def ice_fa2fq(in_fa, ccs_fofn, out_fq):
"""Convert an input FASTA file to an output FASTQ file,
reading QVs from the input ccs.h5 or ccs FOFN.
"""
qver = basQVcacher()
if ccs_fofn:
if ccs_fofn.endswith(".h5"): # Input is a ccs.h5 file not a FOFN.
qver.add_bash5(ccs_fofn)
else: # Input is a ccs FOFN containing multiple ccs.h5 files.
for ccs_fn in get_files_from_fofn(ccs_fofn):
qver.add_bash5(ccs_fn)
bas_handlers = {}
with FastaReader(in_fa) as reader, \
FastqWriter(out_fq) as writer:
for r in reader:
seqid = r.name.split(' ')[0]
movie, hn, s_e = "", "", ""
try:
movie, hn, s_e = seqid.split('/')
hn = int(hn)
except ValueError:
raise ValueError("{seqid} is not a valid CCS read".
format(seqid=seqid))
if ccs_fofn:
try:
bas_file = qver.bas_files[movie][seqid]
if bas_file not in bas_handlers:
bas_handlers[bas_file] = BasH5Reader(bas_file)
except KeyError:
raise IOError("Could not read {s} from input ccs fofn.".
format(s=seqid))
logging.debug("Getting QVs for {name} ...".format(name=r.name))
qvs = get_qv_from_bas_handler(bas_handler=bas_handlers[bas_file],
hn=hn, s_e=s_e,
qv_name="QualityValue")
else: #No quality values provided to pbtranscript.py cluster
qvs = [60]*len(r.sequence) # No information given, have strong belief in the base calls
if len(r.sequence) != len(qvs):
raise ValueError("Sequence and QVs of {r} should be the same!".
format(r=r.name))
writer.writeRecord(r.name, r.sequence, qvs)
for bas_file, bas_handler in bas_handlers.iteritems():
logging.debug("Closing {bas_file} ...".format(bas_file=bas_file))
bas_handler.close()
def ice_fa2fq(in_fa, ccs_fofn, out_fq):
"""Convert an input FASTA file to an output FASTQ file,
reading QVs from the input ccs.h5 or ccs FOFN.
"""
qver = basQVcacher()
if ccs_fofn.endswith(".h5"): # Input is a ccs.h5 file not a FOFN.
qver.add_bash5(ccs_fofn)
else: # Input is a ccs FOFN containing multiple ccs.h5 files.
for ccs_fn in get_files_from_fofn(ccs_fofn):
qver.add_bash5(ccs_fn)
bas_handlers = {}
with FastaReader(in_fa) as reader, \
FastqWriter(out_fq) as writer:
for r in reader:
seqid = r.name.split(' ')[0]
movie, hn, s_e = "", "", ""
try:
movie, hn, s_e = seqid.split('/')
hn = int(hn)
except ValueError:
raise ValueError(
"{seqid} is not a valid CCS read".format(seqid=seqid))
try:
bas_file = qver.bas_files[movie][seqid]
if bas_file not in bas_handlers:
bas_handlers[bas_file] = BasH5Reader(bas_file)
except KeyError:
raise IOError(
"Could not read {s} from input ccs fofn.".format(s=seqid))
logging.debug("Getting QVs for {name} ...".format(name=r.name))
qvs = get_qv_from_bas_handler(bas_handler=bas_handlers[bas_file],
hn=hn,
s_e=s_e,
qv_name="QualityValue")
if len(r.sequence) != len(qvs):
raise ValueError(
"Sequence and QVs of {r} should be the same!".format(
r=r.name))
writer.writeRecord(r.name, r.sequence, qvs)
for bas_file, bas_handler in bas_handlers.iteritems():
logging.debug("Closing {bas_file} ...".format(bas_file=bas_file))
bas_handler.close()
def convert_fofn_to_fasta(fofn_filename,
out_filename,
fasta_out_dir,
force_overwrite=False):
"""
For each .bax.h5 file, create .bax.h5.fasta file and save paths to
out_filename, which should usually be 'input.fasta.fofn'
"""
logging.info("Converting fofn {fofn} to fasta.".format(fofn=fofn_filename))
in_fns = get_files_from_fofn(fofn_filename)
out_fns = []
mkdir(fasta_out_dir)
for in_fn in in_fns:
logging.debug("converting h5 file: {f}.".format(f=in_fn))
if not (in_fn.endswith('.bax.h5') or in_fn.endswith('.bas.h5')):
raise ValueError("fofn file {fofn} ".format(fofn=fofn_filename) +
"should only contain bax/bas.h5 files.")
