def get_info_by_chr(chr, aligned_bases_by_chr, chr_sizes, contigs_fpaths, contig_names_by_refs, one_chromosome=False): if one_chromosome: html_name = qconfig.one_alignment_viewer_name chr_link = os.path.join(qconfig.icarus_dirname, html_name + '.html') else: chr_link = os.path.join(qconfig.icarus_dirname, trim_ref_name(chr) + '.html') chr_name = chr.replace('_', ' ') tooltip = '' if len(chr_name) > 70: short_name = chr[:70] tooltip = chr_name chr_name = short_name + '...' aligned_lengths = [ aligned_len for aligned_len in aligned_bases_by_chr[chr] if aligned_len is not None ] chr_genome = sum(aligned_lengths) * 100.0 / (chr_sizes[chr] * len(contigs_fpaths)) chr_size = chr_sizes[chr] return chr_link, chr_name, chr_genome, chr_size, tooltip
def get_info_by_chr(chr, aligned_bases_by_chr, chr_sizes, contigs_fpaths, contig_names_by_refs, one_chromosome=False): if one_chromosome: html_name = qconfig.one_alignment_viewer_name chr_link = os.path.join(qconfig.icarus_dirname, html_name + '.html') else: chr_link = os.path.join(qconfig.icarus_dirname, trim_ref_name(chr) + '.html') chr_name = chr.replace('_', ' ') tooltip = '' if len(chr_name) > 70: short_name = chr[:70] tooltip = chr_name chr_name = short_name + '...' aligned_lengths = [aligned_len for aligned_len in aligned_bases_by_chr[chr] if aligned_len is not None] chr_genome = sum(aligned_lengths) * 100.0 / (chr_sizes[chr] * len(contigs_fpaths)) chr_size = chr_sizes[chr] return chr_link, chr_name, chr_genome, chr_size, tooltip
def get_html_name(chr, chr_full_names): if len(chr_full_names) == 1: return qconfig.one_alignment_viewer_name return trim_ref_name(chr)