def main(args):
grace.require_shrimp_1()
n_cpus = grace.how_many_cpus()
solid, args = grace.get_flag(args, '--solid')
verbose, args = grace.get_flag(args, '--verbose')
threshold, args = grace.get_option_value(args, '--threshold', str, '68%')
stride, args = grace.get_option_value(args, '--stride', int, 1)
max_shrimps, args = grace.get_option_value(args, '--cpus', int, n_cpus)
batch_size, args = grace.get_option_value(args, '--batch-size', int,
5000000)
input_reference_filenames = []
reads_filenames = []
shrimp_options = ['-h', threshold]
if threshold.endswith('%'):
threshold = -float(threshold[:-1]) / 100.0
else:
threshold = int(threshold)
output_dir = [] #As list so can write to from function. Gah.
def front_command(args):
grace.expect_no_further_options(args)
if len(args) < 1:
return
output_dir.append(args[0])
input_reference_filenames.extend(
[os.path.abspath(filename) for filename in args[1:]])
def reads_command(args):
grace.expect_no_further_options(args)
reads_filenames.extend([[os.path.abspath(filename)]
for filename in args])
def pairs_command(args):
grace.expect_no_further_options(args)
assert len(args) == 2, 'Expected exactly two files in "pairs"'
reads_filenames.append(
[os.path.abspath(filename) for filename in args])
def shrimp_options_command(args):
shrimp_options.extend(args)
grace.execute(
args, {
'reads': reads_command,
'--reads': reads_command,
'pairs': pairs_command,
'shrimp-options': shrimp_options_command,
'--shrimp-options': shrimp_options_command,
}, front_command)
if not output_dir:
print >> sys.stderr, USAGE % n_cpus
return 1
output_dir = output_dir[0]
assert input_reference_filenames, 'No reference files given'
assert reads_filenames, 'No read files given'
for filename in itertools.chain(input_reference_filenames,
*reads_filenames):
assert os.path.exists(filename), '%s does not exist' % filename
if not os.path.isdir(output_dir):
os.mkdir(output_dir)
if solid:
shrimp = 'rmapper-cs'
else:
shrimp = 'rmapper-ls'
reference_filename = os.path.join(output_dir, 'reference.fa')
reference_file = open(reference_filename, 'wb')
total_reference_sequences = 0
total_reference_bases = 0
for input_reference_filename in input_reference_filenames:
for name, sequence in io.read_sequences(input_reference_filename):
#Don't retain any comment
name = name.split()[0]
io.write_fasta(reference_file, name, sequence)
total_reference_sequences += 1
total_reference_bases += len(sequence)
reference_file.close()
print '%s base%s in %s reference sequence%s' % (
grace.pretty_number(total_reference_bases),
's' if total_reference_bases != 1 else '',
grace.pretty_number(total_reference_sequences),
's' if total_reference_sequences != 1 else '')
assert total_reference_bases, 'Reference sequence file is empty'
config = {
'references': input_reference_filenames,
'reads': reads_filenames,
'stride': stride,
'solid': solid,
'threshold': threshold,
}
config_file = open(os.path.join(output_dir, 'config.txt'), 'wb')
pprint.pprint(config, config_file)
config_file.close()
output_filename = os.path.join(output_dir, 'shrimp_hits.txt.gz')
output_file = gzip.open(output_filename, 'wb')
unmapped_filename = os.path.join(output_dir, 'unmapped.fa.gz')
unmapped_file = gzip.open(unmapped_filename, 'wb')
dirty_filenames = set()
dirty_filenames.add(output_filename)
dirty_filenames.add(unmapped_filename)
#warn_low_threshold = True
try: #Cleanup temporary files
N = [0]
def do_shrimp(read_set):
my_number = N[0]
N[0] += 1
tempname = os.path.join(output_dir,
'temp%d-%d.fa' % (os.getpid(), my_number))
tempname_out = os.path.join(
output_dir, 'temp%d-%d.txt' % (os.getpid(), my_number))
dirty_filenames.add(tempname)
dirty_filenames.add(tempname_out)
f = open(tempname, 'wb')
for read_name, read_seq in read_set:
print >> f, '>' + read_name
print >> f, read_seq
f.close()
command = shrimp + ' ' + ' '.join(shrimp_options) + ' ' + \
tempname + ' ' + reference_filename + ' >' + tempname_out
if not verbose:
command += ' 2>/dev/null'
#f = os.popen(command, 'r')
child_pid = os.spawnl(os.P_NOWAIT, '/bin/sh', '/bin/sh', '-c',
command)
#print 'SHRiMP %d running' % my_number
def finalize():
exit_status = os.waitpid(child_pid, 0)[1]
assert exit_status == 0, 'Shrimp indicated an error'