# e.g. m111xxxx.1.bax.h5 ==>
# tmp_out_file = m11xxxx.1.bax.h5.fasta.tmp
# out_file = m11xxxx.1.bax.h5.fasta
in_basename = op.basename(in_fn)
tmp_out_file = op.join(fasta_out_dir, in_basename + '.fasta.tmp')
out_file = op.join(fasta_out_dir, in_basename + '.fasta')
if op.exists(out_file) and not force_overwrite:
logging.debug(
"File {0} already exists. skipping.".format(out_file))
else:
cmd = "pls2fasta {0} {1} ".format(in_fn, tmp_out_file) + \
"-minSubreadLength 300 -minReadScore 750 -trimByRegion"
logging.debug("CMD: {cmd}".format(cmd=cmd))
_out, _code, _msg = backticks(cmd)
if _code != 0:
raise RuntimeError("CMD failed: {cmd}\n".format(cmd=cmd) +
_msg)
trim_subread_flanks(tmp_out_file, out_file)
out_fns.append(out_file)
if op.exists(tmp_out_file):
os.remove(tmp_out_file)
write_files_to_fofn(out_fns, out_filename)
def convert_fofn_to_fasta(fofn_filename, out_filename, fasta_out_dir,
force_overwrite=False):
"""
For each .bax.h5 file, create .bax.h5.fasta file and save paths to
out_filename, which should usually be 'input.fasta.fofn'
"""
logging.info("Converting fofn {fofn} to fasta.".format(fofn=fofn_filename))
in_fns = get_files_from_fofn(fofn_filename)
out_fns = []
mkdir(fasta_out_dir)
for in_fn in in_fns:
logging.debug("converting h5 file: {f}.".format(f=in_fn))
if not (in_fn.endswith('.bax.h5') or in_fn.endswith('.bas.h5')):
raise ValueError("fofn file {fofn} ".format(fofn=fofn_filename) +
"should only contain bax/bas.h5 files.")
# e.g. m111xxxx.1.bax.h5 ==>
# tmp_out_file = m11xxxx.1.bax.h5.fasta.tmp
# out_file = m11xxxx.1.bax.h5.fasta
in_basename = op.basename(in_fn)
tmp_out_file = op.join(fasta_out_dir, in_basename + '.fasta.tmp')
out_file = op.join(fasta_out_dir, in_basename + '.fasta')
if op.exists(out_file) and not force_overwrite:
logging.debug("File {0} already exists. skipping.".format(out_file))
else:
cmd = "pls2fasta {0} {1} ".format(in_fn, tmp_out_file) + \
"-minSubreadLength 300 -minReadScore 750 -trimByRegion"
logging.debug("CMD: {cmd}".format(cmd=cmd))
_out, _code, _msg = backticks(cmd)
if _code != 0:
raise RuntimeError("CMD failed: {cmd}\n".format(cmd=cmd) + _msg)
trim_subread_flanks(tmp_out_file, out_file)
out_fns.append(out_file)
if op.exists(tmp_out_file):
os.remove(tmp_out_file)
write_files_to_fofn(out_fns, out_filename)
def convert_fofn_to_fasta(fofn_filename, out_filename, fasta_out_dir,
force_overwrite=False, cpus=1):
"""
For each .bax.h5 file, create .bax.h5.fasta file and save paths to
out_filename, which should usually be 'input.fasta.fofn'
"""
logging.info("Converting fofn {fofn} to fasta.".format(fofn=fofn_filename))
in_fns = get_files_from_fofn(fofn_filename)
#out_fns = []
mkdir(fasta_out_dir)
# multiprocessing worker stuff
manager = Manager()
in_queue = manager.Queue(len(in_fns))
in_queue_count = 0
outfile_track = {} # expected out file --> (cmd, tmp)
pool = []
out_fns = []
for in_fn in in_fns:
#print >> sys.stderr, "DEBUG: converting h5 file:", in_fn
logging.debug("converting h5 file: {f}.".format(f=in_fn))
if not (in_fn.endswith('.bax.h5') or in_fn.endswith('.bas.h5')):
raise ValueError("fofn file {fofn} ".format(fofn=fofn_filename) +
"should only contain bax/bas.h5 files.")
