def parallel_partition_contigs(asm, assemblies_by_ref, corrected_dirpath,
alignments_fpath_template):
assembly_label = qutils.label_from_fpath(asm.fpath)
corr_assembly_label = qutils.label_from_fpath_for_fname(asm.fpath)
logger.info(' ' + 'processing ' + assembly_label)
added_ref_asm = []
not_aligned_fname = corr_assembly_label + '_not_aligned_anywhere.fasta'
not_aligned_fpath = os.path.join(corrected_dirpath, not_aligned_fname)
contigs = {}
aligned_contig_names = set()
aligned_contigs_for_each_ref = {}
contigs_seq = fastaparser.read_fasta_one_time(asm.fpath)
alignments_fpath = alignments_fpath_template % corr_assembly_label
if os.path.exists(alignments_fpath):
with open(alignments_fpath) as f:
for line in f:
values = line.split()
if values[
0] in contigs_analyzer.ref_labels_by_chromosomes.keys(
):
ref_name = contigs_analyzer.ref_labels_by_chromosomes[
values[0]]
ref_contigs_names = values[1:]
ref_contigs_fpath = os.path.join(
corrected_dirpath,
corr_assembly_label + '_to_' + ref_name + '.fasta')
if ref_name not in aligned_contigs_for_each_ref:
aligned_contigs_for_each_ref[ref_name] = []
for (cont_name, seq) in contigs_seq:
if not cont_name in contigs:
contigs[cont_name] = seq
if cont_name in ref_contigs_names and cont_name not in aligned_contigs_for_each_ref[
ref_name]:
# Collecting all aligned contigs names in order to further extract not aligned
aligned_contig_names.add(cont_name)
aligned_contigs_for_each_ref[ref_name].append(
cont_name)
fastaparser.write_fasta(ref_contigs_fpath,
[(cont_name, seq)], 'a')
ref_asm = Assembly(ref_contigs_fpath, assembly_label)
if ref_asm.name not in added_ref_asm:
if ref_name in assemblies_by_ref:
assemblies_by_ref[ref_name].append(ref_asm)
added_ref_asm.append(ref_asm.name)
if qconfig.space_efficient:
os.remove(alignments_fpath)
# Extraction not aligned contigs
all_contigs_names = set(contigs.keys())
not_aligned_contigs_names = all_contigs_names - aligned_contig_names
fastaparser.write_fasta(not_aligned_fpath,
[(name, contigs[name])
for name in not_aligned_contigs_names])
not_aligned_asm = Assembly(not_aligned_fpath, asm.label)
return assemblies_by_ref, not_aligned_asm
def parallel_partition_contigs(asm, assemblies_by_ref, corrected_dirpath, alignments_fpath_template):
assembly_label = qutils.label_from_fpath(asm.fpath)
corr_assembly_label = qutils.label_from_fpath_for_fname(asm.fpath)
logger.info(' ' + 'processing ' + assembly_label)
added_ref_asm = []
not_aligned_fname = corr_assembly_label + '_not_aligned_anywhere.fasta'
not_aligned_fpath = os.path.join(corrected_dirpath, not_aligned_fname)
contigs = {}
aligned_contig_names = set()
aligned_contigs_for_each_ref = {}
contigs_seq = fastaparser.read_fasta_one_time(asm.fpath)
alignments_fpath = alignments_fpath_template % corr_assembly_label
if os.path.exists(alignments_fpath):
with open(alignments_fpath) as f:
for line in f:
values = line.split()
if values[0] in contigs_analyzer.ref_labels_by_chromosomes.keys():
ref_name = contigs_analyzer.ref_labels_by_chromosomes[values[0]]
ref_contigs_names = values[1:]
ref_contigs_fpath = os.path.join(
corrected_dirpath, corr_assembly_label + '_to_' + ref_name + '.fasta')
if ref_name not in aligned_contigs_for_each_ref:
aligned_contigs_for_each_ref[ref_name] = []
for (cont_name, seq) in contigs_seq:
if not cont_name in contigs:
contigs[cont_name] = seq
if cont_name in ref_contigs_names and cont_name not in aligned_contigs_for_each_ref[ref_name]:
# Collecting all aligned contigs names in order to further extract not aligned
aligned_contig_names.add(cont_name)
aligned_contigs_for_each_ref[ref_name].append(cont_name)
fastaparser.write_fasta(ref_contigs_fpath, [(cont_name, seq)], 'a')
ref_asm = Assembly(ref_contigs_fpath, assembly_label)
if ref_asm.name not in added_ref_asm:
if ref_name in assemblies_by_ref:
assemblies_by_ref[ref_name].append(ref_asm)
added_ref_asm.append(ref_asm.name)
if qconfig.space_efficient:
os.remove(alignments_fpath)
# Extraction not aligned contigs
all_contigs_names = set(contigs.keys())
not_aligned_contigs_names = all_contigs_names - aligned_contig_names
fastaparser.write_fasta(not_aligned_fpath, [(name, contigs[name]) for name in not_aligned_contigs_names])
not_aligned_asm = Assembly(not_aligned_fpath, asm.label)
return assemblies_by_ref, not_aligned_asm