def __init__(self, cogs_file_content):
assert isinstance(cogs_file_content, CogsFileContent)
self.cogs_content = cogs_file_content
spans = [NamedSpan(a.start - 1, a.end - 1, (a.gene,)) for a in self.cogs_content.get_cogs_lines()]
spans = spanning.join(spans)
self.spans = spans
def __init__(self, cogs_file_content, overlap=0):
assert isinstance(cogs_file_content, CogsFileContent)
self.cogs_content = cogs_file_content
self.overlap = overlap
chr_len = cogs_file_content.chr_len
# first get the coding spans & join 'em
coding_spans = [NamedSpan(a.start - 1, a.end, (a.gene,)) for a in self.cogs_content.get_cogs_lines()]
coding_spans = spanning.join(coding_spans)
# then run through and construct the list of complemented spans.
spans = []
prev_span = coding_spans[0]
# for the first span, start at 0 & go to the beginning of the
# first gene.
new_name = [""]
new_name.extend(prev_span.name)
spans.append(NamedSpan(0, prev_span.start + overlap - 1, new_name))
# for each successive region, take the end of the previous gene
# and the start of the next & make a span out of it. account
# for overlaps...
for i in range(1, len(coding_spans)):
span = coding_spans[i]
new_name = []
new_name.extend(prev_span.name)
new_name.extend(span.name)
spans.append(NamedSpan(prev_span.end - overlap + 1, span.start + overlap - 1, new_name))
prev_span = span
new_name = []
new_name.extend(prev_span.name)
new_name.append("")
spans.append(NamedSpan(prev_span.end - overlap + 1, chr_len, new_name))
self.spans = spans
