def screen_maf(qa_file, maf_file):
"""
Screen the .maf file based on the cluster info in the qa_file
"""
clusters = read_clusters(qa_file)
filtered_maf = maf_file + ".filtered"
screened_alignments = set()
for cluster in clusters:
for anchor in cluster:
score = anchor[-1]
if score!=0:
screened_alignments.add(anchor)
fp = file(maf_file)
reader = maf.Reader(fp)
fw = file(filtered_maf, "w")
writer = maf.Writer(fw)
for rec in reader:
alignment = []
for c in rec.components:
chr, left, right, strand, score = c.src, c.forward_strand_start, \
c.forward_strand_end, c.strand, rec.score
alignment.append((chr, left, right, strand, score))
cluster = alignment_to_cluster(alignment)
if cluster[0] in screened_alignments:
writer.write(rec)
fp.close()
print >>sys.stderr, "write (%d) alignments to '%s'" % \
(len(screened_alignments), filtered_maf)
def screen_maf(qa_file, maf_file):
"""
Screen the .maf file based on the cluster info in the qa_file
"""
clusters = read_clusters(qa_file)
filtered_maf = maf_file + ".filtered"
screened_alignments = set()
for cluster in clusters:
for anchor in cluster:
score = anchor[-1]
if score != 0:
screened_alignments.add(anchor)
fp = file(maf_file)
reader = maf.Reader(fp)
fw = file(filtered_maf, "w")
writer = maf.Writer(fw)
for rec in reader:
alignment = []
for c in rec.components:
chr, left, right, strand, score = c.src, c.forward_strand_start, \
c.forward_strand_end, c.strand, rec.score
alignment.append((chr, left, right, strand, score))
cluster = alignment_to_cluster(alignment)
if cluster[0] in screened_alignments:
writer.write(rec)
fp.close()
print >>sys.stderr, "write (%d) alignments to '%s'" % \
(len(screened_alignments), filtered_maf)
def get_depth(fn, q, axis=0):
intervals = []
clusters = read_clusters(fn)
intervals = []
length = 0
for cluster in clusters:
interval = [x[axis][1] for x in cluster]
intervals.append(interval)
length = max(length, max(interval))
length += 1
print >>sys.stderr, length, "total"
depths = np.zeros(length, np.uint8)
for interval in intervals:
start, stop = min(interval), max(interval)
depths[start:stop+1] += 1
cutoff = int(q.split(":")[abs(axis-1)])
exceed_quota = depths[depths>cutoff].shape[0]
anchor_num = sum(len(c) for c in clusters)
cluster_num = len(clusters)
return anchor_num, cluster_num, exceed_quota, length
qa, qb = int(qa), int(qb)
except:
print >> sys.stderr, "quota string should be the form x:x (2:4, 1:3, etc.)"
sys.exit(1)
if options.self_match and qa != qb:
raise Exception, "when comparing genome to itself, " \
"quota must be the same number " \
"(like 1:1, 2:2) you have %s" % options.quota
if qa > 12 or qb > 12:
raise Exception, "quota %s too loose, make it <=12 each" % options.quota
quota = (qa, qb)
self_match = options.self_match
clusters = read_clusters(qa_file, fmt=options.format)
for cluster in clusters:
assert len(cluster) > 0
# below runs `block merging`
if options.merge:
chain = range(len(clusters))
chain = merge_clusters(chain,
clusters,
Dmax=options.Dmax,
min_size=options.min_size)
merged_qa_file = qa_file + ".merged"
fw = file(merged_qa_file, "w")
clusters = [clusters[c] for c in chain]
write_clusters(fw, clusters)
qa, qb = int(qa), int(qb)
except:
print >>sys.stderr, "quota string should be the form x:x (2:4, 1:3, etc.)"
sys.exit(1)
if options.self_match and qa!=qb:
raise Exception, "when comparing genome to itself, " \
"quota must be the same number " \
"(like 1:1, 2:2) you have %s" % options.quota
if qa > 12 or qb > 12:
raise Exception, "quota %s too loose, make it <=12 each" % options.quota
quota = (qa, qb)
self_match = options.self_match
clusters = read_clusters(qa_file, fmt=options.format)
for cluster in clusters:
assert len(cluster) > 0
# below runs `block merging`
if options.merge:
chain = range(len(clusters))
chain = merge_clusters(chain, clusters, Dmax=options.Dmax, min_size=options.min_size)
merged_qa_file = qa_file + ".merged"
fw = file(merged_qa_file, "w")
clusters = [clusters[c] for c in chain]
write_clusters(fw, clusters)
total_len_x, total_len_y = calc_coverage(clusters, self_match=self_match)
