def create_sgr(output_dir, eland_file_path, chr):
eland = ElandFile(eland_file_path, 'r')
output = open(os.path.join(output_dir, chr + ".sgr"), 'w')
signals = {}
for hit in eland:
read_length = len(hit.sequence)
if hit.strand == 'F':
start = int(hit.coordinate)
stop = int(hit.coordinate) + WINDOW
elif hit.strand == 'R':
start = max(int(hit.coordinate) + read_length - WINDOW, 1)
stop = int(hit.coordinate) + read_length
if start in signals:
signals[start] += 1
else:
signals[start] = 1
if stop in signals:
signals[stop] += -1
else:
signals[stop] = -1
sorted_keys = signals.keys()
sorted_keys.sort()
height = 0
for coord in sorted_keys:
height += signals[coord]
s = SGR(chr, coord, height)
output.write(str(s) + "\n")
eland.close()
output.close()
def merge_unique_eland(output, mapped_reads_files, mismatches=2):
eland_out = ElandFile(output, 'w')
for i in mapped_reads_files:
if not os.path.exists(i):
raise Exception("File %s does not exist" % i)
if i.endswith('.bam'):
convert_bam(eland_out, i, mismatches)
continue
if i.endswith('.sam'):
convert_sam(eland_out, i, mismatches)
continue
if 'multi' in i:
eland_in = ElandMultiFile(i, 'r')
elif 'extended' in i:
eland_in = ElandExtendedFile(i, 'r')
else:
eland_in = ElandFile(i, 'r')
total_passed = 0
for i, line in enumerate(eland_in):
best_hits = line.best_matches()
if len(best_hits) == 0:
continue
elif len(best_hits) > 1:
continue # Only merge unique hits
elif best_hits[0].number_of_mismatches() > mismatches:
continue
else:
total_passed += 1
eland_out.write(line.convert_to_eland())
print "unique eland: total lines", i, "total passed", total_passed
eland_in.close()
eland_out.close()
def create_sgr(output_dir, eland_file_path, chr):
eland = ElandFile(eland_file_path, 'r')
output = open(os.path.join(output_dir, chr + ".sgr"), 'w')
signals = {}
for hit in eland:
read_length = len(hit.sequence)
if hit.strand == 'F':
start = int(hit.coordinate)
stop = int(hit.coordinate) + WINDOW
elif hit.strand == 'R':
start = max(int(hit.coordinate) + read_length - WINDOW, 1)
stop = int(hit.coordinate) + read_length
if start in signals:
signals[start] += 1
else:
signals[start] = 1
if stop in signals:
signals[stop] += -1
else:
signals[stop] = -1
sorted_keys = signals.keys()
sorted_keys.sort()
height = 0
for coord in sorted_keys:
height += signals[coord]
s = SGR(chr, coord, height)
output.write(str(s) + "\n")
eland.close()
output.close()
def divide_eland_by_chr(eland_file, genome, output_dir=""):
chr_files = {}
chr_map = get_chr_mapping(genome)
i = ElandFile(eland_file, 'r')
for line in i:
if line.chr_name not in chr_map:
#print "%s not a valid chromosome name, skipping." % line.chr_name
continue
o = open_chr_file(line.chr_name, chr_files, genome, chr_map, output_dir)
o.write(line)
i.close()
for f in chr_files.values():
f.close()
def divide_eland_by_chr(eland_file, genome, output_dir=""):
chr_files = {}
chr_map = get_chr_mapping(genome)
i = ElandFile(eland_file, 'r')
for line in i:
if line.chr_name not in chr_map:
#print "%s not a valid chromosome name, skipping." % line.chr_name
continue
o = open_chr_file(line.chr_name, chr_files, genome, chr_map,
output_dir)
o.write(line)
i.close()
for f in chr_files.values():
f.close()
def open_chr_file(chr_name, chr_files, genome, chr_map, output_dir=""):
if chr_name in chr_files:
return chr_files[chr_name]
else:
f = ElandFile(
os.path.join(output_dir, '%s_eland.txt' % (chr_map[chr_name])),
'w')
chr_files[chr_name] = f
return f
def merge_unique_eland(output, mapped_reads_files, mismatches=2):
print "merge_filter %s to %s" % (','.join(mapped_reads_files), output)
eland_out = ElandFile(output, 'w')
for i in mapped_reads_files:
if not os.path.exists(i):
raise Exception("File %s does not exist" % i)
if i.endswith('.bam'):
convert_bam(eland_out, i, mismatches)
continue
if i.endswith('.sam'):
convert_sam(eland_out, i, mismatches)
continue
if 'multi' in i:
print " multi eland ..."
eland_in = ElandMultiFile(i, 'r')
elif 'extended' in i:
print " extended ..."
eland_in = ElandExtendedFile(i, 'r')
else:
print "ElandFile ..."
eland_in = ElandFile(i, 'r')
total_passed = 0
for i, line in enumerate(eland_in):
best_hits = line.best_matches()
if len(best_hits) == 0:
continue
elif len(best_hits) > 1:
continue # Only merge unique hits
elif best_hits[0].number_of_mismatches() > mismatches:
continue
else:
total_passed += 1
eland_out.write(line.convert_to_eland())
print "best_hits", best_hits
print "unique eland: total lines", i, "total passed", total_passed
eland_in.close()
eland_out.close()