def trf_run_CMD(fas_file, seq, seqtype,softmask=False,tmpdir=None):
if seqtype == 'p':
return fas_file
olddir = os.getcwd()
os.chdir(os.path.dirname(fas_file.name))
f = open(os.devnull, 'w')
util.run_cmd("trf %s 2 7 7 80 10 50 2000 -m -h" % fas_file.name, verbose=False,stdout=f)
fileres = fas_file.name + '.2.7.7.80.10.50.2000.mask'
fileres2 = fas_file.name + '.2.7.7.80.10.50.2000.dat'
result = Read(fileres,sep='\t')
util.run_cmd('rm %s' % fileres, shell=True)
util.run_cmd('rm %s' % fileres2, shell=True)
fas_file.close()
fas_new = tempfile.NamedTemporaryFile(suffix='.fasta', dir=tmpdir)
if softmask:
nresult = []
for seqold,seqnew in zip(seq, result.seq()):
seqnew = ''.join([c1 if c2 != 'N' or c1 == 'N' else c1.lower() for c1,c2 in zip(seqold, seqnew)])
nresult.append(seqnew)
write_fasta_text(result.Get(0)(), nresult, len(nresult), fas_new)
else:
write_fasta_text(result.Get(0)(), result.seq(), len(result), fas_new)
fas_new.flush()
os.chdir(olddir)
return fas_new
def last(data, type, folder=None, pos_mode = 'last', dbargs='', alargs='', lsargs='', probs=0, trf=False, last_split=True, calc_evalue=False,softmask=False,tmpdir=None):
alargs = [alargs]
dbargs = [dbargs]
lsargs = [lsargs]
if probs:
alargs.append('-j %d' % (probs+4))
seq_1 = data[0];
seq_2 = data[1];
if type[0] != type[1]:
if type[0] == 'n' and type[1] == 'p':
util.warning('Reversing order, last supports only Prot to DNA and not DNA to Prot')
seq_1,seq_2 = seq_2,seq_1
type = (type[1],type[0])
if trf:
seq_1 = [s.upper() for s in seq_1]
seq_2 = [s.upper() for s in seq_2]
if not_contains(dbargs, '-c'):
dbargs.append('-c')
if not_contains(alargs, '-u'):
alargs.append('-u2')
title_1 = [ "%d" % i for i in xrange(len(seq_1)) ];
title_2 = [ "%d" % i for i in xrange(len(seq_2)) ];
fas_1 = tempfile.NamedTemporaryFile(suffix='.fasta',dir=tmpdir)
fas_2 = tempfile.NamedTemporaryFile(suffix='.fasta',dir=tmpdir)
res = tempfile.NamedTemporaryFile(suffix='.maf',dir=tmpdir)
db_1 = fas_1.name[:-4]
db_2 = fas_2.name[:-6]
md5_1 = write_fasta_text(title_1, seq_1, len(seq_1), fas_1);
md5_2 = write_fasta_text(title_2, seq_2, len(seq_2), fas_2);
fas_1.flush()
fas_2.flush()
if trf:
fas_1 = trf_run_CMD(fas_1, seq_1, type[0],softmask=softmask, tmpdir=tmpdir)
fas_2 = trf_run_CMD(fas_2, seq_2, type[1],softmask=softmask, tmpdir=tmpdir)
if type[0] != type[1]:
calc_evalue = False
util.run_cmd(last_make_db_CMD(db_1, fas_1.name, type[0], dbargs), verbose=False)
if calc_evalue:
util.run_cmd(last_make_db_CMD(db_2, fas_2.name, type[1], dbargs), verbose=False)
util.run_cmd(last_run_CMD(db_1, type[0], db_2, fas_2.name, type[1], alargs, lsargs, last_split, calc_evalue), shell=True, stdout=res, verbose=False)
res.flush()
data = last_result2(res.name, pos_mode, probs>0, last_split, calc_evalue);
fas_1.close();
fas_2.close();
