def run(self):
base = os.path.split(self.prefix)[1]
annotations = [ ]
sequences = [ ]
for filename in self.filenames:
any = False
if io.is_sequence_file(filename):
sequences.append(filename)
any = True
if annotation.is_annotation_file(filename):
annotations.append(filename)
any = True
assert any, 'File is neither a recognized sequence or annotation file'
cytoband_filename = os.path.join(self.prefix,base+'_cytoband.txt')
property_filename = os.path.join(self.prefix,'property.txt')
gff_filename = os.path.join(self.prefix,base+'.gff')
output_filenames = [ cytoband_filename, property_filename, gff_filename ]
if not os.path.exists(self.prefix):
os.mkdir(self.prefix)
f = open(property_filename,'wb')
print >> f, 'ordered=true'
print >> f, 'id=%s' % base
print >> f, 'name=%s' % (self.name or base)
print >> f, 'cytobandFile=%s_cytoband.txt' % base
print >> f, 'geneFile=%s.gff' % base
print >> f, 'sequenceLocation=%s' % base
f.close()
trivia.As_gff(output=gff_filename,
filenames=annotations,
exclude=[ 'gene', 'source' ]
).run()
f_cyt = open(cytoband_filename,'wb')
for filename in sequences:
for name, seq in io.read_sequences(filename):
assert '/' not in name
f = open(os.path.join(self.prefix, name + '.txt'), 'wb')
f.write(seq)
f.close()
print >> f_cyt, '%s\t0\t%d' % (name, len(seq))
f_cyt.close()
genome_filename = self.prefix + '.genome'
if os.path.exists(genome_filename):
os.unlink(genome_filename)
io.execute(
['zip', '-j', io.abspath(genome_filename)] +
[ io.abspath(item) for item in output_filenames ]
)
for filename in output_filenames:
if os.path.exists(filename):
os.unlink(filename)
def open_bam(filename):
process = io.run([
'samtools',
'view',
'-h',
io.abspath(filename),
])
return process.stdout
def run(self):
workspace = working_directory.Working(self.output_dir)
workspace.setup_reference(self.reference)
workspace.update_param(snp_cost=self.snp_cost)
# assert os.path.exists(self.reference), 'Reference file does not exist'
# reference_filename = workspace._object_filename('reference.fa')
# if os.path.exists(reference_filename):
# os.unlink(reference_filename)
# os.symlink(os.path.relpath(self.reference, self.output_dir), reference_filename)
bam_filename = io.abspath(self.output_dir, "alignments.bam")
bam_prefix = io.abspath(self.output_dir, "alignments")
if sam.is_bam(self.input):
sort_input_filename = self.input
temp_filename = None
else:
temp_filename = io.abspath(self.output_dir, "temp.bam")
sort_input_filename = temp_filename
writer = io.Pipe_writer(temp_filename, ["samtools", "view", "-S", "-b", "-"])
f = open(self.input, "rb")
while True:
data = f.read(1 << 20)
if not data:
break
writer.write(data)
writer.close()
f.close()
grace.status("Sort")
# io.execute([
# 'samtools', 'sort', '-n', sort_input_filename, bam_prefix
# ])
sam.sort_bam(sort_input_filename, bam_prefix, by_name=True)
if temp_filename is not None:
os.unlink(temp_filename)
grace.status("")
def bam_headers(filename):
process = io.run([
'samtools',
'view',
'-H',
io.abspath(filename),
])
headers = process.stdout.read()
assert process.wait() == 0, '"samtools view -H ..." failed'
return headers
def bam_headers(filename):
process = io.run([
'samtools',
'view',
'-H',
io.abspath(filename),
])
headers = process.stdout.read()
assert process.wait() == 0, '"samtools view -H ..." failed'
return headers
def run(self):
workspace = working_directory.Working(self.output_dir)
workspace.setup_reference(self.reference)
workspace.update_param(snp_cost = self.snp_cost)
#assert os.path.exists(self.reference), 'Reference file does not exist'
#reference_filename = workspace._object_filename('reference.fa')
#if os.path.exists(reference_filename):
# os.unlink(reference_filename)
#os.symlink(os.path.relpath(self.reference, self.output_dir), reference_filename)
bam_filename = io.abspath(self.output_dir, 'alignments.bam')
bam_prefix = io.abspath(self.output_dir, 'alignments')
if sam.is_bam(self.input):
