def PS_standard_run(data_obj, ids, shared_blast_folder):
"""
This is the standard mode for a Physcraper run:
update aln and tre as long as new seqs are found, no filtering.
:param data_obj: ATT object
:param ids: IdDict object
:param shared_blast_folder: path to folder for shared blast runs
:return: PS run
"""
if os.path.isfile("{}/scrape_checkpoint.p".format(data_obj.workdir)):
sys.stdout.write("Reloading from pickled scrapefile: scrape\n")
scraper = pickle.load(
open("{}/scrape_checkpoint.p".format(data_obj.workdir), 'rb'))
scraper.repeat = 1
else:
scraper = PhyscraperScrape(data_obj, ids, ingroup_mrca)
# run the analyses
if shared_blast_folder:
scraper.blast_subdir = shared_blast_folder
else:
shared_blast_folder = None
scraper.run_blast_wrapper()
scraper.read_blast_wrapper(blast_dir=shared_blast_folder)
scraper.remove_identical_seqs()
scraper.generate_streamed_alignment()
scraper.dump("scrape_checkpoint.p")
while scraper.repeat == 1:
scraper.data.write_labelled(label="^ot:ottTaxonName")
scraper.data.write_otus("otu_info", schema="table")
if shared_blast_folder:
scraper.blast_subdir = shared_blast_folder
else:
shared_blast_folder = None
scraper.run_blast_wrapper()
scraper.read_blast_wrapper(blast_dir=shared_blast_folder)
scraper.remove_identical_seqs()
scraper.generate_streamed_alignment()
scraper.dump()
write_out_files(scraper)
writeinfofiles.get_additional_GB_info(scraper)
return scraper
def test_filter_length():
workdir = "tests/output/test_selectbylength"
absworkdir = os.path.abspath(workdir)
conf = ConfigObj("tests/data/test.config", interactive=False)
threshold = 2
selectby = "length"
downtorank = "species"
add_unpubl_seq = None
blacklist = None
id_to_spn_addseq_json = None
ingroup_mrca = None
shared_blast_folder = None
data_obj = pickle.load(open("tests/data/precooked/tiny_dataobj.p", 'rb'))
data_obj.workdir = absworkdir
ids = IdDicts(conf, workdir=data_obj.workdir)
ids.acc_ncbi_dict = pickle.load(
open("tests/data/precooked/tiny_acc_map.p", "rb"))
# Now combine the data, the ids, and the configuration into a single physcraper scrape object
filteredScrape = PhyscraperScrape(data_obj, ids)
filteredScrape.blacklist = blacklist
sys.stdout.write("BLASTing input sequences\n")
if shared_blast_folder:
filteredScrape.blast_subdir = shared_blast_folder
else:
shared_blast_folder = None
# filteredScrape.run_blast_wrapper()
filteredScrape.read_blast_wrapper(
blast_dir="tests/data/precooked/fixed/tte_blast_files")
filteredScrape.remove_identical_seqs()
filteredScrape.dump()
sys.stdout.write("Filter the sequences\n")
length_unfiltered = len(filteredScrape.new_seqs_otu_id)
# if threshold is not None:
# filteredScrape.filter_seqs()
length_filtered = len(filteredScrape.new_seqs)
