from bsPlugins import *
from bbcflib.track import track
from bbcflib import genrep
from bbcflib.gfminer.figure import genomeGraph
import os
meta = {'version': "1.0.0",
'author': "BBCF",
'contact': "webmaster-bbcf@epfl.ch"}
in_parameters = [{'id': 'signals_plus', 'type': 'track', 'multiple': 'SigMultiP'},
{'id': 'signals_minus', 'type': 'track', 'multiple': 'SigMultiM'},
{'id': 'features', 'type': 'track', 'multiple': 'FeatMulti'},
{'id': 'assembly', 'type': 'assembly'}]
out_parameters = [{'id': 'genome_graph', 'type': 'pdf'}]
class GenomeGraphForm(BaseForm):
class SigMultiP(twb.BsMultiple):
label='Positive Signals: '
signals_plus = twb.BsFileField(label=' ',
help_text='Signal files (e.g. bedgraph) to plot above the axis',
validator=twb.BsFileFieldValidator(required=False))
class SigMultiM(twb.BsMultiple):
label='Negative Signals: '
signals_minus = twb.BsFileField(label=' ',
help_text='Signal files (e.g. bedgraph) to plot below the axis',
validator=twb.BsFileFieldValidator(required=False))
class FeatMulti(twb.BsMultiple):
label='Features: '
features = twb.BsFileField(label=' ',
help_text='Features files (e.g. bed) to plot as segments on the axis',
validator=twb.BsFileFieldValidator(required=False))
assembly = twf.SingleSelectField(label='Assembly: ',
options=genrep.GenRep().assemblies_available(),
help_text='Reference genome')
submit = twf.SubmitButton(id="submit", value="Plot")
[docs]class GenomeGraphPlugin(BasePlugin):
"""Generates a whole genome overview of several signal and/or feature tracks."""
info = {'title': 'Genome overview graph',
'description': __doc__,
'path': ['Graphics', 'Genome graph'],
'output': GenomeGraphForm,
'in': in_parameters,
'out': out_parameters,
'meta': meta}
def __call__(self, **kw):
assembly = kw.get('assembly') or 'guess'
signals_plus = kw.get('SigMultiP',{}).get('signals_plus', [])
if not isinstance(signals_plus, list): signals_plus = [signals_plus]
signals_minus = kw.get('SigMultiM',{}).get('signals_minus', [])
if not isinstance(signals_minus, list): signals_minus = [signals_minus]
features = kw.get('FeatMulti',{}).get('features', [])
if not isinstance(features, list): features = [features]
sptracks = [track(sig,chrmeta=assembly) for sig in signals_plus if os.path.exists(sig)]
smtracks = [track(sig,chrmeta=assembly) for sig in signals_minus if os.path.exists(sig)]
ftracks = [track(feat,chrmeta=assembly) for feat in features if os.path.exists(feat)]
snames = [t.name for t in sptracks+smtracks+ftracks]
if len(sptracks) > 0:
chrmeta = sptracks[0].chrmeta
elif len(smtracks) > 0:
chrmeta = smtracks[0].chrmeta
elif len(features) > 0:
chrmeta = ftracks[0].chrmeta
else:
raise ValueError("No data provided")
if assembly in [x[0] for x in genrep.GenRep().assemblies_available()]:
chrnames = genrep.Assembly(assembly).chrnames
else:
chrnames = [x[1] for x in sorted([(v['length'],c) for c,v in chrmeta.iteritems()],reverse=True)]
pdf = self.temporary_path(fname='genome_graph.pdf')
_fs = ['chr','start','end','score']
_ff = ['chr','start','end','name']
genomeGraph([(c,chrmeta[c]['length']) for c in chrnames],
[sig.read(fields=_fs) for sig in sptracks],
[sig.read(fields=_fs) for sig in smtracks],
[feat.read(fields=_ff) for feat in ftracks],
output=pdf, new=True, last=True, legend=snames)
self.new_file(pdf, 'genome_graph')
return self.display_time()