res.close()
util.run_cmd('rm %s*' % db_1, shell=True)
if calc_evalue:
util.run_cmd('rm %s*' % db_2, shell=True)
return data
def blast(data, type, folder, reciprocal = True, normalize = False, overwrite = False, blastopts='-num_threads %d' % multiprocessing.cpu_count()):
seq_1 = data[0];
seq_2 = data[1];
title_1 = [ "%d" % i for i in xrange(len(seq_1)) ];
title_2 = [ "%d" % i for i in xrange(len(seq_2)) ];
fas_1 = tempfile.NamedTemporaryFile(delete = False);
fas_2 = tempfile.NamedTemporaryFile(delete = False);
db_1 = "%s.blastdb" % (fas_1.name);
db_2 = "%s.blastdb" % (fas_2.name)
md5_1 = write_fasta_text(title_1, seq_1, len(seq_1), fas_1);
md5_2 = write_fasta_text(title_2, seq_2, len(seq_2), fas_2);
fas_1.close();
fas_2.close();
mkdb_CMDs = [];
blst_CMDs = [];
# perform blast for 12
file_12 = "%s/%s-%s.tsv" % (folder, md5_1, md5_2);
mkdb_CMDs = mkdb_CMDs + [ blast_make_db_CMD(fas_2.name, db_2, type[1]) ];
blst_CMDs = blst_CMDs + [ blast_run_CMD(fas_1.name, db_2, type[0], file_12, blastopts, overwrite) ];
if reciprocal:
# perform blast for 21
file_21 = "%s/%s-%s.tsv" % (folder, md5_2, md5_1);
mkdb_CMDs = mkdb_CMDs + [ blast_make_db_CMD(fas_1.name, db_1, type[1]) ];
blst_CMDs = blst_CMDs + [ blast_run_CMD(fas_2.name, db_1, type[0], file_21, blastopts, overwrite) ];
#fi
if normalize:
# perform blast for 11
file_11 = "%s/%s-%s.tsv" % (folder, md5_1, md5_1);
blst_CMDs = blst_CMDs + [ blast_run_CMD(fas_1.name, db_1, type[0], file_11, blastopts, overwrite) ];
# perform blast for 22
file_22 = "%s/%s-%s.tsv" % (folder, md5_2, md5_2);
blst_CMDs = blst_CMDs + [ blast_run_CMD(fas_2.name, db_2, type[1], file_22, blastopts, overwrite) ];
#fi
util.run_par_cmds(mkdb_CMDs);
util.run_seq_cmds(blst_CMDs);
del_CMDs = [ "rm -f '/tmp/%s'" % f for f in os.listdir('/tmp') if (fnmatch.fnmatch(f, "*%s*" % fas_1.name.split('/')[2])) or (fnmatch.fnmatch(f, "*%s*" % fas_2.name.split('/')[2])) ];
util.run_seq_cmds(del_CMDs);
ab = blast_res_to_dict(file_12); # if reciprocal blast_reciprocal(file_12.name, file_21.name) else blast_res_to_dict(file_12.name)
if reciprocal:
ba = blast_res_to_dict(file_21);
ab = blast_reciprocal(ab, ba);
#fi
if normalize:
aa = blast_res_to_dict(file_11, max=True);
bb = blast_res_to_dict(file_22, max=True);
ab = blast_bitscore_normalize(ab, aa, bb);
#fi
# qseqid sseqid qlen qstart qend slen sstart send length mismatch gapopen pident evalue bitscore
sp_types = (int, int, int, int, int, int, int, int, int, int, int, float, float, float)
ab = [ [ list(p[0]) + h for h in p[1] ] for p in ab.items() ];
ab = [ item for sublist in ab for item in sublist];
if len(ab) == 0:
return tuple([ util.darray([],type) for type in sp_types ] )
#fi
return tuple([ util.darray(row,type) for (type,row) in zip( sp_types, map(lambda *row: list(row), *ab)) ] );