hits = {} # read_name -> [ hit line ]
f = open(tempname_out, 'rb')
for line in f:
if line.startswith('>'):
read_name = line.split(None, 1)[0][1:]
if read_name not in hits:
hits[read_name] = []
hits[read_name].append(line)
f.close()
for read_name, read_seq in read_set:
if read_name in hits:
for hit in hits[read_name]:
output_file.write(hit)
else:
print >> unmapped_file, '>' + read_name
print >> unmapped_file, read_seq
output_file.flush()
unmapped_file.flush()
os.unlink(tempname)
dirty_filenames.remove(tempname)
os.unlink(tempname_out)
dirty_filenames.remove(tempname_out)
#print 'SHRiMP %d finished' % my_number
return finalize
shrimps = []
reader = iter_reads(config)
read_count = 0
while True:
read_set = []
read_set_bases = 0
#Read name should not include comment cruft
# - SHRIMP passes this through
# - might stuff up identification of pairs
for read_name, read_seq in reader:
read_name = read_name.split()[0]
read_set.append((read_name, read_seq))
read_set_bases += len(read_seq)
#if warn_low_threshold and len(read_seq)*7 < threshold: #Require 70% exact match
# sys.stderr.write('\n*** WARNING: Short reads, consider reducing --threshold ***\n\n')
# warn_low_threshold = False
read_count += 1
if read_set_bases >= batch_size: break
if not read_set: break
if len(shrimps) >= max_shrimps:
shrimps.pop(0)()
shrimps.append(do_shrimp(read_set))
grace.status('SHRiMPing %s' % grace.pretty_number(read_count))
while shrimps:
grace.status('Waiting for SHRiMPs to finish %d ' % len(shrimps))
shrimps.pop(0)()
grace.status('')
output_file.close()
dirty_filenames.remove(output_filename)
unmapped_file.close()
dirty_filenames.remove(unmapped_filename)
return 0
finally:
for filename in dirty_filenames:
if os.path.exists(filename):
os.unlink(filename)
def run(self):
grace.require_shrimp_2()
grace.require_samtools()
assert self.references, 'No reference sequences given'
assert self.reads or self.pairs or self.interleaved, 'No reads given'
for pair in self.pairs:
assert len(pair) == 2, 'Two files required in each pair: section'
read_sets = [ ]
for item in self.reads:
read_sets.append( ([item], False) )
for item in self.pairs:
read_sets.append( (item, True) )
for item in self.interleaved:
read_sets.append( ([item], True) )
default_options = { '-E' : None, '-T' : None, '-N' : str(grace.how_many_cpus()), '-n':'2', '-w':'200%',
'-p': 'opp-in', '-I': '0,500', '-X':None }
if self.sam_unaligned:
default_options['--sam-unaligned'] = None
if self.half_paired:
default_options['--half-paired'] = None
else:
default_options['--no-half-paired'] = None
cutoff = '55%' #Default changed in SHRiMP 2.0.2
if '-h' in self.shrimp_options:
cutoff = self.shrimp_options[ self.shrimp_options.index('-h')+1 ]
#Create working directory
workspace = self.get_workspace() #working_directory.Working(self.output_dir, must_exist=False)
workspace.setup_reference(self.references)
reference = workspace.get_reference()
reference_filename = reference.reference_fasta_filename()
#workspace = io.Workspace(self.output_dir)
#
#workspace.update_param(
# shrimp_cutoff = cutoff
#)
#
##Make copy of reference sequences
#
#reference_filename = io.abspath(self.output_dir,'reference.fa')
#reference_file = open(reference_filename,'wb')
#
#reference_genbank_filename = io.abspath(self.output_dir,'reference.gbk')
#reference_genbank_file = open(reference_genbank_filename,'wb')
#any_genbank = [ False ]
#
#def genbank_callback(name, record):
# """ Make a copy of any genbank files passed in. """
# from Bio import SeqIO
#
# SeqIO.write([record], reference_genbank_file, 'genbank')
#
# f = open(os.path.join(
# self.output_dir,
# grace.filesystem_friendly_name(name) + '.gbk'
# ), 'wb')
# SeqIO.write([record], f, 'genbank')
# f.close()
#
# any_genbank[0] = True
#
#for filename in self.references:
# for name, sequence in io.read_sequences(filename, genbank_callback=genbank_callback):
# #Don't retain any comment
# name = name.split()[0]
# io.write_fasta(reference_file, name, sequence.upper())
#
# f = open(os.path.join(
# self.output_dir,
# grace.filesystem_friendly_name(name) + '.fa'
# ), 'wb')
# io.write_fasta(f, name, sequence.upper())
# f.close()
#
#
#reference_file.close()
