def test_group_by(self):
# verify grouping logic
grouped = iters.group_by(len, ['1', '12', 'a', '123', 'ab'])
self.assertEqual({1: ['1', 'a'], 2: ['12', 'ab'], 3: ['123']}, grouped)
# verify it works with any iterable - not only lists
def gen():
yield '1'
yield '12'
grouped = iters.group_by(len, gen())
self.assertEqual({1: ['1'], 2: ['12']}, grouped)
def test_group_by(self):
# verify grouping logic
grouped = iters.group_by(len, ["1", "12", "a", "123", "ab"])
self.assertEqual({1: ["1", "a"], 2: ["12", "ab"], 3: ["123"]}, grouped)
# verify it works with any iterable - not only lists
def gen():
yield "1"
yield "12"
grouped = iters.group_by(len, gen())
self.assertEqual({1: ["1"], 2: ["12"]}, grouped)
def test_group_by(self):
# verify grouping logic
grouped = iters.group_by(len, ['1', '12', 'a', '123', 'ab'])
self.assertEqual({1: ['1', 'a'], 2: ['12', 'ab'], 3: ['123']}, grouped)
# verify it works with any iterable - not only lists
def gen():
yield '1'
yield '12'
grouped = iters.group_by(len, gen())
self.assertEqual({1: ['1'], 2: ['12']}, grouped)
import json
import operator as op
from typing import NamedTuple, Optional
import requests
from Bio.Data import CodonTable
from fn.iters import group_by
REQUEST = "https://www.ebi.ac.uk/proteins/api/coordinates/location/{prot}:{pos}"
_REVMAP = {'A': 'T', 'C': 'G', 'G': 'C', 'T': 'A'}
_STDTABLE = CodonTable.unambiguous_dna_by_id[1]
STDCODE = {
acid: [codon for codon, _ in pairs]
for acid, pairs in group_by(op.itemgetter(1),
_STDTABLE.forward_table.items()).items()
}
_MITOTABLE = CodonTable.unambiguous_dna_by_id[2]
MITOCODE = {
acid: [codon for codon, _ in pairs]
for acid, pairs in group_by(op.itemgetter(1),
_MITOTABLE.forward_table.items()).items()
}
Codon = NamedTuple('Region', [('contig', str), ('transcript', str),
('forward', bool), ('number', int),
('start', int), ('stop', int), ('tstart', int),
('tstop', int)])
_extract_location = op.itemgetter('chromosome', 'ensemblTranslationId',
'geneStart', 'geneEnd')