https://github.com/biocore/taxster
taxster: assigning taxonomy to organisms you've never even heard of
Science Score: 13.0%
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Low similarity (6.9%) to scientific vocabulary
Repository
taxster: assigning taxonomy to organisms you've never even heard of
Basic Info
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- Stars: 2
- Watchers: 9
- Forks: 4
- Open Issues: 3
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Metadata Files
README.md
taxster: assigning taxonomy to organisms you've never even heard of
This library contains tools for working with taxonomic assignment data. This should be considered pre-alpha software. Public APIs can and will change!
Install
pip install https://github.com/biocore/taxster/archive/master.zip
Consensus taxonomy assignments from .uc files
This example illustrates how to apply the consensus taxonomy processing described in Bokulich et al (in preparation). It assumes that you have the test data files included in this repository in ./test-data.
```python import taxster
taxonomymap = {} for line in open('./test-data/uc/tax-map.tsv', 'U'): line = line.strip() if line.startswith('#') or not line: continue fields = line.split('\t') id = fields[0] tax = fields[1].split('; ') taxonomymap[id] = tax
uc = open('./test-data/uc/1.uc', 'U') consensusassignments = taxster.ucconsensusassignments(uc, taxonomymap) ```
If you'd then like to write these out to file, you can do the following. This will write the consensus taxonomy assignments to a file that can be used with biom add-metadata (compatible with biom-format >= 2.1.5, < 2.2.0).
python
f = open('uc-consensus-tax.tsv', 'w')
for id_, (tax, fraction, hits) in consensus_assignments.items():
tax = '; '.join(tax)
f.write('\t'.join(map(str, [id_, tax, fraction, hits])))
f.write('\n')
f.close()
To get help with taxster.uc_consensus_assignments, call:
python
help(taxster.uc_consensus_assignments)
Owner
- Name: biocore
- Login: biocore
- Kind: organization
- Location: Cyberspace
- Website: http://biocore.github.io/
- Repositories: 76
- Profile: https://github.com/biocore
Collaboratively developed bioinformatics software.
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