#reference_genbank_file.close()
#if not any_genbank[0]:
# os.unlink(reference_genbank_filename)
#
## Create an index of the reference sequences
#io.execute([
# 'samtools', 'faidx', reference_filename
#])
#Run shrimp
bam_filename = io.abspath(self.output_dir, 'alignments.bam')
bam_prefix = io.abspath(self.output_dir, 'alignments')
bam_sorted_prefix = io.abspath(self.output_dir, 'alignments_sorted')
temp_filename = io.abspath(self.output_dir, 'temp.bam')
log_filename = io.abspath(self.output_dir, 'shrimp_log.txt')
log_file = open(log_filename, 'wb')
sam_eater = sam.Bam_writer(temp_filename)
#if self.cs:
# program = 'gmapper-cs'
#else:
# program = 'gmapper-ls'
sam_header_sent = [False]
n_seen = [0]
def eat(process):
for line in process.stdout:
if line.startswith('@'):
if sam_header_sent[0]: continue
else:
n_seen[0] += 1
if n_seen[0] % 100000 == 0:
grace.status('%s alignments produced' % grace.pretty_number(n_seen[0]))
sam_eater.write_raw(line)
assert process.wait() == 0, 'shrimp failed'
sam_header_sent[0] = True
def remove_pair_options(options):
for flag in ['-p','-I']:
while flag in options:
pos = options.index(flag)
options = options[:pos] + options[pos+2:]
for flag in ['--half-paired']:
while flag in options:
pos = options.index(flag)
options = options[:pos] + options[pos+1:]
return options
if '--qv-offset' not in self.shrimp_options:
guesses = [ ]
for filenames, is_paired in read_sets:
for filename in filenames:
guesses.append(io.guess_quality_offset(filename))
assert len(set(guesses)) == 1, 'Conflicting quality offset guesses, please specify --qv-offset manually.'
default_options['--qv-offset'] = str(guesses[0])
for filenames, is_paired in read_sets:
options = self.shrimp_options[:]
has_qualities = all(
len( io.read_sequences(filename, qualities=True).next() ) == 3 #A little ugly
for filename in filenames
)
if has_qualities:
options.append( '--fastq' )
# temp_read_filename = io.abspath(working_dir, 'temp.fa')
#else:
# temp_read_filename = io.abspath(working_dir, 'temp.fq')
#try:
#if len(filenames) == 1: # gmapper can cope with gzipped and filenames[0].endswith('.fa') or filenames[0].endswith('.fq'):
# actual_read_filename = filenames[0]
#else:
# actual_read_filename = temp_read_filename
# grace.status('Copying reads')
# f = open(temp_read_filename, 'wb')
# if has_qualities:
# for reads in itertools.izip(*[ io.read_sequences(filename, qualities=True) for filename in filenames ]):
# for name, seq, qual in reads:
# io.write_fastq(f, name, seq, qual)
# else:
# for reads in itertools.izip(*[ io.read_sequences(filename) for filename in filenames ]):
# for name, seq in reads:
# io.write_fasta(f, name, seq)
# f.close()
# grace.status('')
if len(filenames) == 1:
reads_parameters = [ filenames[0] ]
else:
reads_parameters = [ '-1', filenames[0], '-2', filenames[1] ]
for flag in default_options:
if flag not in options:
options.append(flag)
if default_options[flag] is not None:
options.append(default_options[flag])
if not is_paired:
options = remove_pair_options(options)
grace.status('')
full_param = reference.shrimp_command(self.cs, options + reads_parameters)
print >> sys.stderr, 'Running', ' '.join(full_param)
p = io.run(full_param,
stdout=subprocess.PIPE,
stderr=log_file)
eat(p)
#finally:
# if os.path.exists(temp_read_filename):
# os.unlink(temp_read_filename)
log_file.close()
sam_eater.close()
grace.status('Sort')
io.execute([
'samtools', 'sort', '-n', temp_filename, bam_prefix
])
os.unlink(temp_filename)
grace.status('')
def main(args):
grace.require_shrimp_1()
n_cpus = grace.how_many_cpus()
solid, args = grace.get_flag(args, '--solid')
verbose, args = grace.get_flag(args, '--verbose')
threshold, args = grace.get_option_value(args, '--threshold', str, '68%')
stride, args = grace.get_option_value(args, '--stride', int, 1)
max_shrimps, args = grace.get_option_value(args, '--cpus', int, n_cpus)
batch_size, args = grace.get_option_value(args, '--batch-size', int, 5000000)
input_reference_filenames = [ ]
reads_filenames = [ ]
shrimp_options = [ '-h', threshold ]
if threshold.endswith('%'):
threshold = -float(threshold[:-1])/100.0
else:
threshold = int(threshold)
output_dir = [ ] #As list so can write to from function. Gah.
