def _fetch_homebrew(container_dir, distro_config):
"""Fetch homebrew and untar it in the container directory."""
try:
os.stat(os.path.join(container_dir, "bin", "brew"))
return container_for_directory(container_dir, distro_config)
except OSError:
with directory.Navigation(tempdir.TempDir().name):
with TemporarilyDownloadedFile(_HOMEBREW_URL,
filename="brew") as archive_file:
with directory.Navigation(tempdir.TempDir().name) as extract:
_extract_archive(archive_file, extract)
first = os.path.join(extract, os.listdir(extract)[0])
files = [os.path.join(first, p) for p in os.listdir(first)]
for filename in files:
try:
filename_base = os.path.basename(filename)
shutil.move(
filename,
os.path.join(container_dir, filename_base))
except IOError: # suppress(pointless-except)
# Ignore stuff that can't be moved for whatever
# reason. These are all files that generally
# don't matter.
pass
return OSXContainer(container_dir, distro_config["pkgsys"])
def test_input_unrooted_tree(self):
otu61 = os.path.join(path_to_data, '61_otus.gpkg', '61_otus.refpkg')
with tempfile.NamedTemporaryFile(suffix='.fa') as bad_alignment:
with tempdir.TempDir() as tmp:
Create(prerequisites).main(
taxtastic_taxonomy=os.path.join(otu61,
'61_otus_taxonomy.csv'),
taxtastic_seqinfo=os.path.join(otu61,
'61_otus_seqinfo.csv'),
# created with newick_utils:
# nw_prune test/data/61_otus.gpkg/61_otus.refpkg/61_otus.tre 4459468 >test/data/61_otus.without_4459468.tre
unrooted_tree=os.path.join(path_to_data, 'create',
'61_otus.without_4459468.tre'),
sequences=os.path.join(path_to_data, 'create',
'61_otus.without_4459468.fasta'),
alignment=os.path.join(
path_to_data, 'create',
'61_otus.without_4459468.aln.fasta'),
prefix=tmp,
force=True)
gpkg = GraftMPackage.acquire(tmp)
tree = Tree.get(
schema='newick',
data=open(gpkg.reference_package_tree_path()).readline())
self.assertEqual(21, len(tree.leaf_nodes()))
def test_import_math():
# math is an extension module, so this should fail
with tempdir.TempDir() as t:
filename = os.path.join(t, "paper.ap")
paper = ActivePaper(filename, "w")
paper.import_module('math')
paper.close()
def setUp(self):
self.universe = mda.Universe(PSF, [DCD, CRD, DCD, CRD, DCD, CRD, CRD])
self.trajectory = self.universe.trajectory
self.prec = 3
# dummy output DCD file
self.tmpdir = tempdir.TempDir()
self.outfile = self.tmpdir.name + '/chain-reader.dcd'
def setUp(self):
self.universe = mda.Universe(TRZ_psf, TRZ)
self.ag = self.universe.select_atoms('name N')
self.prec = 3
self.tmpdir = tempdir.TempDir()
self.outfile = self.tmpdir.name + '/partial-write-test.pdb'
self.Writer = mda.Writer(self.outfile, n_atoms=len(self.ag))
def setUp(self):
self.universe = mda.Universe(XYZ_psf, XYZ_bz2)
self.prec = 3 # 4 decimals in xyz file
ext = ".xyz"
self.tmpdir = tempdir.TempDir()
self.outfile = self.tmpdir.name + '/xyz-writer' + ext
self.Writer = mda.coordinates.XYZ.XYZWriter
def test_simple_paper():
with tempdir.TempDir() as t:
filename1 = os.path.join(t, "simple1.ap")
filename2 = os.path.join(t, "simple2.ap")
make_simple_paper(filename1)
all_paths = [
'README', 'code', 'code/calc_sine', 'code/initialize', 'data',
'data/frequency', 'data/sine', 'data/time', 'documentation',
'external-dependencies', 'history'
]
all_items = [
'/code/calc_sine', '/code/initialize', '/data/frequency',
'/data/sine', '/data/time'
]
all_deps = {
'/data/sine': ["/code/calc_sine", "/data/frequency", "/data/time"],
'/data/time': [],
'/data/frequency': [],
'/code/calc_sine': [],
'/code/initialize': []
}
sine_deps = ["/code/calc_sine", "/data/frequency", "/data/time"]
hierarchy = [[
'/code/calc_sine', '/code/initialize', '/data/frequency',
