def test():
seqaln = "tests/data/tiny_test_example/test.fas"
mattype = "fasta"
trfn = "tests/data/tiny_test_example/test.tre"
schema_trf = "newick"
workdir = "tests/output/test_own_local"
configfi = "tests/data/test.config"
# configfi = "tests/data/aws.config"
id_to_spn = r"tests/data/tiny_test_example/test_nicespl.csv"
otu_jsonfi = "{}/otu_dict.json".format(workdir)
if not os.path.exists("{}".format(workdir)):
os.makedirs("{}".format(workdir))
conf = ConfigObj(configfi)
ids = IdDicts(conf, workdir=workdir)
if os.path.exists(otu_jsonfi):
print("load json")
else:
otu_json = OtuJsonDict(id_to_spn, ids)
json.dump(otu_json, open(otu_jsonfi, "w"))
wrappers.own_data_run(seqaln, mattype, trfn, schema_trf, workdir,
otu_jsonfi, configfi)
def test():
if not os.path.exists("{}".format(workdir)):
os.makedirs("{}".format(workdir))
conf = ConfigObj(configfi, interactive=False)
ids = IdDicts(conf, workdir=workdir)
if os.path.exists(otu_jsonfi):
print("load json")
otu_json = json.load(open(otu_jsonfi))
else:
otu_json = OtuJsonDict(id_to_spn, ids)
json.dump(otu_json, open(otu_jsonfi, "w"))
# that's the main function
wrappers.own_data_run(seqaln, mattype, trfn, schema_trf, workdir,
otu_jsonfi, configfi)
import json
from physcraper import wrappers, generate_ATT_from_files, AlignTreeTax
#
#
seqaln = "tiny_test_example/test.fas"
mattype = "fasta"
trfn = "tiny_test_example/test.tre"
schema_trf = "newick"
workdir = "test_ods_tiny"
configfi = "tests/data/localblast.config"
id_to_spn = r"tiny_test_example/test_nicespl.csv"
otu_jsonfi = "{}/otu_dict.json".format(workdir)
treshold = 2
selectby = "blast"
downtorank = "species"
add_local_seq = None
id_to_spn_addseq_json = None
if os.path.exists(otu_jsonfi):
otu_json = json.load(open(otu_jsonfi))
else:
otu_json = wrappers.OtuJsonDict(id_to_spn, configfi)
if not os.path.exists(workdir):
os.mkdir(workdir)
json.dump(otu_json, open(otu_jsonfi, "w"))
wrappers.own_data_run(seqaln, mattype, trfn, schema_trf, workdir, treshold,
selectby, downtorank, otu_jsonfi, add_local_seq,
id_to_spn_addseq_json, configfi)
import os
import json
from physcraper import wrappers, OtuJsonDict, ConfigObj, IdDicts
# define here your files
seqaln = "tests/data/tiny_test_example/test.fas"
mattype = "fasta"
trfn = "tests/data/tiny_test_example/test.tre"
schema_trf = "newick"
id_to_spn = r"tests/data/tiny_test_example/test_nicespl.csv"
workdir = "tests/output/tiny_standard_own"
configfi = "tests/data/blubb_localblast.config"
otu_jsonfi = "{}/otu_dict.json".format(workdir)
if not os.path.exists("{}".format(workdir)):
os.makedirs("{}".format(workdir))
conf = ConfigObj(configfi, interactive=False)
ids = IdDicts(conf, workdir=workdir)
if os.path.exists(otu_jsonfi):
print("load json")
otu_json = json.load(open(otu_jsonfi))
else:
otu_json = OtuJsonDict(id_to_spn, ids)
json.dump(otu_json, open(otu_jsonfi, "w"))
# select a wrapper function, depending on what you want to do, see short tutorial:
wrappers.own_data_run(seqaln, mattype, trfn, schema_trf, workdir, otu_jsonfi,
configfi)
id_to_spn = r"tests/data/tiny_test_example/test_nicespl.csv"
workdir = "tests/output/tiny_standard_own"
configfi = "tests/data/test.config"
otu_jsonfi = "{}/otu_dict.json".format(workdir)
ingroup_mrca = None
shared_blast_folder = None
if not os.path.exists("{}".format(workdir)):
os.makedirs("{}".format(workdir))
conf = ConfigObj(configfi, interactive=False)
ids = IdDicts(conf, workdir=workdir)
if os.path.exists(otu_jsonfi):
otu_json = json.load(open(otu_jsonfi))
else:
otu_json = OtuJsonDict(id_to_spn, ids)
json.dump(otu_json, open(otu_jsonfi, "w"))
# select a wrapper function, depending on what you want to do, see short tutorial:
wrappers.own_data_run(seqaln,
mattype,
trfn,
schema_trf,
workdir,
otu_jsonfi,
configfi,
ingroup_mrca=ingroup_mrca,
shared_blast_folder=shared_blast_folder)