.1

3.1.0

3.0.80

3.0.79

3.0.78

3.0.77

3.0.76

3.0.75

3.0.74

3.0.73

3.0.72

3.0.71

3.0.70

3.0.69

3.0.68

3.0.67

3.0.66

3.0.65

3.0.64

3.0.63

3.0.62

3.0.61

3.0.60

3.0.59

3.0.58

3.0.57

3.0.56

3.0.55

3.0.54

3.0.53

3.0.52

3.0.51

3.0.50

3.0.49

3.0.46

3.0.45

3.0.44

3.0.43

3.0.42

3.0.41

3.0.40

3.0.38

3.0.37

3.0.36

3.0.35

3.0.34

3.0.33

3.0.32

3.0.31

3.0.30

3.0.29

3.0.28

3.0.25

3.0.24

3.0.23

3.0.22

3.0.21

3.0.20

3.0.19

3.0.18

3.0.17

3.0.16

3.0.15

3.0.14

3.0.13

3.0.12

3.0.11

3.0.10

3.0.8

3.0.7

3.0.6

3.0.5

3.0.4

3.0.3

3.0.2

3.0.1

2.0.4

2.0.3

2.0.2

2.0.1

2.0.0

1.1.33

1.1.31

1.1.30

1.1.29

1.1.28

1.1.27

1.1.26

1.1.25

1.1.24

1.1.23

1.1.19

1.1.17

1.1.16

1.1.15

1.1.14

1.1.12

1.1.11

1.1.10

1.1.9

1.1.8

1.1.7

1.1.6

1.1.5

1.1.3

1.1.1

1.0.110

1.0.107

1.0.106

1.0.101

1.0.99

1.0.98

1.0.97

1.0.92

1.0.91

1.0.90

1.0.89

1.0.88

1.0.87

1.0.86

1.0.85

1.0.84

1.0.83

1.0.82

1.0.81

1.0.80

1.0.79

1.0.78

1.0.77

1.0.76

1.0.75

1.0.74

1.0.73

1.0.72

1.0.71

1.0.70

1.0.69

1.0.68

1.0.67

1.0.66

1.0.65

1.0.64

1.0.63

1.0.62

1.0.61

1.0.60

1.0.59

1.0.58

1.0.57

1.0.56

1.0.55

1.0.54

1.0.53

1.0.52

1.0.51

1.0.50

1.0.49

1.0.48

1.0.47

1.0.46

1.0.45

1.0.44

1.0.43

1.0.42

1.0.41

1.0.40

1.0.38

1.0.36

1.0.34

1.0.32

1.0.27

1.0.19

1.0.16

1.0.13

1.0.12

1.0.11

1.0.0

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

dark_matter-7.2.4.tar.gz (489.9 kB view details)

Uploaded Source

File details

Details for the file dark_matter-7.2.4.tar.gz.

File metadata

  • Download URL: dark_matter-7.2.4.tar.gz
  • Upload date:
  • Size: 489.9 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: uv/0.9.6

File hashes

Hashes for dark_matter-7.2.4.tar.gz
Algorithm Hash digest
SHA256 8c538ae407a0cc568cde234cfeea77796b8549cc283fc981e7fc952b6f5c9846
MD5 023a4d4c51e7237010af89831311a612
BLAKE2b-256 6790880e3aece1d34a49c70023af0a7054aa63a3e5b9c8cae228428569dea9ae

See more details on using hashes here.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Depot Continuous Integration Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page