def main(args):
# make our error profile report
sys.stderr.write("Reading reference fasta\n")
ref = FastaData(open(args.reference).read())
sys.stderr.write("Reading alignments\n")
epf = ErrorProfileFactory()
if args.random:
bf = None
if args.input_index:
bf = BAMFile(args.input,
reference=ref,
index_file=args.input_index)
bf.read_index(index_file=args.input_index)
else:
bf = BAMFile(args.input, reference=ref)
bf.read_index()
if not bf.has_index():
sys.stderr.write("Random access requires an index be set\n")
z = 0
strand = 'target'
if args.query: strand = 'query'
con = 0
while True:
rname = random.choice(bf.index.get_names())
#print rname
coord = bf.index.get_longest_target_alignment_coords_by_name(rname)
#print coord
if not coord: continue
e = bf.fetch_by_coord(coord)
if e.is_aligned():
epf.add_alignment(e)
z += 1
if z % 100 == 1:
con = epf.get_min_context_count(strand)
sys.stderr.write(
str(z) + " alignments, " + str(con) +
" min context coverage\r")
if args.max_alignments <= z: break
if args.stopping_point <= con: break
else:
bf = BAMFile(args.input, reference=ref)
z = 0
strand = 'target'
if args.query: strand = 'query'
con = 0
for e in bf:
if e.is_aligned():
epf.add_alignment(e)
z += 1
if z % 100 == 1:
con = epf.get_min_context_count(strand)
sys.stderr.write(
str(z) + " alignments, " + str(con) +
" min context coverage\r")
if args.max_alignments <= z: break
if args.stopping_point <= con: break
sys.stderr.write("\n")
sys.stderr.write('working with:' + "\n")
sys.stderr.write(
str(z) + " alignments, " + str(con) + " min context coverage" + "\n")
epf.write_context_error_report(args.tempdir + '/err.txt', strand)
for ofile in args.output:
cmd = args.rscript_path + ' ' + os.path.dirname(
os.path.realpath(__file__)
) + '/plot_base_error_context.r ' + args.tempdir + '/err.txt ' + ofile + ' '
if args.scale:
cmd += ' '.join([str(x) for x in args.scale])
sys.stderr.write(cmd + "\n")
call(cmd.split())
sys.stderr.write("finished\n")
if args.output_raw:
of = open(args.output_raw, 'w')
with open(args.tempdir + "/err.txt") as inf:
for line in inf:
of.write(line)
# Temporary working directory step 3 of 3 - Cleanup
if not args.specific_tempdir:
rmtree(args.tempdir)
def main(args):
sys.stderr.write("Reading our reference Fasta\n")
ref = FastaData(open(args.reference, 'rb').read())
sys.stderr.write("Finished reading our reference Fasta\n")
bf = None
if args.input_index:
bf = BAMFile(args.input, reference=ref, index_file=args.input_index)
bf.read_index(index_file=args.input_index)
else:
bf = BAMFile(args.input, reference=ref)
bf.read_index()
epf = ErrorProfileFactory()
if args.random:
if not bf.has_index():
sys.stderr.write(
"Random access requires our format of index bgi to be set\n")
sys.exit()
z = 0
while True:
rname = random.choice(bf.index.get_names())
coord = bf.index.get_longest_target_alignment_coords_by_name(rname)
if not coord: continue
e = bf.fetch_by_coord(coord)
if e.is_aligned():
epf.add_alignment(e)
z += 1
#print z
if z % 100 == 1:
con = epf.get_alignment_errors().alignment_length
if args.max_length <= con: break
sys.stderr.write(
str(con) + "/" + str(args.max_length) +
" bases from " + str(z) + " alignments\r")
sys.stderr.write("\n")
else:
z = 0
for e in bf:
if e.is_aligned():
epf.add_alignment(e)
z += 1
#print z
if z % 100 == 1:
con = epf.get_alignment_errors().alignment_length
if args.max_length <= con: break
sys.stderr.write(
str(con) + "/" + str(args.max_length) +
" bases from " + str(z) + " alignments\r")
sys.stderr.write("\n")
of = open(args.tempdir + '/report.txt', 'w')
of.write(epf.get_alignment_errors().get_report())
of.close()
for ofile in args.output:
cmd = args.rscript_path + ' ' + os.path.dirname(
os.path.realpath(__file__)
) + '/plot_alignment_errors.r ' + args.tempdir + '/report.txt ' + ofile + ' '
if args.scale:
cmd += ' '.join([str(x) for x in args.scale])
sys.stderr.write(cmd + "\n")
call(cmd.split())
if args.output_raw:
of = open(args.output_raw, 'w')
with open(args.tempdir + "/report.txt") as inf:
for line in inf:
of.write(line)
of.close()
if args.output_stats:
of = open(args.output_stats, 'w')
of.write(epf.get_alignment_errors().get_stats())
of.close()
sys.stderr.write("finished\n")
# Temporary working directory step 3 of 3 - Cleanup
if not args.specific_tempdir:
rmtree(args.tempdir)
