from bsPlugins import *
from bbcflib.gfminer.stream import overlap
from bbcflib.track import track
from bbcflib import genrep
class OverlapForm(BaseForm):
child = twd.HidingTableLayout()
features = twb.BsFileField(label='Features file: ',
help_text='Upload your own file',
validator=twb.BsFileFieldValidator(required=True))
filter = twb.BsFileField(label='Filter file: ',
help_text='Upload your own file',
validator=twb.BsFileFieldValidator(required=True))
format = twf.SingleSelectField(label='Output format: ',
options=["txt","bed","sql","bedGraph","bigWig"],
validator=twc.Validator(required=True),
help_text='Format of the output file')
assembly = twf.SingleSelectField(label='Assembly: ',
options=genrep.GenRep().assemblies_available(),
help_text='Reference genome')
submit = twf.SubmitButton(id="submit", value="Submit")
meta = {'version': "1.0.0",
'author': "BBCF",
'contact': "webmaster-bbcf@epfl.ch"}
in_parameters = [{'id': 'filter', 'type': 'userfile', 'required': True},
{'id': 'features', 'type': 'track', 'required': True},
{'id': 'format', 'type': 'text'},
{'id': 'assembly', 'type': 'assembly'}]
out_parameters = [{'id': 'filtered', 'type': 'track'}]
[docs]class OverlapPlugin(BasePlugin):
"""Returns only the regions of the first input file that overlap
(or contain) some feature from the second ('filter')."""
info = {
'title': 'Overlap',
'description': __doc__,
'path': ['Intervals', 'Overlap'],
'output': OverlapForm,
'in': in_parameters,
'out': out_parameters,
'meta': meta,
}
def __call__(self, **kw):
# Set assembly
assembly_id = kw.get('assembly')
chrmeta = "guess"
if assembly_id:
assembly = genrep.Assembly(assembly_id)
chrmeta = assembly.chrmeta
# Set features track
assert os.path.exists(str(kw.get('features'))), "Features file not found: '%s'"%kw.get("features")
features = track(kw['features'], chrmeta=chrmeta or None )
chrmeta = features.chrmeta
# Set filter track
assert os.path.exists(str(kw.get('filter'))), "Filter file not found: '%s'"%kw.get("filter")
filter = track(kw.get('filter'), chrmeta=chrmeta or None)
# Main
format = kw.get('format',features.format)
output = self.temporary_path(fname=features.name+'_filtered.'+format)
tout = track(output, format, fields=filter.fields,
chrmeta=chrmeta, info={'datatype':'qualitative'})
for chrom in chrmeta:
tout.write(overlap(features.read(chrom),filter.read(chrom)), chrom=chrom,clip=True)
tout.close()
self.new_file(output, 'filtered')
return self.display_time()