sort_input_filename = self.input
temp_filename = None
else:
temp_filename = io.abspath(self.output_dir, 'temp.bam')
sort_input_filename = temp_filename
writer = io.Pipe_writer(temp_filename, ['samtools', 'view', '-S', '-b', '-'])
f = open(self.input, 'rb')
while True:
data = f.read(1<<20)
if not data: break
writer.write(data)
writer.close()
f.close()
grace.status('Sort')
#io.execute([
# 'samtools', 'sort', '-n', sort_input_filename, bam_prefix
#])
sam.sort_bam(sort_input_filename, bam_prefix, by_name=True)
if temp_filename is not None:
os.unlink(temp_filename)
grace.status('')
def run(self):
workspace = working_directory.Working(self.output_dir)
workspace.setup_reference(self.reference)
workspace.update_param(snp_cost = self.snp_cost)
#assert os.path.exists(self.reference), 'Reference file does not exist'
#reference_filename = workspace._object_filename('reference.fa')
#if os.path.exists(reference_filename):
# os.unlink(reference_filename)
#os.symlink(os.path.relpath(self.reference, self.output_dir), reference_filename)
bam_filename = io.abspath(self.output_dir, 'alignments.bam')
bam_prefix = io.abspath(self.output_dir, 'alignments')
if sam.is_bam(self.input):
sort_input_filename = self.input
temp_filename = None
else:
temp_filename = io.abspath(self.output_dir, 'temp.bam')
sort_input_filename = temp_filename
writer = io.Pipe_writer(temp_filename, ['samtools', 'view', '-S', '-b', '-'])
f = open(self.input, 'rb')
while True:
data = f.read(1<<20)
if not data: break
writer.write(data)
writer.close()
f.close()
grace.status('Sort')
io.execute([
'samtools', 'sort', '-n', sort_input_filename, bam_prefix
])
if temp_filename is not None:
os.unlink(temp_filename)
grace.status('')
def __init__(self, filename):
assert os.path.exists(filename), filename + ' does not exist'
if is_bam(filename):
self.process = io.run([
'samtools',
'view',
io.abspath(filename),
])
## Godawful hack
#self.process.stdout = io.process_buffer(self.process.stdout)
self.file = self.process.stdout
else:
self.process = None
self.file = io.open_possibly_compressed_file(filename)
def __init__(self, filename):
assert os.path.exists(filename), filename + ' does not exist'
if is_bam(filename):
self.process = io.run([
'samtools',
'view',
io.abspath(filename),
])
## Godawful hack
#self.process.stdout = io.process_buffer(self.process.stdout)
self.file = self.process.stdout
else:
self.process = None
self.file = io.open_possibly_compressed_file(filename)
def open_bam(filename):
process = io.run([
'samtools', 'view', '-h',
io.abspath(filename),
])
return process.stdout
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'
io.check_name_uniqueness(self.reads, self.pairs, self.interleaved)
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))
#Create working directory
workspace = self.get_workspace()
workspace.setup_reference(self.references)
workspace.update_param(snp_cost=25)
reference = workspace.get_reference()
reference_filename = reference.reference_fasta_filename()
cores = min(self.cores, legion.coordinator().get_cores())
default_options = {
'-E': None,
'-T': None,
'-N': str(cores),
'-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]
#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)
sam_header_sent = [False]
n_seen = [0]
def eat(f):
for line in f:
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)
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
for i, (filenames, is_paired) in enumerate(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')
if len(filenames) == 1:
reads_parameters = [filenames[0]]
else:
reads_parameters = ['-1', filenames[0], '-2', filenames[1]]
if '--qv-offset' not in self.shrimp_options:
#guesses = [ ]
#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])
default_options['--qv-offset'] = str(
io.guess_quality_offset(*filenames))
default_options['--read-group'] = '%s,%s' % (
workspace.name.replace(',',
'_'), workspace.name.replace(',', '_'))