def front_command(args):
grace.expect_no_further_options(args)
if len(args) < 1:
return
output_dir.append(args[0])
input_reference_filenames.extend(
[ os.path.abspath(filename) for filename in args[1:] ])
def reads_command(args):
grace.expect_no_further_options(args)
reads_filenames.extend([ [ os.path.abspath(filename) ] for filename in args])
def pairs_command(args):
grace.expect_no_further_options(args)
assert len(args) == 2, 'Expected exactly two files in "pairs"'
reads_filenames.append([ os.path.abspath(filename) for filename in args ])
def shrimp_options_command(args):
shrimp_options.extend(args)
grace.execute(args, {
'reads': reads_command,
'--reads': reads_command,
'pairs': pairs_command,
'shrimp-options': shrimp_options_command,
'--shrimp-options': shrimp_options_command,
}, front_command)
if not output_dir:
print >> sys.stderr, USAGE % n_cpus
return 1
output_dir = output_dir[0]
assert input_reference_filenames, 'No reference files given'
assert reads_filenames, 'No read files given'
for filename in itertools.chain(input_reference_filenames, *reads_filenames):
assert os.path.exists(filename), '%s does not exist' % filename
if not os.path.isdir(output_dir):
os.mkdir(output_dir)
if solid:
shrimp = 'rmapper-cs'
else:
shrimp = 'rmapper-ls'
reference_filename = os.path.join(output_dir,'reference.fa')
reference_file = open(reference_filename,'wb')
total_reference_sequences = 0
total_reference_bases = 0
for input_reference_filename in input_reference_filenames:
for name, sequence in io.read_sequences(input_reference_filename):
#Don't retain any comment
name = name.split()[0]
io.write_fasta(reference_file, name, sequence)
total_reference_sequences += 1
total_reference_bases += len(sequence)
reference_file.close()
print '%s base%s in %s reference sequence%s' % (
grace.pretty_number(total_reference_bases), 's' if total_reference_bases != 1 else '',
grace.pretty_number(total_reference_sequences), 's' if total_reference_sequences != 1 else '')
assert total_reference_bases, 'Reference sequence file is empty'
config = {
'references' : input_reference_filenames,
'reads' : reads_filenames,
'stride' : stride,
'solid': solid,
'threshold': threshold,
}
config_file = open(os.path.join(output_dir, 'config.txt'), 'wb')
pprint.pprint(config, config_file)
config_file.close()
output_filename = os.path.join(output_dir, 'shrimp_hits.txt.gz')
output_file = gzip.open(output_filename, 'wb')
unmapped_filename = os.path.join(output_dir, 'unmapped.fa.gz')
unmapped_file = gzip.open(unmapped_filename, 'wb')
dirty_filenames = set()
dirty_filenames.add(output_filename)
dirty_filenames.add(unmapped_filename)
#warn_low_threshold = True
try: #Cleanup temporary files
N = [0]
def do_shrimp(read_set):
my_number = N[0]
N[0] += 1
tempname = os.path.join(output_dir,'temp%d-%d.fa' % (os.getpid(),my_number))
tempname_out = os.path.join(output_dir,'temp%d-%d.txt' % (os.getpid(),my_number))
dirty_filenames.add(tempname)
dirty_filenames.add(tempname_out)
f = open(tempname,'wb')
for read_name, read_seq in read_set:
print >> f, '>' + read_name
print >> f, read_seq
f.close()
command = shrimp + ' ' + ' '.join(shrimp_options) + ' ' + \
tempname + ' ' + reference_filename + ' >' + tempname_out
if not verbose:
command += ' 2>/dev/null'
#f = os.popen(command, 'r')
child_pid = os.spawnl(os.P_NOWAIT,'/bin/sh','/bin/sh','-c',command)
#print 'SHRiMP %d running' % my_number
def finalize():
exit_status = os.waitpid(child_pid, 0)[1]
assert exit_status == 0, 'Shrimp indicated an error'
hits = { } # read_name -> [ hit line ]
f = open(tempname_out,'rb')
for line in f:
if line.startswith('>'):
read_name = line.split(None,1)[0][1:]
if read_name not in hits:
hits[read_name] = [ ]
hits[read_name].append(line)
