A compilation of bioinformatic and computation biology inspired python tools

Navigation

Verified details

These details have been verified by PyPI
Maintainers
Avatar for xonq from gravatar.com xonq

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License: GNU Lesser General Public License v3 or later (LGPLv3+)
  • Author: xonq
  • Requires: Python >=3.0, <4
Classifiers

Project description

Now supports prokaryotes too!



PURPOSE

Bring broadscale comparative genomics to the masses.

Mycotools is a compilation of computational biology tools and database MycotoolsDB software that facilitate large-scale prokaryote and fungal comparative genomics. MycotoolsDB locally assimilates all NCBI and MycoCosm (Joint Genome Institute) genomes into a database schema with uniform file curation, scalability, and automation as guiding principles.

  • Installation is as simple as updateDB.py --init <DIR>. No more limited and incomplete databases.
  • updateDB.py --update brings the database to the current date. No more database obsolecence in the wake of accelerating genome availability.
  • The MycotoolsDB (MTDB) uniformly curates the numerous notorious iterations of the gff, allowing for reliable analyses and format expectations from multiple eras.
  • The .mtdb database format enables swift transitions from analyses with datasets of 100,000s genomes to as few as a lineage of interest. No more scrambling to acquire files for an analysis.

Mycotools is currently available as a beta subset of the full suite, excluding the database assimilation tools. MycotoolsDB is currently restricted to Ohio Supercomputer Center - if you are interested in early access, please email konkelzach@protonmail.com.


By integrating with the curated MycotoolsDB, Mycotools aids routine-complex tasks like retrieving gff or fasta accessions; running and compiling fastas of MycotoolsDB BLAST/hmmsearches; biology-based database manipulation tools; automated phylogenetic analysis pipelines from blast to Pfam extraction to tree prediction, etc etc. Mycotools includes sets of utilities that also enable easy acquisition of batches of sequence data using ncbiDwnld.py and jgiDwnld.py.


USAGE

Check out README.md for install and the USAGE.md for a guide.


CITING

If Mycotools contribute to your analysis, please cite this git repository (gitlab.com/xonq/mycotools) and mention the Mycotools version in line.












Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for xonq from gravatar.com xonq

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License: GNU Lesser General Public License v3 or later (LGPLv3+)
  • Author: xonq
  • Requires: Python >=3.0, <4
Classifiers