'/data/time'
], ['/data/sine']]
check_hdf5_file(filename1, all_paths, sine_deps)
check_paper(filename1, all_items, all_deps, hierarchy)
with ActivePaper(filename1, "r") as paper:
paper.rebuild(filename2)
check_hdf5_file(filename2, all_paths, sine_deps)
check_paper(filename2, all_items, all_deps, hierarchy)
def test_cycle(self):
otu_table = \
[['gene','sample','sequence','num_hits','coverage','taxonomy'],
['ribosomal_protein_L11_rplK_gpkg','minimal','GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC','7','14.4',
'Root; k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'],
['ribosomal_protein_S2_rpsB_gpkg','minimal','CGTCGTTGGAACCCAAAAATGAAAAAATATATCTTCACTGAGAGAAATGGTATTTATATC','6','12.2',
'Root; k__Bacteria; p__Firmicutes; c__Bacilli'],
['ribosomal_protein_S17_gpkg','minimal','GCTAAATTAGGAGACATTGTTAAAATTCAAGAAACTCGTCCTTTATCAGCAACAAAACGT','9','18.8',
'Root; k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus']]
otu_table = "\n".join(["\t".join(x) for x in otu_table])
with tempdir.TempDir() as tmp:
db_path = os.path.join(tmp, 'my.sdb')
collection = OtuTableCollection()
collection.add_otu_table(StringIO.StringIO(otu_table))
SequenceDatabase.create_from_otu_table(db_path, collection)
db2 = SequenceDatabase.acquire(db_path)
s1 = db2.extract_sequence(1)
self.assertEqual('ribosomal_protein_L11_rplK_gpkg', s1.marker)
self.assertEqual('minimal',s1.sample_name)
self.assertEqual('GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',s1.sequence)
self.assertEqual(7, s1.count)
self.assertEqual('Root; k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales', s1.taxonomy)
s3 = db2.extract_sequence(3)
self.assertEqual('GCTAAATTAGGAGACATTGTTAAAATTCAAGAAACTCGTCCTTTATCAGCAACAAAACGT',s3.sequence)
self.assertEqual('Root; k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus', s3.taxonomy)
self.assertEqual(os.path.join(db_path,"sequences.fasta"), db2.sequences_fasta_file)
def test_groups():
with tempdir.TempDir() as t:
filename = os.path.join(t, "paper.ap")
paper = ActivePaper(filename, 'w')
group = paper.data.create_group('group')
subgroup = group.create_group('subgroup')
group['data1'] = np.arange(10)
group['data2'] = 42
assert sorted([g.name for g in paper.iter_groups()]) \
== ['/data/group', '/data/group/subgroup']
assert sorted(list(node for node in group)) \
== ['data1', 'data2', 'subgroup']
assert group['data1'][...].shape == (10,)
assert group['data2'][...] == 42
assert paper.data.parent is paper.data
assert group.parent is paper.data
assert group['data1'].parent is group
assert group['data2'].parent is group
script = paper.create_calclet("script",
"""
from activepapers.contents import data
assert data.parent is data
assert data._codelet is not None
assert data._codelet.path == '/code/script'
group = data['group']
assert group.parent is data
assert group._codelet is not None
assert group._codelet.path == '/code/script'
""")
script.run()
paper.close()
def setup(self):
self.tmpdir = td.TempDir()
self.old_path = os.getcwd()
self.resources = os.path.join(self.old_path, 'mdpow', 'tests',
'testing_resources')
m = pybol.Manifest(os.path.join(self.resources, 'manifest.yml'))
m.assemble('base', self.tmpdir.name)
def test_dummy_datasets():
with tempdir.TempDir() as t:
filename = os.path.join(t, "paper.ap")
paper = ActivePaper(filename, 'w')
paper.data.create_dataset("frequency", data = 0.2)
paper.data.create_dataset("time", data=0.1*np.arange(100))
calc_angular = paper.create_calclet("calc_angular",
"""
from activepapers.contents import data, snapshot
import numpy as np
frequency = data['frequency'][...]
time = data['time'][...]
