def test_example_data_md5s():
data_dir = helpers.data_dir()
data = [
i.strip().split() for i in '''
3735b696b3a416a59f8755eaf5664e5a sine-hg38-0.bedgraph.bw
73ad8ba3590d0895810d069599b0e443 sine-hg38-1.bedgraph.bw
85478d1ecc5906405ccb43d1ca426d29 sine-hg38-2.bedgraph.bw
55ac2603c31b232dacfdaba07d8a25eb sine-no1-1000.bedgraph.bw
b8c983862c58fee6afa99382634ab2d8 sine-no1-100.bedgraph.bw
35fa6ac3453e2bbd503c40a1d15afc65 random-hg38-0.bigBed
3c94c294f8376f625f3701dee7641997 random-hg38-1.bigBed
3bed0726e452d677f33979b2ed1c65d6 random-hg38-2.bigBed
72934b760f1f5ee8f99d596536ef8b4c random-no1-0.bigBed
19116a3295e5679cb79ffc8904fa5abe random-no1-1.bigBed
d628cd0d3b91d8426bb9d0f99b39be52 random-no1-2.bigBed
'''.splitlines(False)
if not i.strip().startswith('#') and len(i.strip()) > 0
]
# for some reason, only faToTwoBit under py27 results in a different md5 than under py3.
if sys.version_info[0] == 3:
data.append(('ba2fd8b22bcad65bb6583da937ff5222', 'newOrg1.2bit'))
success = True
for md5, fn in data:
fn = os.path.join(data_dir, fn)
obs = hashlib.md5(open(fn, 'rb').read()).hexdigest()
success = success and (obs == md5)
print(obs, md5, fn)
assert success
def test_example_data_md5s():
data_dir = helpers.data_dir()
data = [i.strip().split() for i in '''
3735b696b3a416a59f8755eaf5664e5a sine-hg38-0.bedgraph.bw
73ad8ba3590d0895810d069599b0e443 sine-hg38-1.bedgraph.bw
85478d1ecc5906405ccb43d1ca426d29 sine-hg38-2.bedgraph.bw
55ac2603c31b232dacfdaba07d8a25eb sine-no1-1000.bedgraph.bw
b8c983862c58fee6afa99382634ab2d8 sine-no1-100.bedgraph.bw
35fa6ac3453e2bbd503c40a1d15afc65 random-hg38-0.bigBed
3c94c294f8376f625f3701dee7641997 random-hg38-1.bigBed
3bed0726e452d677f33979b2ed1c65d6 random-hg38-2.bigBed
72934b760f1f5ee8f99d596536ef8b4c random-no1-0.bigBed
19116a3295e5679cb79ffc8904fa5abe random-no1-1.bigBed
d628cd0d3b91d8426bb9d0f99b39be52 random-no1-2.bigBed
'''.splitlines(False) if not i.strip().startswith('#') and len(i.strip()) > 0]
# for some reason, only faToTwoBit under py27 results in a different md5 than under py3.
if sys.version_info[0] == 3:
data.append(('ba2fd8b22bcad65bb6583da937ff5222', 'newOrg1.2bit'))
success = True
for md5, fn in data:
fn = os.path.join(data_dir, fn)
obs = hashlib.md5(open(fn, 'rb').read()).hexdigest()
success = success and (obs == md5)
print(obs, md5, fn)
assert success
import os
import subprocess
import pybedtools
from trackhub import helpers
data_dir = helpers.data_dir()
chromsizes = pybedtools.genome_registry.dm3.euchromatic
g = pybedtools.chromsizes_to_file(chromsizes)
# Make some randomized bigBed files
for i in range(3):
x = (
pybedtools.BedTool("chr2L 0 10000000", from_string=True)
.window_maker(g=g, w=1000 * (i + 1))
.shuffle(g=g, seed=i)
.sort()
)
out = os.path.join(data_dir, "random-dm3-%s.bigBed" % i)
cmds = ["bedToBigBed", x.fn, g, out]
p = subprocess.Popen(cmds)
p.communicate()
# make some sine waves for bigWigs
import numpy as np
def sine(factor):
import os
from textwrap import dedent
import warnings
import pytest
import tempfile
from trackhub import upload
from trackhub.helpers import data_dir
from trackhub import Hub, GenomesFile, Genome, Track, CompositeTrack, \
TrackDb, ViewTrack, SuperTrack, AggregateTrack
d = data_dir()
class TestUpload(object):
def setup(self):
with pytest.warns(DeprecationWarning):
self.hub = Hub(
hub='example_hub',
short_label='example hub',
long_label='an example hub for testing',
email='*****@*****.**')
self.genomes_file = GenomesFile()
self.genome = Genome('dm3')
self.trackdb = TrackDb()
self.tracks = [
Track(
name='track1',
tracktype='bigBed',
local_fn=os.path.join(d, 'random-hg38-0.bigBed'),
remote_fn='1.bigbed',
),
import os
import random
import subprocess
from collections import OrderedDict
import pybedtools
import numpy as np
from trackhub import helpers
random.seed(0)
np.random.seed(0)
data_dir = helpers.data_dir()
chromsizes = OrderedDict([("chr1", (0, 100000)), ("chr2", (0, 75000)),
("chr3", (0, 50000))])
def random_dna(length, chars="ATGC"):
return ''.join(random.choice(chars) for _ in range(length)) + "\n"
fasta = open(os.path.join(data_dir, "newOrg1.fa"), "w")
for chrom, size in chromsizes.items():
fasta.write(">" + chrom + "\n")
n, r = divmod(size[1], 80)
for _ in range(n):
fasta.write(random_dna(80))
fasta.write(random_dna(r))
cmds = ["faToTwoBit", fasta.name, fasta.name[0:-2] + "2bit"]
import os
from textwrap import dedent
import pytest
import tempfile
from trackhub import upload
from trackhub.helpers import data_dir
from trackhub import Hub, GenomesFile, Genome, Track, CompositeTrack, \
TrackDb, ViewTrack, SuperTrack, AggregateTrack
d = data_dir()
class TestUpload(object):
def setup(self):
self.hub = Hub(
hub='example_hub',
short_label='example hub',
long_label='an example hub for testing',
email='*****@*****.**')
self.genomes_file = GenomesFile()
self.genome = Genome('dm3')
self.trackdb = TrackDb()
self.tracks = [
Track(
name='track1',
tracktype='bigBed',
source=os.path.join(d, 'random-hg38-0.bigBed')
),
Track(
name='track2',
tracktype='bigWig',