def generate_backbone(self):
_LOG.info("Reading input sequences: %s" %(self.options.sequence_file))
sequences = MutableAlignment()
sequences.read_file_object(self.options.sequence_file)
if (options().backbone_size is None):
options().backbone_size = min(100,int(.20*sequences.get_num_taxa()))
_LOG.info("Backbone size set to: %d" %(options().backbone_size))
backbone_sequences = sequences.get_hard_sub_alignment(random.sample(sequences.keys(), options().backbone_size))
[sequences.pop(i) for i in backbone_sequences.keys()]
_LOG.info("Writing query and backbone set. ")
query = get_temp_file("query", "backbone", ".fas")
backbone = get_temp_file("backbone", "backbone", ".fas")
_write_fasta(sequences, query)
_write_fasta(backbone_sequences, backbone)
_LOG.info("Generating sate backbone alignment and tree. ")
satealignJob = SateAlignJob()
moleculeType = options().molecule
if (options().molecule == 'amino'):
moleculeType = 'protein'
satealignJob.setup(backbone,options().backbone_size,self.options.outdir,moleculeType,options().cpu)
satealignJob.run()
satealignJob.read_results()
options().placement_size = self.options.backbone_size
options().alignment_file = open(self.options.outdir + "/sate.fasta")
options().tree_file = open(self.options.outdir + "/sate.fasttree")
_LOG.info("Backbone alignment written to %s.\nBackbone tree written to %s" % (options().alignment_file, options().tree_file))
options().fragment_file = query
def check_options(self):
self.check_outputprefix()
options().info_file = "A_dummy_value"
# Check to see if tree/alignment/fragment file provided, if not,
# generate it from sequence file
if ((not options().tree_file is None)
and (not options().alignment_file is None)
and (not options().sequence_file is None)):
options().fragment_file = options().sequence_file
elif ((options().tree_file is None)
and (options().alignment_file is None)
and (not options().sequence_file is None)):
self.generate_backbone()
else:
_LOG.error(
("Either specify the backbone alignment and tree and query "
"sequences or only the query sequences. Any other "
"combination is invalid"))
exit(-1)
sequences = MutableAlignment()
sequences.read_file_object(open(self.options.alignment_file.name))
backbone_size = sequences.get_num_taxa()
if options().backbone_size is None:
options().backbone_size = backbone_size
assert options().backbone_size == backbone_size, (
("Backbone parameter needs to match actual size of backbone; "
"backbone parameter:%s backbone_size:%s") %
(options().backbone_size, backbone_size))
if options().placement_size is None:
options().placement_size = options().backbone_size
return ExhaustiveAlgorithm.check_options(self)
def check_options(self):
options().info_file = "A_dummy_value"
#Check to see if tree/alignment/fragment file provided, if not, generate it
#from sequence file
if not options().tree_file is None and not options(
).alignment_file is None and not options().sequence_file is None:
options().fragment_file = options().sequence_file
elif options().tree_file is None and options(
).alignment_file is None and not options().sequence_file is None:
self.generate_backbone()
else:
_LOG.error(
"Either specify the backbone alignment and tree and query sequences or only the query sequences. Any other combination is invalid"
)
exit(-1)
sequences = MutableAlignment()
sequences.read_file_object(open(self.options.alignment_file.name))
backbone_size = sequences.get_num_taxa()
if options().backbone_size is None:
options().backbone_size = backbone_size
assert options().backbone_size == backbone_size, (
"Backbone parameter needs to match actual size of backbone; backbone parameter:%s backbone_size:%s"
% (options().backbone_size, backbone_size))
if options().placement_size is None:
options().placement_size = options().backbone_size
if options().alignment_size is None:
_LOG.info(
"Alignment subset size not given. Calculating subset size. ")
alignment = MutableAlignment()
alignment.read_file_object(open(self.options.alignment_file.name))
if (options().molecule == 'amino'):
_LOG.warning(
"Automated alignment subset selection not implemented for protein alignment. Setting to 10."