angular = data.create_group('angular')
angular.attrs['time'] = data['time'].ref
angular.create_dataset("time", data=data['time'].ref)
angular.create_dataset("sine", data=np.sin(2.*np.pi*frequency*time))
""")
calc_angular.run()
paper.replace_by_dummy('/data/angular/sine')
dummy = paper.data_group['angular/sine']
assert dummy.attrs.get('ACTIVE_PAPER_GENERATING_CODELET') \
== '/code/calc_angular'
assert dummy.attrs.get('ACTIVE_PAPER_DUMMY_DATASET', False)
passed = True
try:
paper.replace_by_dummy('/data/time')
except AssertionError:
passed = False
assert not passed
paper.close()
def test_modified_scripts():
with tempdir.TempDir() as t:
filename = os.path.join(t, "paper.ap")
paper = ActivePaper(filename, 'w')
script = paper.create_calclet("script",
"""
from activepapers.contents import data
data.create_dataset('foo', data=42)
group = data.create_group('group1')
group.mark_as_data_item()
group['value'] = 1
group = data.create_group('group2')
group['value'] = 2
""")
script.run()
items = sorted([item.name for item in paper.iter_items()])
assert items == ['/code/script', '/data/foo',
'/data/group1', '/data/group2/value']
assert (paper.data['foo'][...] == 42)
assert (paper.data['group1/value'][...] == 1)
assert (paper.data['group2/value'][...] == 2)
script = paper.create_calclet("script",
"""
from activepapers.contents import data
data.create_dataset('foo', data=1)
""")
script.run()
items = sorted([item.name for item in paper.iter_items()])
assert items == ['/code/script', '/data/foo']
assert (paper.data['foo'][...] == 1)
paper.close()
def test_biom_hello_world(self):
insert_otu_table = [
self.headers,
[
'4.12.ribosomal_protein_L11_rplK', 'insert',
'CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG',
'1', '2.44',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
],
[
'4.12.ribosomal_protein_L11_rplK', 'insert',
'CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTtttCAAGCAGGTGTG',
'2', '2.94',
'Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
]
]
with tempdir.TempDir() as tmp:
with tempfile.NamedTemporaryFile(suffix='.otu_table.csv',
mode='w') as n:
n.write("\n".join(["\t".join(x)
for x in insert_otu_table] + ['']))
n.flush()
extern.run(
"%s summarise --biom_prefix '%s' --input_otu_tables '%s'" %
(path_to_script, os.path.join(tmp, "mybiom"), n.name))
self.assertEqual(
['mybiom.4.12.ribosomal_protein_L11_rplK.biom'],
os.listdir(tmp))
self.assertEqual(
'# Constructed from biom file\n#OTU ID\tinsert\ttaxonomy\nRoot; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG\t1.0\tRoot; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales\nRoot; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTtttCAAGCAGGTGTG\t2.0\tRoot; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales',
extern.run(
"biom convert -i '%s' -o /dev/stdout --to-tsv --header-key taxonomy"
% os.path.join(
tmp,
'mybiom.4.12.ribosomal_protein_L11_rplK.biom')))
def test_clustering(self):
otu_table = [
self.headers,
[
'ribosomal_protein_L11_rplK_gpkg', 'minimal',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'7', '4.95',
'Root; k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
],
[
'ribosomal_protein_L11_rplK_gpkg', 'minimal',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATA',
'6', '4.95', 'Root; k__Bacteria; p__Firmicutes; c__Bacilli'
], #last base only is different to first sequence
[
'ribosomal_protein_S17_gpkg', 'minimal',
'GCTAAATTAGGAGACATTGTTAAAATTCAAGAAACTCGTCCTTTATCAGCAACAAAACGT',
'9', '4.95',
'Root; k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus'
