def read_lwcfile(infile, scale, normalize=True):
"""
Cannot handle very large file
:param infile: a string for path, or file object
:param normalize: boolean. If true, shift to make leftmost point 0
:param scale: a number. All head and tail values will be divided by this num
:return:
"""
items = tabular.read(infile, LWC_TABLE, castfunc=list)
if normalize:
minpos = min(min(item['head'], item['tail']) for item in items)
else:
minpos = 0.
for item in items:
element = get_defaults(polygon_style=dict(fill=item['color']))
# print(element, file=sys.stderr)
head = min(item['head'], item['tail'])
tail = max(item['head'], item['tail'])
if item['strand'] == '-':
element['head'] = (tail - minpos) * 1. / scale
element['tail'] = (head - minpos) * 1. / scale
else:
element['head'] = (head - minpos) * 1. / scale
element['tail'] = (tail - minpos) * 1. / scale
# element['']
element['text'] = item['name']
yield element
def render(cls, args, outfile):
recgens = [tabular.read(fn) for fn in args.filenames]
records = itertools.chain(*recgens)
aggregator = tabular.Aggregator(aggregator)
if args.function == 'count':
# groups = aggregator
pass
def read_tblout(infile):
"""
Read tabfile generated by `hmmscan --tblout`
:param infile: a string or a file like opject
"""
return tabular.read(infile, TBLOUT_FIELDS)
def read_fmt6(infile):
return tabular.read(infile, fieldlist_default, sep='\t')
def read_fmt6m(infile):
return tabular.read(infile, fieldlist_mini)
def read_fmt7a(infile):
return tabular.read(infile, fieldlist_all, sep='\t')