)
options().alignment_size = 10
else:
(averagep, maxp) = alignment.get_p_distance()
align_size = 10
if (averagep > .60):
while (align_size * 2 < alignment.get_num_taxa()):
align_size = align_size * 2
_LOG.info(
"Average p-distance of backbone is %f0.2. Alignment subset size set to %d. "
% (averagep, align_size))
options().alignment_size = align_size
return ExhaustiveAlgorithm.check_options(self)
def generate_backbone(self):
_LOG.info("Reading input sequences: %s" %(self.options.sequence_file))
sequences = MutableAlignment()
sequences.read_file_object(self.options.sequence_file)
fragments = MutableAlignment()
if (options().median_full_length is not None):
if (options().median_full_length == -1):
seq_lengths = sorted([len(seq) for seq in sequences.values()])
lengths = len(seq_lengths)
if lengths % 2:
options().median_full_length = (seq_lengths[lengths / 2] + seq_lengths[lengths / 2 - 1]) / 2.0
else:
options().median_full_length = seq_lengths[lengths / 2]
(min_length,max_length) = (int(options().median_full_length*(1-options().backbone_threshold)),int(options().median_full_length*(1+options().backbone_threshold)))
frag_names = [name for name in sequences if len(sequences[name]) > max_length or len(sequences[name]) < min_length]
if (len(frag_names) > 0):
fragments = sequences.get_hard_sub_alignment(frag_names)
[sequences.pop(i) for i in fragments.keys()]
if (options().backbone_size is None):
options().backbone_size = min(1000,int(sequences.get_num_taxa()))
_LOG.info("Backbone size set to: %d" %(options().backbone_size))
if (options().backbone_size > len(sequences.keys())):
options().backbone_size = len(sequences.keys())
backbone_sequences = sequences.get_hard_sub_alignment(random.sample(sequences.keys(), options().backbone_size))
[sequences.pop(i) for i in backbone_sequences.keys()]
_LOG.info("Writing backbone set. ")
backbone = get_temp_file("backbone", "backbone", ".fas")
_write_fasta(backbone_sequences, backbone)
_LOG.info("Generating pasta backbone alignment and tree. ")
pastaalignJob = PastaAlignJob()
moleculeType = options().molecule
if (options().molecule == 'amino'):
moleculeType = 'protein'
pastaalignJob.setup(backbone,options().backbone_size,self.options.outdir,moleculeType,options().cpu)
pastaalignJob.run()
pastaalignJob.read_results()
options().placement_size = self.options.backbone_size
options().alignment_file = open(self.options.outdir + "/pasta.fasta")
options().tree_file = open(self.options.outdir + "/pasta.fasttree")
_LOG.info("Backbone alignment written to %s.\nBackbone tree written to %s" % (options().alignment_file, options().tree_file))
sequences.set_alignment(fragments)
if (len(sequences) == 0):
_LOG.info("No query sequences to align. Final alignment saved as %s" % self.get_output_filename("alignment.fasta"))
shutil.copyfile(self.options.outdir + "/pasta.fasta", self.get_output_filename("alignment.fasta"))
sys.exit(0)
else:
query = get_temp_file("query", "backbone", ".fas")
options().fragment_file = query
_write_fasta(sequences, query)
def check_options(self):
options().info_file = "A_dummy_value"
#Check to see if tree/alignment/fragment file provided, if not, generate it
#from sequence file
if not options().tree_file is None and not options().alignment_file is None and not options().sequence_file is None:
options().fragment_file = options().sequence_file
elif options().tree_file is None and options().alignment_file is None and not options().sequence_file is None:
self.generate_backbone()
else:
_LOG.error("Either specify the backbone alignment and tree and query sequences or only the query sequences. Any other combination is invalid")
exit(-1)
sequences = MutableAlignment()
sequences.read_file_object(open(self.options.alignment_file.name))
backbone_size = sequences.get_num_taxa()
if options().backbone_size is None:
options().backbone_size = backbone_size
assert options().backbone_size == backbone_size, ("Backbone parameter needs to match actual size of backbone; backbone parameter:%s backbone_size:%s"
%(options().backbone_size, backbone_size))
if options().placement_size is None:
options().placement_size = options().backbone_size
if options().alignment_size is None:
_LOG.info("Alignment subset size not given. Calculating subset size. ")
alignment = MutableAlignment()
alignment.read_file_object(open(self.options.alignment_file.name))
if (options().molecule == 'amino'):
_LOG.warning("Automated alignment subset selection not implemented for protein alignment. Setting to 10.")
options().alignment_size = 10
else:
(averagep,maxp) = alignment.get_p_distance()
align_size = 10
if (averagep > .60):
while (align_size*2 < alignment.get_num_taxa()):
align_size = align_size * 2
_LOG.info("Average p-distance of backbone is %f0.2. Alignment subset size set to %d. " % (averagep,align_size))
options().alignment_size = align_size
return ExhaustiveAlgorithm.check_options(self)
def check_options(self):
options().info_file = "A_dummy_value"
#Check to see if tree/alignment/fragment file provided, if not, generate it
#from sequence file
if not options().tree_file is None and not options().alignment_file is None and not options().sequence_file is None:
options().fragment_file = options().sequence_file
elif options().tree_file is None and options().alignment_file is None and not options().sequence_file is None:
self.generate_backbone()
else:
_LOG.error("Either specify the backbone alignment and tree and query sequences or only the query sequences. Any other combination is invalid")
