def main():
'''
Script execution starts here.
'''
args = get_arguments()
if args.align and not find_program('muscle'):
quit_with_error(
'Muscle must be installed to produce an aligned output.')
gene_seqs = dict(load_fasta_file(args.gene_seqs))
gene_seqs = {
fix_allele_name(name): seq
for name, seq in gene_seqs.iteritems()
}
mlst = MlstScheme(scheme_table=args.scheme)
seqs_by_type_and_gene = {} # key = ST value = list of gene sequences
for st_num in get_types(args, mlst):
seqs_by_type_and_gene[st_num] = []
alleles = mlst.type_to_alleles[st_num]
for allele in alleles:
if allele not in gene_seqs:
quit_with_error('Allele ' + allele +
' not in gene sequence FASTA')
seqs_by_type_and_gene[st_num].append(gene_seqs[allele])
if args.align:
seqs_by_type_and_gene = align_seqs(seqs_by_type_and_gene,
args.muscle_args)
cat_seqs = sorted([(st, ''.join(seqs))
for st, seqs in seqs_by_type_and_gene.iteritems()])
save_fasta(cat_seqs, args.out)
def align_seqs(seqs_by_type, muscle_args):
'''
Uses Muscle to align the sequences. Alignments are performed independently for each gene (the
sequences will be concatenated later).
'''
st_nums = seqs_by_type.keys()
aligned_seqs_by_type = {st_num: [] for st_num in st_nums}
gene_count = len(seqs_by_type.itervalues().next())
command = ['muscle'] + muscle_args.split()
for i in range(gene_count):
gene_seqs = [(st_num, seqs[i])
for st_num, seqs in seqs_by_type.iteritems()]
muscle_input = ''
for gene_seq in gene_seqs:
muscle_input += '>' + str(gene_seq[0]) + '\n'
muscle_input += add_line_breaks_to_sequence(gene_seq[1], 60)
process = subprocess.Popen(command,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
muscle_output, err = process.communicate(input=muscle_input)
if '*** ERROR ***' in err:
muscle_error = err.split('*** ERROR ***')[1].strip()
quit_with_error('Muscle alignment failed\n' + muscle_error)
if 'Invalid command line option' in err:
muscle_error = err.split('\n')[0].strip()
quit_with_error('Muscle alignment failed\n' + muscle_error)
aligned_seqs = load_fasta_lines(muscle_output)
for st_num, seq in aligned_seqs:
aligned_seqs_by_type[int(st_num)].append(seq)
return aligned_seqs_by_type
def align_seqs(seqs_by_type, muscle_args):
"""
Uses Muscle to align the sequences. Alignments are performed independently for each gene (the
sequences will be concatenated later).
"""
st_nums = seqs_by_type.keys()
aligned_seqs_by_type = {st_num: [] for st_num in st_nums}
gene_count = len(seqs_by_type.itervalues().next())
command = ["muscle"] + muscle_args.split()
for i in range(gene_count):
gene_seqs = [(st_num, seqs[i]) for st_num, seqs in seqs_by_type.iteritems()]
muscle_input = ""
for gene_seq in gene_seqs:
muscle_input += ">" + str(gene_seq[0]) + "\n"
muscle_input += add_line_breaks_to_sequence(gene_seq[1], 60)
process = subprocess.Popen(command, stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
muscle_output, err = process.communicate(input=muscle_input)
if "*** ERROR ***" in err:
muscle_error = err.split("*** ERROR ***")[1].strip()
quit_with_error("Muscle alignment failed\n" + muscle_error)
if "Invalid command line option" in err:
muscle_error = err.split("\n")[0].strip()
quit_with_error("Muscle alignment failed\n" + muscle_error)
aligned_seqs = load_fasta_lines(muscle_output)
for st_num, seq in aligned_seqs:
aligned_seqs_by_type[int(st_num)].append(seq)
return aligned_seqs_by_type
def main():
"""
Script execution starts here.
"""
args = get_arguments()
if args.align and not find_program("muscle"):
quit_with_error("Muscle must be installed to produce an aligned output.")
gene_seqs = dict(load_fasta_file(args.gene_seqs))
gene_seqs = {fix_allele_name(name): seq for name, seq in gene_seqs.iteritems()}
mlst = MlstScheme(scheme_table=args.scheme)
seqs_by_type_and_gene = {} # key = ST value = list of gene sequences
for st_num in get_types(args, mlst):
seqs_by_type_and_gene[st_num] = []
alleles = mlst.type_to_alleles[st_num]
for allele in alleles:
if allele not in gene_seqs:
quit_with_error("Allele " + allele + " not in gene sequence FASTA")
seqs_by_type_and_gene[st_num].append(gene_seqs[allele])
if args.align:
seqs_by_type_and_gene = align_seqs(seqs_by_type_and_gene, args.muscle_args)
cat_seqs = sorted([(st, "".join(seqs)) for st, seqs in seqs_by_type_and_gene.iteritems()])
save_fasta(cat_seqs, args.out)
def get_types(args, mlst):
"""
This function returns a list of the sequence types to output based on the user's arguments.
It also checks for problems with the chosen types.
"""
if args.all:
types = mlst.type_to_alleles.keys()
if not types:
quit_with_error("The given MLST scheme has no sequence types.")
else:
types = args.types.split(",")
types = sorted([string_to_int(x) for x in types])
if None in types:
quit_with_error("One or more sequence types is incorrectly formatted.")
for st_num in types:
if st_num not in mlst.type_to_alleles:
quit_with_error("Sequence type " + str(st_num) + " is not in the given MLST scheme.")
if len(types) != len(set(types)):
quit_with_error("Not all sequence types are unique (there are duplicates).")
return types
def get_types(args, mlst):
'''
This function returns a list of the sequence types to output based on the user's arguments.
It also checks for problems with the chosen types.
'''
if args.all:
types = mlst.type_to_alleles.keys()
if not types:
quit_with_error('The given MLST scheme has no sequence types.')
else:
types = args.types.split(',')
types = sorted([string_to_int(x) for x in types])
if None in types:
quit_with_error('One or more sequence types is incorrectly formatted.')
for st_num in types:
if st_num not in mlst.type_to_alleles:
quit_with_error('Sequence type ' + str(st_num) +
' is not in the given MLST scheme.')
if len(types) != len(set(types)):
quit_with_error(
'Not all sequence types are unique (there are duplicates).')
return types