def read_known_motifs(motif_dbs, _DEBUG = False):
"""Given a list of xml file names, this function tries to load the motifs
in those databases
"""
DATA_DIR = os.path.join(settings.DEPLOY_DIR, 'database')
known_motifs = MotifList()
for db in motif_dbs:
if _DEBUG: print "loading (time): %s (%s)" % (db, time.ctime())
tmp = MotifList()
tmp.from_xml_file(os.path.join(DATA_DIR, db))
known_motifs.extend(tmp)
if _DEBUG: print "load Complete (time): %s (%s)" % (db, time.ctime())
return known_motifs
def read_known_motifs(motif_dbs, _DEBUG=False):
"""Given a list of xml file names, this function tries to load the motifs
in those databases
"""
DATA_DIR = os.path.join(settings.DEPLOY_DIR, 'database')
known_motifs = MotifList()
for db in motif_dbs:
if _DEBUG: print("loading (time): %s (%s)" % (db, time.ctime()))
tmp = MotifList()
tmp.from_xml_file(os.path.join(DATA_DIR, db))
known_motifs.extend(tmp)
if _DEBUG: print("load Complete (time): %s (%s)" % (db, time.ctime()))
return known_motifs
if opts.new_motifs_dir is None:
new_motifs_path = opts.new_motifs_file
else:
new_motifs_path = os.path.join(opts.new_motifs_dir,
opts.new_motifs_file)
# set BED file path
bed_path = os.path.join(opts.bed_dir, opts.bed_file)
# set FASTA file path
fasta_path = os.path.join(opts.fasta_dir, opts.fasta_file)
# retrieve known motifs
motifs = MotifList()
if known_motifs_path is not None:
motifs.from_xml_file(known_motifs_path)
# retrieve new motifs if new motifs file is specified by user
if new_motifs_path is not None:
new_motifs = MotifList()
new_motifs.from_xml_file(new_motifs_path)
#motifs.append(new_motifs)
motifs += new_motifs
# scan all motifs for the desired motif ID
if opts.pssm_file is None:
for motif in motifs:
if motif.id == motif_id:
desired_motif = motif
break
else: #use a pssm as the flatfile
else:
if opts.new_motifs_dir is None:
new_motifs_path = opts.new_motifs_file
else:
new_motifs_path = os.path.join(opts.new_motifs_dir, opts.new_motifs_file)
# set BED file path
bed_path = os.path.join(opts.bed_dir, opts.bed_file)
# set FASTA file path
fasta_path = os.path.join(opts.fasta_dir, opts.fasta_file)
# retrieve known motifs
motifs = MotifList()
if known_motifs_path is not None:
motifs.from_xml_file(known_motifs_path)
# retrieve new motifs if new motifs file is specified by user
if new_motifs_path is not None:
new_motifs = MotifList()
new_motifs.from_xml_file(new_motifs_path)
#motifs.append(new_motifs)
motifs += new_motifs
# scan all motifs for the desired motif ID
if opts.pssm_file is None:
for motif in motifs:
if motif.id == motif_id:
desired_motif = motif
break
else: #use a pssm as the flatfile