]
]
otu_table = "\n".join(["\t".join(x) for x in otu_table])
with tempfile.NamedTemporaryFile() as f:
f.write(otu_table)
f.flush()
with tempdir.TempDir() as d:
cmd = "{} makedb --db_path {}/db --otu_table {} --clustering_divergence 3".format(
path_to_script, d, f.name)
subprocess.check_call(cmd, shell=True)
cmd = "%s query --query_sequence %s --db %s/db" % (
path_to_script,
'AGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC', # first sequence with an extra A at the start
d)
expected = [
[
'query_name', 'query_sequence', 'divergence',
'num_hits', 'sample', 'marker', 'hit_sequence',
'taxonomy'
],
[
'unnamed_sequence',
'AGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'1', '7', 'minimal', 'ribosomal_protein_L11_rplK_gpkg',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'Root; k__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales'
],
[
'unnamed_sequence',
'AGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATC',
'2', '6', 'minimal', 'ribosomal_protein_L11_rplK_gpkg',
'GGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTGAACATA',
'Root; k__Bacteria; p__Firmicutes; c__Bacilli'
]
]
self.assertEqualOtuTable(
expected, subprocess.check_output(cmd, shell=True))
def setUp(self):
self.tmpdir = tempdir.TempDir()
self.outfile = self.tmpdir.name + '/ncdf-write-vels-force.ncdf'
self.prec = 3
self.top = XYZ_mini
self.n_atoms = 3
self.ts1 = mda.coordinates.TRJ.Timestep(self.n_atoms,
velocities=True,
forces=True)
self.ts1._pos[:] = np.arange(self.n_atoms * 3).reshape(self.n_atoms, 3)
self.ts1._velocities[:] = np.arange(self.n_atoms * 3).reshape(
self.n_atoms, 3) + 100
self.ts1._forces[:] = np.arange(self.n_atoms * 3).reshape(
self.n_atoms, 3) + 200
self.ts2 = mda.coordinates.TRJ.Timestep(self.n_atoms,
velocities=True,
forces=True)
self.ts2._pos[:] = np.arange(self.n_atoms * 3).reshape(
self.n_atoms, 3) + 300
self.ts2._velocities[:] = np.arange(self.n_atoms * 3).reshape(
self.n_atoms, 3) + 400
self.ts2._forces[:] = np.arange(self.n_atoms * 3).reshape(
self.n_atoms, 3) + 500
def init_gpg(keys):
t = tempdir.TempDir()
gpg = gnupg.GPG(homedir=t.name)
gpg.temp_dir = t
for key in keys:
gpg.import_keys(key)
return gpg
def _fetch_choco(container_dir, distro_config):
"""Fetch chocolatey and install it in the container directory."""
try:
os.stat(os.path.join(container_dir, "bin", "choco.exe"))
return container_for_directory(container_dir, distro_config)
except OSError:
with tempdir.TempDir() as download_dir:
with directory.Navigation(download_dir):
_execute_no_output(
["setx", "ChocolateyInstall", container_dir])
# Also set the variable in the local environment
# too, so that it gets propagated down to our
# children
os.environ["ChocolateyInstall"] = container_dir
try:
os.makedirs(container_dir)
except OSError as error:
if error.errno != errno.EEXIST:
raise error
_execute_no_output([
"powershell", "-NoProfile", "-ExecutionPolicy", "Bypass",
"-Command", _CHOCO_INSTALL_CMD
])
# Reset variable back to original state to prevent
# polluting the user's registry
_execute_no_output(["setx", "ChocolateyInstall", ""])
return WindowsContainer(container_dir, distro_config["pkgsys"])
def setUp(self):
self.universe = mda.Universe(GRO)
self.prec = 2 # 3 decimals in file in nm but MDAnalysis is in A
ext = ".gro"
self.tmpdir = tempdir.TempDir()
self.outfile = self.tmpdir.name + '/gro-writer' + ext
self.outfile2 = self.tmpdir.name + '/gro-writer2' + ext
def make(self):
import tarfile, bz2, os.path, sys, os
