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)
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)