# e.g. m111xxxx.1.bax.h5 ==>
# tmp_out_file = m11xxxx.1.bax.h5.fasta.tmp
# out_file = m11xxxx.1.bax.h5.fasta
in_basename = op.basename(in_fn)
tmp_out_file = op.join(fasta_out_dir, in_basename + '.fasta.tmp')
out_file = op.join(fasta_out_dir, in_basename + '.fasta')
if op.exists(out_file) and not force_overwrite:
logging.debug("File {0} already exists. skipping.".format(out_file))
out_fns.append(out_file)
if op.exists(tmp_out_file):
os.remove(tmp_out_file)
else:
cmd = "pls2fasta {in_fn} ".format(in_fn=real_upath(in_fn)) + \
" {out} ".format(out=real_upath(tmp_out_file)) + \
"-minSubreadLength 300 -minReadScore 750 -trimByRegion"
print >> sys.stderr, "DEBUG: putting in queue:", cmd, tmp_out_file, out_file
in_queue.put((cmd, tmp_out_file, out_file))
in_queue_count += 1
outfile_track[out_file] = (cmd, tmp_out_file)
print >> sys.stderr, "DEBUG: put in queue:", cmd, tmp_out_file, out_file
cpus = min(cpus, in_queue_count) # cap max CPU if there's fewer files to convert
for i in xrange(cpus):
p = Process(target=convert_fofn_to_fasta_worker, args=(in_queue,))
pool.append(p)
#error_flag = False
# starting & joining pool worakers
for p in pool:
p.start()
#print >> sys.stderr, "Starting worker", p.name
for p in pool:
#print >> sys.stderr, "Waiting join", p.name
p.join(timeout=1200)
if p.is_alive(): p.terminate()
# check that all files exists
# if it does not, force to run locally
for out_file,(cmd, tmp_out_file) in outfile_track.iteritems():
in_queue.put((cmd, tmp_out_file, out_file))
convert_fofn_to_fasta_worker(in_queue)
out_fns.append(out_file)
#if error_flag:
# raise Exception, "Unable to successfuly run convert_fofn_to_fasta, ABORT!"
write_files_to_fofn(out_fns, out_filename)
def convert_fofn_to_fasta(fofn_filename, out_filename, fasta_out_dir,
force_overwrite=False, cpus=1):
"""
For each .bax.h5 file, create .bax.h5.fasta file and save paths to
out_filename, which should usually be 'input.fasta.fofn'
"""
logging.info("Converting fofn {fofn} to fasta.".format(fofn=fofn_filename))
in_fns = get_files_from_fofn(fofn_filename)
#out_fns = []
mkdir(fasta_out_dir)
# multiprocessing worker stuff
manager = Manager()
in_queue = manager.Queue(len(in_fns))
in_queue_count = 0
outfile_track = {} # expected out file --> (cmd, tmp)
pool = []
out_fns = []
for in_fn in in_fns:
#print >> sys.stderr, "DEBUG: converting h5 file:", in_fn
logging.debug("converting h5 file: {f}.".format(f=in_fn))
if not (in_fn.endswith('.bax.h5') or in_fn.endswith('.bas.h5')):
raise ValueError("fofn file {fofn} ".format(fofn=fofn_filename) +
"should only contain bax/bas.h5 files.")