import tempdir
#Temporary Directory
td = tempdir.TempDir()
tempPath = td.name
os.chdir(tempPath)
#Parse files
self.parseDesc()
self.parseFiles()
if (self.parseINSTALL()):
self.createINSTALL()
#Create PKGINFO inside the temporary directory
self.createPKGINFO()
name = self.desc["pkgname"] + "-" + self.desc["pkgver"] + ".pkg.tar.bz2"
completePath = os.path.join(self.pkgDest, name)
pkg = tarfile.open(completePath, mode=self.comp, dereference=False)
for file in self.files:
try:
pkg.add(file)
except:
string = "Was not able to add the " + file + " of package: " + self.desc[
'pkgname'] + "\n Please run repac again as root \n"
sys.stderr.write(string)
#sys.exit()
pkg.close()
td.dissolve()
def test_alignment_rereplication(self):
gpkg = os.path.join(path_to_data,'61_otus.gpkg')
test_sequences=""">FCC0WM1ACXX:2:2208:12709:74426#GTCCAGAA_2/1
ACACTGCCCAGACACCTACGGGTGGCTGCAGTCGAGGATCTTCGGCAATGGGCGAAAGCCTGACCGAGCGACGCCGCGTGTGGGATGAAGGCCCTCGGGT
>FCC0WM1ACXX:2:2208:12709:74426#GTCCAGAA/1
ACACTGCCCAGACACCTACGGGTGGCTGCAGTCGAGGATCTTCGGCAATGGGCGAAAGCCTGACCGAGCGACGCCGCGTGTGGGATGAAGGCCCTCGGGT
>FCC0WM1ACXX:2:2208:12709:74426#GTCCAGAA/2
CGGGGTATCTAATCCCGTTCGCTCCCCTAGCTTTCGTGCCTCAGCGTCAGAAAAGACCCAGTGAGCCGCTTTCGCCCCCGGTGTTCCTTAGGATATCAAC
"""
expected_rereplicated_alignment=""">FCC0WM1ACXX:2:2208:12709:74426#GTCCAGAA/2
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TTGATATCCTAAGGAACACCGGGGGCGAAAGCGGCTCACTGGGTCTTCTGACGCTGAGGCACGAAAGCTAGGGGAGCGAACGGGATTAGATACCCC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>FCC0WM1ACXX:2:2208:12709:74426#GTCCAGAA_2/1
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACACTGCCCAGACACCTACGGGTGGCTGCAGTCGAGGATCTTCGGCAATGGGCGAAAGCCTGACCGAGCGACGCCGCGTGTGGGATGAAGGCCCTCGGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
>FCC0WM1ACXX:2:2208:12709:74426#GTCCAGAA/1
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACACTGCCCAGACACCTACGGGTGGCTGCAGTCGAGGATCTTCGGCAATGGGCGAAAGCCTGACCGAGCGACGCCGCGTGTGGGATGAAGGCCCTCGGG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------""".split()
with tempfile.NamedTemporaryFile(suffix=".fa") as tf:
tf.write(test_sequences)
tf.flush()
with tempdir.TempDir() as tmp:
cmd = "%s graft --forward %s --graftm_package %s --output_directory %s --force" % (path_to_script,
tf.name,
gpkg,
tmp)
extern.run(cmd)
filename=os.path.splitext(os.path.basename(tf.name))[0]
observed_rereplicated_alignment = [x.strip() for x in open(os.path.join(tmp, filename, "%s_hits.aln.fa" % filename))]
self.assertEquals(expected_rereplicated_alignment,
observed_rereplicated_alignment)
def test_search_hmms_input(self):
with tempdir.TempDir() as tmp:
gpkg = tmp + ".gpkg"
Create(prerequisites).main(
sequences=os.path.join(path_to_data, 'create',
'homologs.trimmed.unaligned.faa'),
taxonomy=os.path.join(
path_to_data, 'create',
'homologs.tax2tree.rerooted.decorated.tree-consensus-strings'
),
hmm=os.path.join(
path_to_data, 'create', 'first5.hmm'
), # an HMM created from just the first 5 sequences
search_hmm_files=[
os.path.join(path_to_data, 'create', 'homologs.hmm')
],
prefix=gpkg,
threads=5)
self.assertEqual(
'NAME first10\n',
open(GraftMPackageVersion2.acquire(
gpkg).alignment_hmm_path()).readlines()[1])
self.assertEqual(
1, len(GraftMPackageVersion2.acquire(gpkg).search_hmm_paths()))
self.assertEqual(
'NAME homologs.trimmed.aligned\n',
open(
GraftMPackageVersion2.acquire(gpkg).search_hmm_paths()
[0]).readlines()[1])
def test_returns_data_as_is(self):
with tempdir.TempDir() as d:
tempfile = os.path.join(d.name, 'tempfile')
