varq-py 0.3.1

VarQ API wrapper for Python.

varq-py is an API wrapper for sending, managing and retrieving jobs sent to the VarQ (2.0) backend rewritten in Go.

Install

Requires Python >= 3.6

pip install varq-py

Usage

Available fields and methods can be found in uniprot.py, job.py and structure.py.

Examples

UniProt data

You can get the contents of some fields for a given UniProt accession ID using get_unp. It doesn't send or start a new job, it only takes advantage of the retrieving, parsing and referencing that the backend already does (GET /api/uniprot/:unpID).

>>> from varq import VarQ
>>> api = VarQ("http", "localhost:8888")

>>> unp = api.get_unp("P06280")

>>> print(unp.name)
Alpha-galactosidase A

>>> print(unp.sequence)
MQLRNPELHLGCALALRFLALVSWDIPGARALDNGLARTPTMGWLHWERFMCNLDCQEEPDSCISEKLFMEMAELMVSEGWKDAGYEYLCIDDCWMAPQRDSEGRLQADPQRFPHGIRQLANYVHSKGLKLGIYADVGNKTCAGFPGSFGYYDIDAQTFADWGVDLLKFDGCYCDSLENLADGYKHMSLALNRTGRSIVYSCEWPLYMWPFQKPNYTEIRQYCNHWRNFADIDDSWKSIKSILDWTSFNQERIVDVAGPGGWNDPDMLVIGNFGLSWNQQVTQMALWAIMAAPLFMSNDLRHISPQAKALLQDKDVIAINQDPLGKQGYQLRQGDNFEVWERPLSGLAWAVAMINRQEIGGPRSYTIAVASLGKGVACNPACFITQLLPVKRKLGFYEWTSRLRSHINPTGTVLLQLENTMQMSLKDLL

>>> print(unp.pdb_ids)
['1R46', '1R47', '3GXN', '3GXP', '3GXT', '3HG2', '3HG3', '3HG4', '3HG5', '3LX9', '3LXA', '3LXB', '3LXC', '3S5Y', '3S5Z', '3TV8', '4NXS', '6IBK', '6IBM', '6IBR', '6IBT']

>>> print(unp.ptms.glycosilation_sites)
[GlycoSite(position=139, note='N-linked (GlcNAc...) asparagine'), GlycoSite(position=192, note='N-linked (GlcNAc...) asparagine'), GlycoSite(position=215, note='N-linked (GlcNAc...) asparagine')]

>>> print(unp.variants[0])
Variant(id='VAR_077365', position=3, from_aa='L', to_aa='P', change='L3P', note='L -> P (polymorphism; does not affect enzyme activity; dbSNP:rs150547672)', evidence='ECO:0000269|PubMed:26415523', dbsnp='rs150547672', clinvar=ClinVar(variation_id='42464', name='NM_000169.3(GLA):c.8T>C (p.Leu3Pro)', clin_sig='Conflicting interpretations of pathogenicity', clin_sig_simple=0, review_status='criteria provided, conflicting interpretations', phenotypes='Cardiovascular phenotype;Deoxygalactonojirimycin response;Fabry disease;not specified'))

Sending and retrieving jobs

# Start two jobs for UniProt P06280, PDBs 1R46 and 1R47, 92 D -> F and 231 D -> F substitutions.
j1 = api.new_job("P06280", "1R46", ["D92F", "D231F"])
j2 = api.new_job("P06280", "1R47", ["D92F", "D231F"])

# Starting new jobs is a non-blocking operation.
>>> print(j1.status)
(1, 'processing')
>>> print(j2.status)
(0, 'in queue')

# ... that means, go grab a coffee and check again later.
>>> print(j1.status)
(2, 'done')
>>> print(j2.status)
(2, 'done')

# Positions passed are from the UniProt sequence and mapped internally to the structure, unless stated otherwise.
>>> print(j1.sas_ddg("D92F"), j1.binding(92), j1.buried(92), j1.near_ligands(92))
>>> print(j2.sas_ddg("D92F"), j1.binding(92), j2.buried(92), j2.near_ligands(92))
-1.44298 False True ['EDO']
-3.95959 False True ['GAL']

# Errors
>>> print(j1.buried(1))
# varq.job.PositionError: UniProt position not included in PDB structure.

>>> j1.sas_ddg("G666W")
# varq.job.NotFoundInResults: SAS not found in FoldX results.

# Retrieve a job (in any current status) by ID.
from varq.job import Job

>>> j = Job("http", "localhost:8888", "8cfcfd9355e5fcb97bdf5c02641a100a16870d36c74d73dd4f6d11ce398264f0")
>>> print(j.status)
(1, 'in queue')