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)
with io.pipe_from(full_param, stderr=log_file, cores=cores) as f:
eat(f)
log_file.close()
sam_eater.close()
grace.status('Sort')
#io.execute([
# 'samtools', 'sort', '-n', temp_filename, bam_prefix
#])
sam.sort_bam(temp_filename, bam_prefix, by_name=True, cores=self.cores)
os.unlink(temp_filename)
grace.status('')
def absolutize(filename):
if options.prefix is not None:
return options.prefix + filename
else:
return io.abspath(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"
io.check_name_uniqueness(self.reads, self.pairs, self.interleaved)
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))
# Create working directory
workspace = self.get_workspace()
workspace.setup_reference(self.references)
workspace.update_param(snp_cost=25)
reference = workspace.get_reference()
reference_filename = reference.reference_fasta_filename()
cores = min(self.cores, legion.coordinator().get_cores())
default_options = {
"-E": None,
"-T": None,
"-N": str(cores),
"-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]
# 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)
sam_header_sent = [False]
n_seen = [0]
def eat(f):
for line in f:
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)
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
for i, (filenames, is_paired) in enumerate(read_sets):
options = self.shrimp_options[:]
has_qualities = all(
len(io.read_sequences(filename, qualities=True).next()) == 3 for filename in filenames # A little ugly
)
if has_qualities:
options.append("--fastq")
if len(filenames) == 1:
reads_parameters = [filenames[0]]
else:
reads_parameters = ["-1", filenames[0], "-2", filenames[1]]
if "--qv-offset" not in self.shrimp_options:
guesses = []
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])
default_options["--read-group"] = "%s,%s" % (
workspace.name.replace(",", "_"),
workspace.name.replace(",", "_"),
)
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)
with io.pipe_from(full_param, stderr=log_file, cores=cores) as f:
eat(f)
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 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'
io.check_name_uniqueness(self.reads, self.pairs, self.interleaved)
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) )
#Create working directory
workspace = self.get_workspace()
workspace.setup_reference(self.references)
workspace.update_param(snp_cost=25)
reference = workspace.get_reference()
reference_filename = reference.reference_fasta_filename()
cores = min(self.cores, legion.coordinator().get_cores())
default_options = {
'-E' : None,
'-T' : None,
'-N' : str(cores),
'-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 ]
#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)
sam_header_sent = [False]
n_seen = [0]
def eat(f):
for line in f:
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)
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
for i, (filenames, is_paired) in enumerate(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' )
if len(filenames) == 1:
reads_parameters = [ filenames[0] ]
else:
reads_parameters = [ '-1', filenames[0], '-2', filenames[1] ]
if '--qv-offset' not in self.shrimp_options:
#guesses = [ ]
#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])
default_options['--qv-offset'] = str( io.guess_quality_offset(*filenames) )
default_options['--read-group'] = '%s,%s' % (
workspace.name.replace(',','_'),
workspace.name.replace(',','_')
)
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)
with io.pipe_from(full_param,
stderr=log_file,
cores=cores) as f:
eat(f)
log_file.close()
sam_eater.close()
grace.status('Sort')
#io.execute([
# 'samtools', 'sort', '-n', temp_filename, bam_prefix
#])
sam.sort_bam(temp_filename, bam_prefix, by_name=True, cores=self.cores)
os.unlink(temp_filename)
grace.status('')
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 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('')