p = self.program(tempfile)
d = Data('id', 'payload')
self.assertEqual(d, p.run(d))
def test_hello_world(self):
with tempdir.TempDir() as tmp:
with tempdir.TempDir() as tmp2:
cmd1 = "%s create --verbosity 2 --sequences %s --alignment %s --taxonomy %s --rerooted_tree %s --output %s" \
%(path_to_script,
os.path.join(path_to_data,'create','homologs.trimmed.unaligned.faa'),
os.path.join(path_to_data,'create','homologs.trimmed.aligned.faa'),
os.path.join(path_to_data,'create','homologs.tax2tree.rerooted.decorated.tree-consensus-strings'),
os.path.join(path_to_data,'create','homologstre.tree'),
tmp+".gpkg")
extern.run(cmd1)
cmd2 = "%s graft --verbosity 2 --graftm_package %s --forward %s --output_directory %s" \
% (path_to_script,
"%s.gpkg" % tmp,
os.path.join(path_to_data,'create','test.faa'),
tmp2+"_")
extern.run(cmd2)
def setUp(self):
self.universe = mda.Universe(self.topology, self.filename)
self.prec = 5
ext = ".ncdf"
self.tmpdir = tempdir.TempDir()
self.outfile = os.path.join(self.tmpdir.name, 'ncdf-writer-1' + ext)
self.outtop = os.path.join(self.tmpdir.name, 'ncdf-writer-top.pdb')
self.Writer = mda.coordinates.TRJ.NCDFWriter
def test_published_paper():
with tempdir.TempDir() as t:
library.library = [t]
ap = ActivePaperExploration("doi:10.6084/m9.figshare.808595")
import time_series
ts = np.arange(10)
assert time_series.integral(ts, 1)[-1] == 40.5
ap.close()
def test_krona(self):
archive = '{"fields": ["gene", "sample", "sequence", "num_hits", "coverage", "taxonomy", "read_names", "nucleotides_aligned", "taxonomy_by_known?"], "singlem_package_sha256s": ["2b2afe0114de20451fccfe74360756376dc83d001d890e84e322ab0833eca6ba", "7f406a73d8bb176994055cb966ff350e208986d12c8215722686c17c26e548c7", "735b44ae547c133163cb7d40f417292c35423864d00c95e7f1b32091b27d46c5", "8fc6dcce2766cc01defb3b5c689a1ed8ce9d59b725c67e58c2044dafaae908b3", "172df49937742b8411d41d217500d862567374401eaf393b25107b22ac630202", "4cb1bf226bf28d8198ed5c29e8a76df411d96a6c3ce1256af16887b9a184b0a6", "d473d3ae677e6e46202461ccdedb2aef23c0a10a3412422586b37e397ca37294", "431a2860bb890cd1c7193c565cbf0cc227850cba36fb17fe94df686e74ee9b11", "faa663527bb9aea63cef03859311f2e7f55fe98590a5ec85c5ba85815a6fd13e", "a0daf111380e6e499ad9c10c3ac413aa9016c7503dd459825100168524bff0d1", "aba631d4735aeb9d2dfbbbfee1c0739bf9e99ad6532a3be04ff627f3e6efdae2", "bba10c1feb0c26bdf46aa3d1dcb992744a699cde5cf02bb2728f8397378b342f", "4d91dd794b25fd256508f0814f6a2d31e20dc85e0aa9ea405031398565276768", "9b23c524a6210af0706eea7252c2d378888029f141b9305c3e88cbac3fd83f88", "50a209417b455a48bc67702d6a3809a172c57f00785d8c705a3322e6e2a71f72"], "version": 1, "alignment_hmm_sha256s": ["dd9b7e283598360b89ec91ff3f5c509361a6108a2eadc44bfb29646b1510f6b7", "b1bb943c3449a78f937db960bfdf6b2bed641388d33fce3cb2d5f69e79946ea6", "de92c90f2c83e380ae3953972fb63fcb8ce868dab87a305f9f1811b84ffb3d39", "453ed4a62608a4aec36117a2dd1a276709ff6b130ecb8d7b1612926bfab25527", "20cc450cf4157ecf1772e0325d4d8ed400b597d888a5cb5044ca69098f935656", "4b0bf5b3d7fd2ca16e54eed59d3a07eab388f70f7078ac096bf415f1c04731d9", "7cbba7ba0ed58d21c7519ba3fcef0abe43378e5c38c985b0d5e0e5219f141d92", "4a3bbe5ac594ef3c7c820e74544828e19eca68bf860d64f928729eb4530fce4e", "06a4bed0a765971b891ca4a4bf5680aeef4a4a249ce0c028798c0e912f0ccfb4", "2678fe218ca860a2d88bdbf76935d8c78a00ab6603a041a432505d754ef08250", "b54ff98aa03ab31af39c737a569b23ee4ed9296c8ea088562bfb3db87c38fe4a", "4ae31f14067bf183f38dca20f2aefb580e5ff25848881dd988908b70b67761bb", "d7bb3d544133f38110a329712b3ace7e7d7c989dafa3815d2d5a292b4c575f50", "7639bb919ef54f7baff3ed3a8c924efca97ed375cf4120a6e05d98fd6ef52cbb", "6923b889888ea34fabf463b2c8ad5fe23c94828f1a2631a07601f246f5e87150"], "otus": [["4.11.ribosomal_protein_L10", "minimal", "TTACGTTCACAATTACGTGAAGCTGGTGTTGAGTATAAAGTATACAAAAACACTATGGTA", 