def write_misasm_broken_ctgs(contigs_file,
breaks,
out_prefix,
in_gff=None,
in_gff_name=None):
current_path = os.getcwd()
os.chdir('ctg_alignments')
if in_gff and in_gff_name:
with open(in_gff_name, 'w') as f:
for i in in_gff.keys():
for j in in_gff[i]:
f.write(str(j) + '\n')
x = SeqReader("../../" + contigs_file)
f = open(out_prefix + ".misasm.break.fa", 'w')
for header, seq in x.parse_fasta():
header = header[1:]
if header not in breaks:
f.write(">" + header + "\n")
f.write(seq + "\n")
else:
# Break the contig
ctg_len = len(seq)
break_list = [0] + sorted(breaks[header]) + [ctg_len]
for i in range(len(break_list) - 1):
f.write(">" + header + "_misasm_break:" + str(break_list[i]) +
"-" + str(break_list[i + 1]) + "\n")
f.write(seq[break_list[i]:break_list[i + 1]] + "\n")
os.chdir(current_path)
def make_gaps_tree(in_file):
# A dictionary to store an interval tree for each chromosome header.
all_trees = dict()
x = SeqReader(in_file)
if in_file.endswith(".gz"):
for header, sequence in x.parse_gzip_fasta():
# Remove the greater than sign and only get first token if delimited by spaces
header = header[1:].split(' ')[0]
all_trees[header] = IntervalTree()
gap_sequence = GapSequence(sequence)
all_coordinates = [(m.start(0), m.end(0))
for m in gap_sequence.get_gap_coords()]
for i in all_coordinates:
all_trees[header][i[0]:i[1]] = i
else:
for header, sequence in x.parse_fasta():
# Remove the greater than sign and only get first token if delimited by spaces
header = header[1:].split(' ')[0]
all_trees[header] = IntervalTree()
gap_sequence = GapSequence(sequence)
all_coordinates = [(m.start(0), m.end(0))
for m in gap_sequence.get_gap_coords()]
for i in all_coordinates:
all_trees[header][i[0]:i[1]] = i
return all_trees
def create_pseudomolecules(in_contigs_file, in_unique_contigs, gap_size):
"""
Need to make a translation table for easy lift-over.
:param in_contigs_file:
:param in_unique_contigs:
:param gap_size:
:return:
"""
# First, read all of the contigs into memory
remaining_contig_headers = []
all_seqs = dict()
x = SeqReader('../' + in_contigs_file)
for header, seq in x.parse_fasta():
remaining_contig_headers.append(header.split(' ')[0])
all_seqs[header.split(' ')[0]] = seq
# Get all reference chromosomes
all_chroms = sorted(
list(
set([
in_unique_contigs[i].ref_chrom
for i in in_unique_contigs.keys()
])))
# Iterate through each orderings file and store sequence in a dictionary
all_pms = dict()
for this_chrom in all_chroms:
all_pms[this_chrom] = ''
orderings_file = 'orderings/' + this_chrom + '_orderings.txt'
orderings = get_orderings(orderings_file)
for line in orderings:
# Mark that we have seen this contig
remaining_contig_headers.pop(
remaining_contig_headers.index('>' + line[0]))
if line[1] == '+':
all_pms[this_chrom] += all_seqs['>' + line[0]]
all_pms[this_chrom] += ''.join('N' for i in range(gap_size))
else:
assert line[1] == '-'
all_pms[this_chrom] += reverse_complement(all_seqs['>' +
line[0]])
all_pms[this_chrom] += ''.join('N' for i in range(gap_size))
all_pms[this_chrom] += '\n'
# Get unincorporated sequences and place them in Chr0
all_pms['Chr0'] = ''
for header in remaining_contig_headers:
all_pms['Chr0'] += all_seqs[header]
all_pms['Chr0'] += ''.join('N' for i in range(gap_size))
all_pms['Chr0'] += '\n'
# Write the final sequences out to a file
with open('ragoo.fasta', 'w') as f:
f.write('>Chr0_RaGOO\n')
f.write(all_pms['Chr0'])
for header in all_chroms:
f.write('>' + header + '_RaGOO\n')
f.write(all_pms[header])
def create_pseudomolecules(in_contigs_file,
in_unique_contigs,
gap_size,
chr0=True):
"""
Need to make a translation table for easy lift-over.
:param in_contigs_file:
:param in_unique_contigs:
:param gap_size:
:return:
"""
# First, read all of the contigs into memory
remaining_contig_headers = []
all_seqs = OrderedDict()
x = SeqReader(in_contigs_file)
for header, seq in x.parse_fasta():
remaining_contig_headers.append(header.split(' ')[0])
all_seqs[header.split(' ')[0]] = seq
# Get all reference chromosomes
all_chroms = sorted(
list(
set([
in_unique_contigs[i].ref_chrom
for i in in_unique_contigs.keys()
])))
# Iterate through each orderings file and store sequence in a dictionary
all_pms = dict()
pad = ''.join('N' for i in range(gap_size))
for this_chrom in all_chroms:
orderings_file = 'orderings/' + this_chrom + '_orderings.txt'
orderings = get_orderings(orderings_file)
if orderings:
seq_list = []
for line in orderings:
# Mark that we have seen this contig
remaining_contig_headers.pop(
remaining_contig_headers.index('>' + line[0]))
if line[1] == '+':
seq_list.append(all_seqs['>' + line[0]])
else:
assert line[1] == '-'
seq_list.append(reverse_complement(all_seqs['>' +
line[0]]))
all_pms[this_chrom] = pad.join(seq_list)
all_pms[this_chrom] += '\n'
# Get unincorporated sequences and place them in Chr0
if remaining_contig_headers:
if chr0:
chr0_headers = []
chr0_seq_list = []
for header in remaining_contig_headers:
chr0_headers.append(header)
chr0_seq_list.append(all_seqs[header])
all_pms['Chr0'] = pad.join(chr0_seq_list)
all_pms['Chr0'] += '\n'
# Write out the list of chr0 headers
f_chr0_g = open('groupings/Chr0_contigs.txt', 'w')
f_chr0_o = open('orderings/Chr0_orderings.txt', 'w')
for i in chr0_headers:
f_chr0_g.write(i[1:] + "\t" + "0" + '\n')
f_chr0_o.write(i[1:] + '\t' + "+" + '\t' + "0" + '\t' + "0" +
'\n')
f_chr0_g.close()
f_chr0_o.close()
else:
# Instead of making a chromosome 0, add the unplaced sequences as is.
for header in remaining_contig_headers:
all_pms[header[1:]] = all_seqs[header] + "\n"
f_chr0_g = open('groupings/' + header[1:] + '_contigs.txt',
'w')
f_chr0_o = open('orderings/' + header[1:] + '_orderings.txt',
'w')
f_chr0_g.write(header[1:] + "\t" + "0" + '\n')
f_chr0_o.write(header[1:] + '\t' + "+" + '\t' + "0" + '\t' +
"0" + '\n')
f_chr0_g.close()
f_chr0_o.close()
# Write the final sequences out to a file
with open('ragoo.fasta', 'w') as f:
for out_header in all_pms:
f.write(">" + out_header + "_RaGOO\n")
f.write(all_pms[out_header])
def read_gz_contigs(in_file):
d = dict()
x = SeqReader(in_file)
for header, seq in x.parse_gzip_fasta():
d[header.replace('>', '').split(' ')[0]] = seq
return d