def get_alignment_as_string(id, no, fmt="emboss"):
session = Session()
query = session.query(ParcaJob).filter(ParcaJob.id == id)
if query.count() == 0:
return "ERROR: Wrong id", ""
job = query.first()
if job.status != ST_DONE:
return "ERROR: Job not complete", ""
res = json.loads(job.alignments)
inf = json.loads(job.alignment_infos)
if no >= len(res):
return "ERROR: Wrong alignment number", ""
gep = job.gep
gop = inf[no]["MinGOP"], inf[no]["MaxGOP"]
al = res[no]["data"]
mn = job.matrix_name
matr = parca.__dict__[job.matrix_name]
name1 = job.name1
name2 = job.name2
seq1 = job.sequence1
seq2 = job.sequence2
finish_datetime = job.finish_datetime
m = inf[no]["m"]
err = ""
s = ""
try:
s = bioformats.proteins_alignment_to_string(
al, seq1, seq2, name1, name2, fmt, matr, mn, gep, gop, finish_datetime, "parca-soap-server", None, m
)
except bioformats.BioFormatException as e:
err = "ERROR: " + str(e.text)
log.error("Tried to get '%s' representaion of %d:%d: %s" % (fmt, job.id, no, e.text))
return err, s
als = _base.get_pareto_alignments(seq1,seq2,gep,matrix,40)
err = _base.get_last_error()
if len(err)>0:
sys.stderr.write("Error: "+err+"\n")
sys.exit(7)
primary = _util.get_primary_alignments(als)
gops = _util.calculate_gops(primary)
for index, pa in enumerate(primary):
#out.write("\n# Score = %i, Deletions = %i, Gaps = %i \n" % (pa.m, pa.d, pa.g))
gop = gops[index]
s = bioformats.proteins_alignment_to_string(
pa.data,
seq1,
seq2,
name1,
name2,
outfmt,
matrix,
mn,
gep,
gop,
rundate,
"parca",
outname,
pa.m
)
#s = _util.alignment_to_string(seq1,seq2,pa.data,cps,matrix,60)
out.write(s+"\n")
out.close()
else: sys.stderr.write("PASSED\n")
_ = "Test 5. Check output formats"
sys.stderr.write(_+"... ")
try:
for outfmt in ["CLUSTAL", "FASTA", "FASTQ", "EMBOSS"]:
for index, al in enumerate(alns):
gop = gops[index]
s = bioformats.proteins_alignment_to_string(
al.data,
reference[seq_names[0]],
reference[seq_names[1]],
seq_names[0],
seq_names[1],
outfmt,
matrix,
"BLOSUM62",
1.0,
gop,
None,
"selftest",
None,
al.m
)
f = open(RESOURCE_PATH+"/test03/ref/reference"+str(index)+"."+outfmt.lower(), "r")
ref_s = f.read()
f.close()
assert s==ref_s
except:
failed[4] = True
if failed[4]: sys.stderr.write("FAILED\n")
else: sys.stderr.write("PASSED\n")
