def add_contig_structure_data(data_str, structure, ref_contigs, chr_full_names, contig_names_by_refs,
used_chromosomes, links_to_chromosomes, chr_names_by_id):
for el in structure:
if isinstance(el, Alignment):
if el.ref_name in ref_contigs:
num_chr = ref_contigs.index(el.ref_name)
# corr_len = sum(chr_lengths[:num_chr+1])
else:
# corr_len = -int(el.end)
if el.ref_name not in used_chromosomes:
used_chromosomes.append(el.ref_name)
if contig_names_by_refs:
other_ref_name = contig_names_by_refs[el.ref_name]
links_to_chromosomes.append('links_to_chromosomes["' + el.ref_name + '"] = "' +
get_html_name(other_ref_name, chr_full_names) + '";')
corr_el_start = el.start
corr_el_end = el.end
data_str.append('{corr_start: ' + str(corr_el_start) + ',corr_end: ' +
str(corr_el_end) + ',start:' + str(el.unshifted_start) + ',end:' + str(el.unshifted_end) +
',start_in_contig:' + str(el.start_in_contig) + ',end_in_contig:' +
str(el.end_in_contig) + ',IDY:' + el.idy + ',chr: "' + chr_names_by_id[el.ref_name] + '"},')
elif type(el) == str:
ms_description, ms_type = parse_misassembly_info(el)
data_str.append('{contig_type: "M", mstype: "' + ms_type + '", msg: "' + ms_description + '"},')
return data_str
def add_contig(cum_length, contig, not_used_nx, assemblies_n50, assembly, contigs, contig_size_lines, num, structures_by_labels,
only_nx=False, has_aligned_contigs=True):
end_contig = cum_length + contig.size
marks = []
align = None
for nx in not_used_nx:
if assemblies_n50[assembly][nx] == contig.size and \
(num + 1 >= len(contigs) or contigs[num + 1].size != contig.size):
marks.append(nx)
marks = ', '.join(marks)
genes = ['{start:' + str(gene.start) + ',end:' + str(gene.end) + '}' for gene in contig.genes]
if marks:
not_used_nx = [nx for nx in not_used_nx if nx not in marks]
marks = ', marks: "' + marks + '"' if marks else ''
if not only_nx or marks:
structure = []
if structures_by_labels and assembly in structures_by_labels:
assembly_structure = structures_by_labels[assembly]
for el in assembly_structure[contig.name]:
if isinstance(el, Alignment):
structure.append('{contig:"' + contig.name + '",corr_start: ' + str(el.start) + ',corr_end: ' +
str(el.end) + ',start:' + str(el.unshifted_start) + ',end:' + str(el.unshifted_end) +
',start_in_contig:' + str(el.start_in_contig) + ',end_in_contig:' +
str(el.end_in_contig) + ',size:' + str(contig.size) + ',IDY:' + el.idy + ',chr:"' + el.ref_name + '"},')
elif type(el) == str:
ms_description, ms_type = parse_misassembly_info(el)
structure.append('{contig_type: "M", mstype: "' + ms_type + '", msg: "' + ms_description + '"},')
if has_aligned_contigs and not contig.contig_type:
contig.contig_type = 'unaligned'
align = '{name:"' + contig.name + '",size:' + str(contig.size) + marks + ',contig_type: "' + contig.contig_type + \
'",structure:[' + ''.join(structure) + ']' + (',genes:[' + ','.join(genes) + ']' if qconfig.gene_finding else '') + '},'
return end_contig, contig_size_lines, align, not_used_nx
