Python own_data_run Exemples

Exemple #1

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)

Exemple #2

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)

Exemple #3

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)

Exemple #4

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)

Exemple #5

Fichier : tiny_standard_ownfile.py Projet : DalavanCloud/physcraper

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)