f.close()
for read_name, read_seq in read_set:
if read_name in hits:
for hit in hits[read_name]:
output_file.write(hit)
else:
print >> unmapped_file, '>' + read_name
print >> unmapped_file, read_seq
output_file.flush()
unmapped_file.flush()
os.unlink(tempname)
dirty_filenames.remove(tempname)
os.unlink(tempname_out)
dirty_filenames.remove(tempname_out)
#print 'SHRiMP %d finished' % my_number
return finalize
shrimps = [ ]
reader = iter_reads(config)
read_count = 0
while True:
read_set = [ ]
read_set_bases = 0
#Read name should not include comment cruft
# - SHRIMP passes this through
# - might stuff up identification of pairs
for read_name, read_seq in reader:
read_name = read_name.split()[0]
read_set.append((read_name, read_seq))
read_set_bases += len(read_seq)
#if warn_low_threshold and len(read_seq)*7 < threshold: #Require 70% exact match
# sys.stderr.write('\n*** WARNING: Short reads, consider reducing --threshold ***\n\n')
# warn_low_threshold = False
read_count += 1
if read_set_bases >= batch_size: break
if not read_set: break
if len(shrimps) >= max_shrimps:
shrimps.pop(0)()
shrimps.append( do_shrimp(read_set) )
grace.status('SHRiMPing %s' % grace.pretty_number(read_count))
while shrimps:
grace.status('Waiting for SHRiMPs to finish %d ' % len(shrimps) )
shrimps.pop(0)()
grace.status('')
output_file.close()
dirty_filenames.remove(output_filename)
unmapped_file.close()
dirty_filenames.remove(unmapped_filename)
return 0
finally:
for filename in dirty_filenames:
if os.path.exists(filename):
os.unlink(filename)
def run(self):
grace.require_shrimp_2()
grace.require_samtools()
assert self.references, 'No reference sequences given'
assert self.reads or self.pairs or self.interleaved, 'No reads given'
for pair in self.pairs:
assert len(pair) == 2, 'Two files required in each pair: section'
read_sets = []
for item in self.reads:
read_sets.append(([item], False))
for item in self.pairs:
read_sets.append((item, True))
for item in self.interleaved:
read_sets.append(([item], True))
default_options = {
'-E': None,
'-T': None,
'-N': str(grace.how_many_cpus()),
'-n': '2',
'-w': '200%',
'-p': 'opp-in',
'-I': '0,500',
'-X': None
}
if self.sam_unaligned:
default_options['--sam-unaligned'] = None
if self.half_paired:
default_options['--half-paired'] = None
else:
default_options['--no-half-paired'] = None
cutoff = '55%' #Default changed in SHRiMP 2.0.2
if '-h' in self.shrimp_options:
cutoff = self.shrimp_options[self.shrimp_options.index('-h') + 1]
#Create working directory
workspace = self.get_workspace(
) #working_directory.Working(self.output_dir, must_exist=False)
workspace.setup_reference(self.references)
reference = workspace.get_reference()
reference_filename = reference.reference_fasta_filename()
#workspace = io.Workspace(self.output_dir)
#
#workspace.update_param(
# shrimp_cutoff = cutoff
#)
#
##Make copy of reference sequences
#
#reference_filename = io.abspath(self.output_dir,'reference.fa')
#reference_file = open(reference_filename,'wb')
#
#reference_genbank_filename = io.abspath(self.output_dir,'reference.gbk')
#reference_genbank_file = open(reference_genbank_filename,'wb')
#any_genbank = [ False ]
#
#def genbank_callback(name, record):
# """ Make a copy of any genbank files passed in. """
# from Bio import SeqIO
#
# SeqIO.write([record], reference_genbank_file, 'genbank')
#
# f = open(os.path.join(
# self.output_dir,
# grace.filesystem_friendly_name(name) + '.gbk'
# ), 'wb')
# SeqIO.write([record], f, 'genbank')
# f.close()
#
# any_genbank[0] = True
#
#for filename in self.references:
# for name, sequence in io.read_sequences(filename, genbank_callback=genbank_callback):
# #Don't retain any comment
# name = name.split()[0]
# io.write_fasta(reference_file, name, sequence.upper())
#
# f = open(os.path.join(
# self.output_dir,
# grace.filesystem_friendly_name(name) + '.fa'
# ), 'wb')
# io.write_fasta(f, name, sequence.upper())
# f.close()
#
#
#reference_file.close()
#reference_genbank_file.close()
#if not any_genbank[0]:
# os.unlink(reference_genbank_filename)
#
## Create an index of the reference sequences
#io.execute([
# 'samtools', 'faidx', reference_filename
#])
#Run shrimp
bam_filename = io.abspath(self.output_dir, 'alignments.bam')
bam_prefix = io.abspath(self.output_dir, 'alignments')
bam_sorted_prefix = io.abspath(self.output_dir, 'alignments_sorted')
temp_filename = io.abspath(self.output_dir, 'temp.bam')
log_filename = io.abspath(self.output_dir, 'shrimp_log.txt')
log_file = open(log_filename, 'wb')
sam_eater = sam.Bam_writer(temp_filename)
#if self.cs:
# program = 'gmapper-cs'
#else:
# program = 'gmapper-ls'
sam_header_sent = [False]
n_seen = [0]
def eat(process):
for line in process.stdout:
if line.startswith('@'):
if sam_header_sent[0]: continue
else:
n_seen[0] += 1
if n_seen[0] % 100000 == 0:
grace.status('%s alignments produced' %
grace.pretty_number(n_seen[0]))
sam_eater.write_raw(line)
assert process.wait() == 0, 'shrimp failed'
sam_header_sent[0] = True
def remove_pair_options(options):
for flag in ['-p', '-I']:
while flag in options:
pos = options.index(flag)
options = options[:pos] + options[pos + 2:]
for flag in ['--half-paired']:
while flag in options:
pos = options.index(flag)
options = options[:pos] + options[pos + 1:]
return options
if '--qv-offset' not in self.shrimp_options:
guesses = []
for filenames, is_paired in read_sets:
for filename in filenames:
guesses.append(io.guess_quality_offset(filename))
assert len(
set(guesses)
) == 1, 'Conflicting quality offset guesses, please specify --qv-offset manually.'
default_options['--qv-offset'] = str(guesses[0])
for filenames, is_paired in read_sets:
options = self.shrimp_options[:]
has_qualities = all(
len(io.read_sequences(filename, qualities=True).next()) ==
3 #A little ugly
for filename in filenames)
if has_qualities:
options.append('--fastq')
# temp_read_filename = io.abspath(working_dir, 'temp.fa')
#else:
# temp_read_filename = io.abspath(working_dir, 'temp.fq')
#try:
#if len(filenames) == 1: # gmapper can cope with gzipped and filenames[0].endswith('.fa') or filenames[0].endswith('.fq'):
# actual_read_filename = filenames[0]
#else:
# actual_read_filename = temp_read_filename
# grace.status('Copying reads')
# f = open(temp_read_filename, 'wb')
# if has_qualities:
# for reads in itertools.izip(*[ io.read_sequences(filename, qualities=True) for filename in filenames ]):
# for name, seq, qual in reads:
# io.write_fastq(f, name, seq, qual)
# else:
# for reads in itertools.izip(*[ io.read_sequences(filename) for filename in filenames ]):
# for name, seq in reads:
# io.write_fasta(f, name, seq)
# f.close()
# grace.status('')
if len(filenames) == 1:
reads_parameters = [filenames[0]]
else:
reads_parameters = ['-1', filenames[0], '-2', filenames[1]]
for flag in default_options:
if flag not in options:
options.append(flag)
if default_options[flag] is not None:
options.append(default_options[flag])
if not is_paired:
options = remove_pair_options(options)
grace.status('')
full_param = reference.shrimp_command(self.cs,
options + reads_parameters)
print >> sys.stderr, 'Running', ' '.join(full_param)
p = io.run(full_param, stdout=subprocess.PIPE, stderr=log_file)
eat(p)
#finally:
# if os.path.exists(temp_read_filename):
# os.unlink(temp_read_filename)
log_file.close()
sam_eater.close()
grace.status('Sort')
io.execute(['samtools', 'sort', '-n', temp_filename, bam_prefix])
os.unlink(temp_filename)
grace.status('')
