def run_ptp(self, jp):
full_aln = SeqGroup(self.epa_alignment)
species_list = epa_2_ptp(epa_jp=jp,
ref_jp=self.refjson,
full_alignment=full_aln,
min_lw=0.5,
debug=self.cfg.debug)
self.cfg.log.debug("Species clusters:")
if fout:
fo2 = open(fout + ".species", "w")
else:
fo2 = None
for sp_cluster in species_list:
translated_taxa = []
for taxon in sp_cluster:
origin_taxon_name = EpacConfig.strip_query_prefix(taxon)
translated_taxa.append(origin_taxon_name)
s = ",".join(translated_taxa)
if fo2:
fo2.write(s + "\n")
self.cfg.log.debug(s)
if fo2:
fo2.close()
def checkinput(self, query_fname, minp=0.9):
formats = [
"fasta", "phylip", "iphylip", "phylip_relaxed", "iphylip_relaxed"
]
for fmt in formats:
try:
self.seqs = SeqGroup(sequences=query_fname, format=fmt)
break
except:
self.cfg.log.debug("Guessing input format: not " + fmt)
if self.seqs == None:
self.cfg.exit_user_error(
"Invalid input file format: %s\nThe supported input formats are fasta and phylip"
% query_fname)
if self.ignore_refalign:
self.cfg.log.info(
"Assuming query file contains reference sequences, skipping the alignment step...\n"
)
self.write_combined_alignment()
return
self.query_count = len(self.seqs)
# add query seq name prefix to avoid confusion between reference and query sequences
self.seqs.add_name_prefix(EpacConfig.QUERY_SEQ_PREFIX)
self.seqs.write(format="fasta", outfile=self.tmpquery)
self.cfg.log.info("Checking if query sequences are aligned ...")
entries = self.seqs.get_entries()
seql = len(entries[0][1])
aligned = True
for entri in entries[1:]:
l = len(entri[1])
if not seql == l:
aligned = False
break
if aligned and len(self.seqs) > 1:
self.cfg.log.info("Query sequences are aligned")
refalnl = self.refjson.get_alignment_length()
if refalnl == seql:
self.cfg.log.info(
"Merging query alignment with reference alignment")
self.merge_alignment(self.seqs)
else:
self.cfg.log.info(
"Merging query alignment with reference alignment using MUSCLE"
)
self.require_muscle()
refaln = self.refjson.get_alignment(fout=self.tmp_refaln)
m = muscle(self.cfg)
self.epa_alignment = m.merge(refaln, self.tmpquery)
else:
self.cfg.log.info("Query sequences are not aligned")
self.cfg.log.info(
"Align query sequences to the reference alignment using HMMER")
self.require_hmmer()
self.align_to_refenence(self.noalign, minp=minp)
def load_reduced_refalign(self):
formats = ["fasta", "phylip_relaxed"]
for fmt in formats:
try:
self.reduced_refalign_seqs = SeqGroup(
sequences=self.reduced_refalign_fname, format=fmt)
break
except:
pass
if self.reduced_refalign_seqs == None:
errmsg = "FATAL ERROR: Invalid input file format in %s! (load_reduced_refalign)" % self.reduced_refalign_fname
self.cfg.exit_fatal_error(errmsg)
def load_alignment(self):
in_file = self.cfg.align_fname
self.input_seqs = None
formats = [
"fasta", "phylip_relaxed", "iphylip_relaxed", "phylip", "iphylip"
]
for fmt in formats:
try:
self.input_seqs = SeqGroup(sequences=in_file, format=fmt)
break
except:
self.cfg.log.debug("Guessing input format: not " + fmt)
if self.input_seqs == None:
self.cfg.exit_user_error(
"Invalid input file format: %s\nThe supported input formats are fasta and phylip"
% in_file)
def setUp(self):
cfg = EpacTrainerConfig()
cfg.debug = True
testfile_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)),
"testfiles")
tax_fname = os.path.join(testfile_dir, "test.tax")
phy_fname = os.path.join(testfile_dir, "test.phy")
tax = Taxonomy(EpacConfig.REF_SEQ_PREFIX, tax_fname)
seqs = SeqGroup(sequences=phy_fname, format="phylip")
self.inval = InputValidator(cfg, tax, seqs, False)
self.expected_mis_ids = ["Missing1", "Missing2"]
self.expected_dups = ["DupSeq(01)", "DupSeq02"]
self.expected_merges = [
self.inval.taxonomy.seq_rank_id(sid) for sid in self.expected_dups
]
