Skip to main content

A compilation of bioinformatic and computation biology inspired python tools

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


Release history Release notifications | RSS feed

Download files

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

Source Distribution

mycotools-0.26.43.tar.gz (106.5 kB view details)

Uploaded Source

Built Distribution

mycotools-0.26.43-py3-none-any.whl (217.6 kB view details)

Uploaded Python 3

File details

Details for the file mycotools-0.26.43.tar.gz.

File metadata

  • Download URL: mycotools-0.26.43.tar.gz
  • Upload date:
  • Size: 106.5 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.1 CPython/3.10.6

File hashes

Hashes for mycotools-0.26.43.tar.gz
Algorithm Hash digest
SHA256 d62f9275692666379bec5fcbc14df0c3500fa8495c50d01f11a3576d087c06f9
MD5 e2c0656a236fa5f84d5181366c45fd3b
BLAKE2b-256 77b74a490e3ecd3343a06f5731a2dc75c0be9d548f064ff246a25ea0f23751ab

See more details on using hashes here.

File details

Details for the file mycotools-0.26.43-py3-none-any.whl.

File metadata

  • Download URL: mycotools-0.26.43-py3-none-any.whl
  • Upload date:
  • Size: 217.6 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.1 CPython/3.10.6

File hashes

Hashes for mycotools-0.26.43-py3-none-any.whl
Algorithm Hash digest
SHA256 67316bd0735c771d0630e767ea9f8203dc728f20f1bc982a92e104047b5e4f7c
MD5 c0a30df0192e6c5e4cb34a05ab75c7c9
BLAKE2b-256 89241774f52d1c96cc841a49e46cb86b6c83504fe974f99888799151824999ec

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