Release history Release notifications | RSS feed

0.32.5

0.32.4

0.32.3

0.32.2

0.32.1

0.31.49

0.31.48

0.31.47

0.31.46

0.31.45

0.31.44

0.31.43

0.31.42

0.31.41

0.31.40

0.31.39

0.31.38

0.31.37

0.31.36

0.31.35

0.31.34

0.31.33

0.31.32

0.31.31

0.31.30

0.31.29

0.31.28

0.31.27

0.31.26

0.31.25

0.31.24

0.31.23

0.31.22

0.31.21

0.31.20

0.31.19

0.31.18

0.31.17

0.31.16

0.31.15

0.31.14

0.31.13

0.31.12

0.31.11

0.31.10

0.31.9

0.31.8

0.31.7

0.31.6

0.31.5

0.31.4

0.31.3

0.31.2

0.31.1

0.31.0

0.30.95

0.30.94

0.30.93

0.30.91

0.30.90

0.30.89

0.30.88

0.30.87

0.30.86

0.30.85

0.30.84

0.30.83

0.30.82

0.30.81

0.30.80

0.30.79

0.30.78

0.30.77

0.30.76

0.30.75

0.30.74

0.30.73

0.30.72

0.30.71

0.30.70

0.30.69

0.30.68

0.30.67

0.30.66

0.30.65

0.30.64

0.30.63

0.30.62

0.30.61

0.30.60

0.30.59

0.30.58

0.30.57

0.30.56

0.30.55

0.30.54

0.30.53

0.30.52

0.30.51

0.30.50

0.30.49

0.30.48

0.30.47

0.30.46

0.30.45

0.30.44

0.30.43

0.30.42

0.30.41

0.30.40

0.30.39

0.30.38

0.30.37

0.30.36

0.30.35

0.30.33

0.30.32

0.30.31

0.30.30

0.30.29

0.30.28

0.30.27

0.30.26

0.30.25

0.30.24

0.30.23

0.30.22

0.30.21

0.30.20

0.30.18

0.30.17

0.30.16

0.30.15

0.30.14

0.30.13

0.30.12

0.30.11

0.30.10

0.30.9

0.30.7

0.30.6

0.30.5

0.30.4

0.30.3

0.30.2

0.30.1

0.27.36

0.27.35

0.27.34

0.27.33

0.27.32

0.27.31

0.27.30

0.27.29

0.27.28

0.27.27

0.27.26

0.27.25

0.27.24

0.27.23

0.27.22

0.27.21

0.27.20

0.27.19

0.27.18

0.27.17

0.27.16

0.27.15

0.27.14

0.27.13

0.27.12

This version

0.27.11

0.27.10

0.27.9

0.27.8

0.27.7

0.27.6

0.27.5

0.27.4

0.27.3

0.27.2

0.26.45

0.26.44

0.26.43

0.26.42

0.26.41

0.26.40

0.26.39

0.26.38

0.26.37

0.26.36

0.26.35

0.26.34

0.26.33

0.26.32

0.26.31

0.26.30

0.26.29

0.26.28

0.26.27

0.26.26

0.26.25

0.26.24

0.26.23

0.26.22

0.26.21

0.26.19

0.26.18

0.26.17

0.26.14

0.26.13

0.26.12

0.26.11

0.26.10

0.26.9

0.26.8

0.26.7

0.26.5

0.26.4

0.26.3

0.26.2

0.26.1

0.26

0.25

0.24

0.23

0.22

0.21

0.20

0.19

0.18

0.16

0.15

0.15b1 pre-release

0.14

0.13

0.12

0.11b24 pre-release

0.11b23 pre-release

0.11b22 pre-release

0.11b21 pre-release

0.11b20 pre-release

0.11b19 pre-release

0.11b18 pre-release

0.11b17 pre-release

0.11b16 pre-release

0.11b15 pre-release

0.11b14 pre-release

0.11b12 pre-release

0.11b11 pre-release

0.11b10 pre-release

0.11b9 pre-release

0.11b6 pre-release

0.11b5 pre-release

0.11b4 pre-release

0.11b2 pre-release

0.11b1 pre-release

0.10b12 pre-release

0.10b11 pre-release

0.10b10 pre-release

0.10b9 pre-release

0.10b8 pre-release

0.10b7 pre-release

0.10b6 pre-release

0.10b5 pre-release

0.10b4 pre-release

0.10b3 pre-release

0.10b2 pre-release

0.10b1 pre-release

0.9b37 pre-release

0.9b36 pre-release

0.9b35 pre-release

0.9b34 pre-release

0.9b33 pre-release

0.9b32 pre-release

0.9b31 pre-release

0.9b30 pre-release

0.9b29 pre-release

0.9b28 pre-release

0.9b27 pre-release

0.9b26 pre-release

0.9b25 pre-release

0.9b24 pre-release

0.9b23 pre-release

0.9b22 pre-release

0.9b21 pre-release

0.9b20 pre-release

0.9b19 pre-release

0.9b18 pre-release

0.9b17 pre-release

0.9b16 pre-release

0.9b15 pre-release

0.9b14 pre-release

0.9b13 pre-release

0.9b12 pre-release

0.9b10 pre-release

0.9b9 pre-release

0.9b8 pre-release

0.9b7 pre-release

0.9b6 pre-release

0.9b5 pre-release

0.9b4 pre-release

0.9b3 pre-release

0.9b2 pre-release

0.9b1 pre-release

0.5.25

0.5.23

0.5.22

0.5.20

0.5.19

0.5.18

0.5.17

0.5.15

0.5.14

0.5.13

0.5.12

0.5.11

0.5.10

0.5.9

0.5.8

0.5.7

0.5.6

0.5.5

0.5.4

0.5.3

0.5.1

0.5.1b1 pre-release

0.5.1b0 pre-release

0.5.0b0 pre-release

Download files

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

Source Distribution

mycotools-0.27.11.tar.gz (111.7 kB view details)

Uploaded Source

Built Distribution

mycotools-0.27.11-py3-none-any.whl (237.0 kB view details)

Uploaded Python 3

File details

Details for the file mycotools-0.27.11.tar.gz.

File metadata

  • Download URL: mycotools-0.27.11.tar.gz
  • Upload date:
  • Size: 111.7 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.1 CPython/3.10.6

File hashes

Hashes for mycotools-0.27.11.tar.gz
Algorithm Hash digest
SHA256 7e5d28268b86bc18fe28d2aceb6404333ee3c44b2b60b26bb9b7e194a0e1fa35
MD5 671683685e980708365ee975a11dbbd8
BLAKE2b-256 3b94b29b0341df113f212295a81f1885175c208379ae93beddb133ac05721b5f

See more details on using hashes here.

File details

Details for the file mycotools-0.27.11-py3-none-any.whl.

File metadata

  • Download URL: mycotools-0.27.11-py3-none-any.whl
  • Upload date:
  • Size: 237.0 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.1 CPython/3.10.6

File hashes

Hashes for mycotools-0.27.11-py3-none-any.whl
Algorithm Hash digest
SHA256 5765b87e0d734e34054ea000e3076fa7135ad4d2a1f1e68ea24209d57e53e553
MD5 2591062fa6db1573f4c9dd5a09c5b4be
BLAKE2b-256 55ef3a8926635f943ecec173012128963a81bbd039edbbed1660a52be916f977

See more details on using hashes here.

Supported by

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