def run_cmfinder(Q, nodes_to_index, sets_for_nodes, prefix, fasta_filename):
import tempfile, miscCMF
old_dir = os.popen("pwd").read().strip()
MOTIF_DIR = '../../MOTIF_DIR/experiment'
prefix_dir = tempfile.mkdtemp(dir=MOTIF_DIR, prefix=prefix)
F = FastaReader(fasta_filename)
os.chdir(prefix_dir)
handle = open( os.path.basename(prefix_dir)+'.fna', 'w' )
for q in Q:
m = sets_for_nodes[q]
acc_id = nodes_to_index[m['nodes_ind']]
handle.write(">{0}({1}-{2})\n".format(acc_id,m['start'],m['end']))
handle.write("{0}\n".format(F[acc_id].seq[m['start']:(m['end']+1)]))
handle.close()
# run CMfinder
os.system("cmfinder.pl -def " + handle.name)
# rank the motifs with rank_cmfinder.pl
os.system("rank_cmfinder.pl -w -rank \"{0}.*.motif.*\" {0}.summary".format(handle.name))
# run pfold_pscore, the summary is written to <fna_name>.pscore.summary
# and in addition we get back a descending sorted list of (lod,motif)
pscores = miscCMF.pfold_pscore(motif_dir='.')
print >> sys.stderr, "prefix dir is", prefix_dir
# take the highest pscore motif, cmbuild then cmsearch the original fasta
# TODO: change behaviour later?
scan_result = None
if len(pscores) > 0:
scan_result = run_infernal(motif=pscores[0][1], scan_filename=fasta_filename,\
output_prefix=pscores[0][1]+'.Rfam')
print >> sys.stderr, "scan result is...", scan_result
print >> sys.stderr, "prefix dir is", prefix_dir
os.chdir(old_dir)
return os.path.basename(prefix_dir), scan_result
def rank_motifs(dir_of_motif_dir, webdir, use_pscore=True, use_rankpl=False):
"""
Exactly one of use_pscore/use_rankpl should be True.
"""
assert os.path.isdir(webdir)
if not operator.xor(use_pscore, use_rankpl):
raise Exception, "exactly use_pscore/use_rankpl should be True!"
total_ranks = []
dir_of_motif_dir = os.path.abspath( dir_of_motif_dir )
for d in os.listdir(dir_of_motif_dir):
dd = os.path.join( dir_of_motif_dir, d )
if not os.path.isdir(dd):
continue
print >> sys.stderr, "ranking motifs for directory {0}...".format(d)
with ToDirAndBack(dd):
fam_o,count_o,clique_size,ids_hit = eval_original_fna( d + '.fna' )
if use_rankpl:
ranks = miscCMF.rank_cmfinder_score( dd )
else: # use pscore
ranks = miscCMF.pfold_pscore( dd )
if len(ranks) == 0:
if fam_o is not None:
# if this clique originally was a ncRNA clique, if so,
# we put it in total_ranks but with a rank of -1.0
total_ranks.append( MotifRankInfo(fam='NA',\
count=0,\
motif_size=0,\
motif_filename=d+'.fna',\
fam_o=fam_o,\
count_o=count_o,\
clique_size=clique_size,\
rank=MotifRankInfo.NO_MOTIF_RANK) )
print >> sys.stderr, "copying fastafile {0} to webdir {1}".format(d+'.fna',webdir)
os.system("cp {fasta} {webdir}".format(fasta=d+'.fna', webdir=webdir))
continue
rank_index,motif_filename = ranks[0] # for now take just the top rank motif
fam,count,motif_size = read_cmfinder_motif(motif_filename)
total_ranks.append( MotifRankInfo(fam=fam,\
count=count,\
motif_size=motif_size,\
motif_filename=os.path.basename(motif_filename)+'.html',\
fam_o=fam_o,\
count_o=count_o,\
clique_size=clique_size,\
rank=rank_index) )
# use Zasha's script to create a colorful alignment html, then copy it to web directory
os.system("perl ~/lib/perl/StockholmUnblock.pl {0} tmp.unblocked".format(motif_filename))
os.system("cmzasha --GSC-weighted-consensus tmp.unblocked tmp 3 0.97 0.9 0.75 4 0.97 0.9 0.75 0.5 0.05")
os.system("perl -I/homes/gws/lachesis/lib/perl ~/lib/perl/FancifyStockholm.pl "\
"-noWarnParseHitId -forNewMotifsWeb -noURL -highlightCovarying tmp {0}.html".format(motif_filename))
os.system("cp {motif}.html {webdir}".format(motif=motif_filename, webdir=webdir))
os.system("cp tmp.unblocked {webdir}/{motif}.unblocked".format(motif=os.path.basename(motif_filename),webdir=webdir))
return total_ranks