# e.g. m111xxxx.1.bax.h5 ==>
# tmp_out_file = m11xxxx.1.bax.h5.fasta.tmp
# out_file = m11xxxx.1.bax.h5.fasta
in_basename = op.basename(in_fn)
tmp_out_file = op.join(fasta_out_dir, in_basename + '.fasta.tmp')
out_file = op.join(fasta_out_dir, in_basename + '.fasta')
if op.exists(out_file) and not force_overwrite:
logging.debug("File {0} already exists. skipping.".format(out_file))
out_fns.append(out_file)
if op.exists(tmp_out_file):
os.remove(tmp_out_file)
else:
cmd = "pls2fasta {in_fn} ".format(in_fn=real_upath(in_fn)) + \
" {out} ".format(out=real_upath(tmp_out_file)) + \
"-minSubreadLength 300 -minReadScore 750 -trimByRegion"
print >> sys.stderr, "DEBUG: putting in queue:", cmd, tmp_out_file, out_file
in_queue.put((cmd, tmp_out_file, out_file))
in_queue_count += 1
outfile_track[out_file] = (cmd, tmp_out_file)
print >> sys.stderr, "DEBUG: put in queue:", cmd, tmp_out_file, out_file
cpus = min(cpus, in_queue_count) # cap max CPU if there's fewer files to convert
for i in xrange(cpus):
p = Process(target=convert_fofn_to_fasta_worker, args=(in_queue,))
pool.append(p)
#error_flag = False
# starting & joining pool worakers
for p in pool:
p.start()
#print >> sys.stderr, "Starting worker", p.name
for p in pool:
#print >> sys.stderr, "Waiting join", p.name
p.join(timeout=1200)
if p.is_alive(): p.terminate()
# check that all files exists
# if it does not, force to run locally
for out_file,(cmd, tmp_out_file) in outfile_track.iteritems():
in_queue.put((cmd, tmp_out_file, out_file))
convert_fofn_to_fasta_worker(in_queue)
out_fns.append(out_file)
#if error_flag:
# raise Exception, "Unable to successfuly run convert_fofn_to_fasta, ABORT!"
write_files_to_fofn(out_fns, out_filename)
def convert_fofn_to_fasta(fofn_filename,
out_filename,
fasta_out_dir,
force_overwrite=False,
cpus=1):
"""
For each .bax.h5 file, create .bax.h5.fasta file and save paths to
out_filename, which should usually be 'input.fasta.fofn'
"""
logging.info("Converting fofn {fofn} to fasta.".format(fofn=fofn_filename))
in_fns = get_files_from_fofn(fofn_filename)
#out_fns = []
mkdir(fasta_out_dir)
# multiprocessing worker stuff
manager = Manager()
out_fns = manager.list()
in_queue = manager.Queue(99999)
pool = []
for i in xrange(cpus):
p = Process(target=convert_fofn_to_fasta_worker,
args=(in_queue, out_fns))
pool.append(p)
for in_fn in in_fns:
#print >> sys.stderr, "DEBUG: converting h5 file:", in_fn
logging.debug("converting h5 file: {f}.".format(f=in_fn))
if not (in_fn.endswith('.bax.h5') or in_fn.endswith('.bas.h5')):
raise ValueError("fofn file {fofn} ".format(fofn=fofn_filename) +
"should only contain bax/bas.h5 files.")
# e.g. m111xxxx.1.bax.h5 ==>
# tmp_out_file = m11xxxx.1.bax.h5.fasta.tmp
# out_file = m11xxxx.1.bax.h5.fasta
in_basename = op.basename(in_fn)
tmp_out_file = op.join(fasta_out_dir, in_basename + '.fasta.tmp')
out_file = op.join(fasta_out_dir, in_basename + '.fasta')
if op.exists(out_file) and not force_overwrite:
logging.debug(
"File {0} already exists. skipping.".format(out_file))
out_fns.append(out_file)
if op.exists(tmp_out_file):
os.remove(tmp_out_file)
else:
cmd = "pls2fasta {in_fn} ".format(in_fn=real_upath(in_fn)) + \
" {out} ".format(out=real_upath(tmp_out_file)) + \
"-minSubreadLength 300 -minReadScore 750 -trimByRegion"
print >> sys.stderr, "DEBUG: putting in queue:", cmd, tmp_out_file, out_file
in_queue.put((cmd, tmp_out_file, out_file))
print >> sys.stderr, "DEBUG: put in queue:", cmd, tmp_out_file, out_file
# logging.debug("CMD: {cmd}".format(cmd=cmd))
# _out, _code, _msg = backticks(cmd)
# if _code != 0:
# raise RuntimeError("CMD failed: {cmd}\n".format(cmd=cmd) + _msg)
# trim_subread_flanks(tmp_out_file, out_file)
# out_fns.append(out_file)
# if op.exists(tmp_out_file):
# os.remove(tmp_out_file)
# starting & joining pool worakers
for p in pool:
p.start()
#print >> sys.stderr, "Starting worker", p.name
for p in pool:
#print >> sys.stderr, "Waiting join", p.name
p.join()
write_files_to_fofn(out_fns, out_filename)