2, 4.878048780487805, "Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales; f__Staphylococcaceae; g__Staphylococcus", ["HWI-ST1243:156:D1K83ACXX:7:1106:18671:79482", "HWI-ST1243:156:D1K83ACXX:7:1105:19152:28331"], [60, 60], false], ["4.12.ribosomal_protein_L11_rplK", "minimal", "CCTGCAGGTAAAGCGAATCCAGCACCACCAGTTGGTCCAGCATTAGGTCAAGCAGGTGTG", 4, 9.75609756097561, "Root; d__Bacteria; p__Firmicutes; c__Bacilli; o__Bacillales", ["HWI-ST1243:156:D1K83ACXX:7:1109:18214:9910", "HWI-ST1243:156:D1K83ACXX:7:1103:21187:63124", "HWI-ST1243:156:D1K83ACXX:7:1108:10813:6928", "HWI-ST1243:156:D1K83ACXX:7:1105:12385:81842"], [60, 60, 60, 60], false]]}'
table_collection = OtuTableCollection()
table_collection.add_archive_otu_table(StringIO(archive))
with tempdir.TempDir() as tmp:
Summariser.summarise(krona_output=os.path.join(tmp, 'KronaOK.html'),
table_collection=table_collection)
self.assertTrue(os.path.exists(os.path.join(tmp,'KronaOK.html')))
def setUp(self):
self.temp = tempdir.TempDir()
self.store_dir = os.path.join(os.path.abspath(self.temp.name),
'test_data')
self.app = main({}, **settings)
self.storage_location = 'https://storage.onroerenderfgoed.be/'
collections_include(self.app, self.store_dir)
self.testapp = TestApp(self.app)
def test_module_paper():
with tempdir.TempDir() as t:
filename1 = os.path.join(t, "paper1.ap")
filename2 = os.path.join(t, "paper2.ap")
make_paper_with_module(filename1, 42)
check_paper_with_module(filename1, 42)
make_paper_with_module(filename2, 0)
check_paper_with_module(filename2, 0)
def test_min_aligned_percent(self):
# test it doesn't raise with a lower check limit
with tempdir.TempDir() as tmp:
Create(prerequisites).main(
alignment=os.path.join(path_to_data, 'create',
'homologs.trimmed.aligned.faa'),
taxonomy=os.path.join(
path_to_data, 'create',
'homologs.tax2tree.rerooted.decorated.tree-consensus-strings'
),
sequences=os.path.join(path_to_data, 'create',
'homologs.trimmed.unaligned.faa'),
rerooted_tree=os.path.join(path_to_data, 'create',
'decorated.tree'),
min_aligned_percent=0.5,
prefix=tmp + ".gpkg",
threads=5)
original_alignment_length = len(
open(
os.path.join(
tmp + '.gpkg',
os.path.basename(tmp) + '.gpkg.refpkg',
'homologs_deduplicated_aligned.fasta')).readlines())
with tempdir.TempDir() as tmp:
Create(prerequisites).main(
alignment=os.path.join(path_to_data, 'create',
'homologs.trimmed.aligned.faa'),
taxonomy=os.path.join(
path_to_data, 'create',
'homologs.tax2tree.rerooted.decorated.tree-consensus-strings'
),
sequences=os.path.join(path_to_data, 'create',
'homologs.trimmed.unaligned.faa'),
#rerooted_tree=os.path.join(path_to_data,'create','decorated.tree'),
min_aligned_percent=0.9,
prefix=tmp + ".gpkg",
threads=5)
self.assertEqual(
original_alignment_length - 4, # 2 sequences get removed
len(
open(
os.path.join(tmp + '.gpkg',
os.path.basename(tmp) + '.gpkg.refpkg',
'homologs_deduplicated_aligned.fasta')).
readlines()))
def setUp(self):
self.universe = mda.Universe(PRMncdf, NCDF)
self.prec = 6
ext = ".ncdf"
self.tmpdir = tempdir.TempDir()
self.outfile = self.tmpdir.name + '/ncdf-writer-1' + ext
self.outtop = self.tmpdir.name + '/ncdf-writer-top.pdb'
self.Writer = mda.coordinates.TRJ.NCDFWriter
