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136 | #(c) 2013-2014 by Authors
#This file is a part of Ragout program.
#Released under the BSD license (see LICENSE file)
from itertools import repeat
import logging
from ragout.parsers.fasta_parser import write_fasta_dict, reverse_complement
logger = logging.getLogger()
def output_links(scaffolds, out_links):
"""
Outputs pretty table with information about adjacencies
"""
HEADER = ["contig_1", "contig_2", "gap", "ref_support", "~>"]
COL_GAP = 4
with open(out_links, "w") as f:
for scf in scaffolds:
rows = []
for left, right in zip(scf.contigs[:-1], scf.contigs[1:]):
supp_genomes = ",".join(sorted(left.link.supporting_genomes))
supp_assembly = "*" if left.link.supporting_assembly else " "
rows.append([str(left), str(right), str(left.link.gap),
supp_genomes, supp_assembly])
col_widths = repeat(0)
for row in [HEADER] + rows:
col_widths = [max(len(v), w) for v, w in zip(row, col_widths)]
line_len = sum(col_widths) + COL_GAP * len(col_widths)
#header
f.write("-" * line_len + "\n")
f.write(scf.name + "\n")
f.write("-" * line_len + "\n")
for hdr, width in zip(HEADER, col_widths):
f.write(hdr + (" " * (width - len(hdr) + COL_GAP)))
f.write("\n" + "-" * line_len + "\n")
#values
for row in rows:
for val, width in zip(row, col_widths):
f.write(val + (" " * (width - len(val) + COL_GAP)))
f.write("\n")
f.write("-" * line_len + "\n\n")
def output_fasta(contigs_fasta, scaffolds, out_file):
"""
Outputs scaffodls to file in "fasta" format
"""
logger.info("Generating FASTA output")
used_contigs = set()
out_fasta_dict = {}
scf_length = []
total_contigs = 0
total_len = 0
for scf in scaffolds:
scf_seqs = []
for contig in scf.contigs:
###
sep = contig.seq_name.find("[")
if sep == -1:
seq_name = contig.seq_name
cont_seq = contigs_fasta[contig.seq_name]
else:
seq_name = contig.seq_name[:sep]
seg_start, seg_end = \
map(int, contig.seq_name[sep + 1 : -1].split(":"))
cont_seq = contigs_fasta[seq_name][seg_start:seg_end]
###
used_contigs.add(seq_name)
total_contigs += 1
total_len += len(cont_seq)
if contig.sign < 0:
cont_seq = reverse_complement(cont_seq)
if contig.link.gap >= 0:
scf_seqs.append(cont_seq)
scf_seqs.append("N" * contig.link.gap)
else:
scf_seqs.append(cont_seq[:contig.link.gap])
scf_seq = "".join(scf_seqs)
scf_length.append(len(scf_seq))
out_fasta_dict[scf.name] = scf_seq
write_fasta_dict(out_fasta_dict, out_file)
#add some statistics
used_unique = 0
used_len = 0
unused_count = 0
unused_len = 0
for h in contigs_fasta:
if h in used_contigs:
used_unique += 1
used_len += len(contigs_fasta[h])
else:
unused_count += 1
unused_len += len(contigs_fasta[h])
assembly_len = unused_len + used_len
used_perc = 100 * float(used_len) / assembly_len
unused_perc = 100 * float(unused_len) / assembly_len
contigs_length = [len(c) for c in contigs_fasta.values()]
logger.info("Assembly statistics:\n\n"
"\tScaffolds:\t\t{0}\n"
"\tUnique contigs:\t\t{1}\n"
"\tUnique contigs length:\t{2} ({3:2.4}%)\n"
"\tTotal contigs:\t\t{4}\n"
"\tTotal contigs length:\t{5}\n"
"\tUnused contigs count:\t{6}\n"
"\tUnused contigs length:\t{7} ({8:2.4}%)\n"
"\tContigs N50: \t\t{9}\n"
"\tScaffolds N50:\t\t{10}\n"
.format(len(scaffolds), used_unique, used_len, used_perc,
total_contigs, total_len, unused_count, unused_len,
unused_perc,
_calc_n50(contigs_length, unused_len + used_len),
_calc_n50(scf_length, unused_len + used_len)))
def _calc_n50(scaffolds_lengths, assembly_len):
n50 = 0
sum_len = 0
for l in sorted(scaffolds_lengths, reverse=True):
sum_len += l
if sum_len > assembly_len / 2:
n50 = l
break
return n50
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