exit(-1)
sequences = MutableAlignment()
sequences.read_file_object(open(self.options.alignment_file.name))
backbone_size = sequences.get_num_taxa()
if options().backbone_size is None:
options().backbone_size = backbone_size
assert options().backbone_size == backbone_size, ("Backbone parameter needs to match actual size of backbone; backbone parameter:%s backbone_size:%s"
%(options().backbone_size, backbone_size))
if options().placement_size is None:
options().placement_size = options().backbone_size
return ExhaustiveAlgorithm.check_options(self)
def generate_backbone(self):
_LOG.info("Reading input sequences: %s" % (self.options.sequence_file))
sequences = MutableAlignment()
sequences.read_file_object(self.options.sequence_file)
if (options().backbone_size is None):
options().backbone_size = min(100,
int(.20 * sequences.get_num_taxa()))
_LOG.info("Backbone size set to: %d" % (options().backbone_size))
backbone_sequences = sequences.get_hard_sub_alignment(
random.sample(sequences.keys(),
options().backbone_size))
[sequences.pop(i) for i in backbone_sequences.keys()]
_LOG.info("Writing query and backbone set. ")
query = get_temp_file("query", "backbone", ".fas")
backbone = get_temp_file("backbone", "backbone", ".fas")
_write_fasta(sequences, query)
_write_fasta(backbone_sequences, backbone)
_LOG.info("Generating sate backbone alignment and tree. ")
satealignJob = SateAlignJob()
moleculeType = options().molecule
if (options().molecule == 'amino'):
moleculeType = 'protein'
satealignJob.setup(backbone,
options().backbone_size, self.options.outdir,
moleculeType,
options().cpu)
satealignJob.run()
satealignJob.read_results()
options().placement_size = self.options.backbone_size
options().alignment_file = open(self.options.outdir + "/sate.fasta")
options().tree_file = open(self.options.outdir + "/sate.fasttree")
_LOG.info(
"Backbone alignment written to %s.\nBackbone tree written to %s" %
(options().alignment_file, options().tree_file))
options().fragment_file = query
def generate_backbone(self):
_LOG.info("Reading input sequences: %s" % (self.options.sequence_file))
sequences = MutableAlignment()
sequences.read_file_object(self.options.sequence_file)
sequences.degap()
fragments = MutableAlignment()
if (options().median_full_length is not None
or options().full_length_range is not None):
if (options().median_full_length == -1):
seq_lengths = sorted(
[len(seq) for seq in list(sequences.values())])
lengths = len(seq_lengths)
l2 = int(lengths / 2)
if lengths % 2:
options().median_full_length = (seq_lengths[l2] +
seq_lengths[l2 + 1]) / 2.0
else:
options().median_full_length = seq_lengths[l2]
if options().full_length_range is not None:
L = sorted(int(x) for x in options().full_length_range.split())
min_length = L[0]
max_length = L[1]
else:
(min_length,
max_length) = (int(options().median_full_length *
(1 - options().backbone_threshold)),
int(options().median_full_length *
(1 + options().backbone_threshold)))
_LOG.info(
"Full length sequences are set to be from %d to %d character long"
% (min_length, max_length))
frag_names = [
name for name in sequences if len(sequences[name]) > max_length
or len(sequences[name]) < min_length
]
if (len(frag_names) > 0):
_LOG.info("Detected %d fragmentary sequences" %
len(frag_names))
fragments = sequences.get_hard_sub_alignment(frag_names)
[sequences.pop(i) for i in list(fragments.keys())]
if (options().backbone_size is None):
options().backbone_size = min(1000, int(sequences.get_num_taxa()))
_LOG.info("Backbone size set to: %d" % (options().backbone_size))
if (options().backbone_size > len(list(sequences.keys()))):
options().backbone_size = len(list(sequences.keys()))
sample = sorted(
random.sample(sorted(list(sequences.keys())),
options().backbone_size))
backbone_sequences = sequences.get_hard_sub_alignment(sample)
_LOG.debug("Backbone: %s" % (sorted(list(backbone_sequences.keys()))))
[sequences.pop(i) for i in list(backbone_sequences.keys())]
_LOG.info("Writing backbone set. ")
backbone = get_temp_file("backbone", "backbone", ".fas")
_write_fasta(backbone_sequences, backbone)
_LOG.info("Generating pasta backbone alignment and tree. ")
pastaalignJob = PastaAlignJob()
moleculeType = options().molecule
if (options().molecule == 'amino'):
moleculeType = 'protein'
pastaalignJob.setup(backbone,
options().backbone_size, moleculeType,
options().cpu, **vars(options().pasta))
pastaalignJob.run()
(a_file, t_file) = pastaalignJob.read_results()
shutil.copyfile(t_file, self.get_output_filename("pasta.fasttree"))
shutil.copyfile(a_file, self.get_output_filename("pasta.fasta"))
options().placement_size = self.options.backbone_size
options().alignment_file = open(
self.get_output_filename("pasta.fasta"))
options().tree_file = open(self.get_output_filename("pasta.fasttree"))
_LOG.info(
"Backbone alignment written to %s.\nBackbone tree written to %s" %
(options().alignment_file, options().tree_file))
sequences.set_alignment(fragments)
if (len(sequences) == 0):
sequences = MutableAlignment()
sequences.read_file_object(open(self.options.alignment_file.name))
self.results = ExtendedAlignment(fragment_names=[])
self.results.set_alignment(sequences)
_LOG.info(
"No query sequences to align. Final alignment saved as %s" %
self.get_output_filename("alignment.fasta"))
self.output_results()
sys.exit(0)
else:
query = get_temp_file("query", "backbone", ".fas")
options().fragment_file = query
_write_fasta(sequences, query)
