from bsPlugins import *
from bein import execution
from bbcflib import genrep
from bbcflib.common import fasta_composition
from bbcflib.motif import save_motif_profile
from bbcflib.track import track, FeatureStream
import os
g = genrep.GenRep()
available_motifs = g.motifs_available()
assembly_list = g.assemblies_available()
input_types = [(0, 'Fasta upload'), (1, 'Select regions from genome')]
input_map = {0: ['fastafile'], 1: ['regions']}
meta = {'version': "1.0.0",
'author': "BBCF",
'contact': "webmaster-bbcf@epfl.ch"}
in_parameters = [{'id': 'input_type', 'type': 'radio'},
{'id': 'fastafile', 'type': 'userfile'},
{'id': 'background', 'type': 'txt'},
{'id': 'assembly', 'type': 'assembly'},
{'id': 'regions', 'type': 'track'},
{'id': 'motifs', 'type': 'list'},
{'id': 'customMotif', 'type': 'txt'},
{'id': 'threshold', 'type': 'float', 'required': True}]
out_parameters = [{'id': 'motif_track', 'type': 'track'}]
class MotifScanForm(BaseForm):
child = twd.HidingTableLayout()
input_type = twd.HidingRadioButtonList(label='Sequence source: ',
options=input_types,
value=0,
mapping=input_map)
fastafile = twb.BsFileField(label='Fasta file: ', help_text='Sequences to scan')
regions = twb.BsFileField(label='Regions: ', help_text='Genomic regions to scan (e.g. bed)',
validator=twb.BsFileFieldValidator())
assembly = twf.SingleSelectField(label='Assembly: ', options=assembly_list,
prompt_text=None,
help_text='Assembly to fetch sequences from')
background = twb.BsFileField(label='Background: ',
help_text='File of background frequencies (default: genome-wide frequencies)')
motifs = twf.MultipleSelectField(label='Motifs: ', options=available_motifs,
help_text='Select motifs to be scanned')
customMotif = twb.BsFileField(label='Custom motif: ',
help_text='An optional custom/additional motif to scan (.mat)')
threshold = twf.TextField(label='Threshold: ', value='0.0')
submit = twf.SubmitButton(id="submit", value='Scan sequences')
[docs]class MotifScanPlugin(BasePlugin):
"""Scan motifs PWM on a set of a sequences"""
info = {
'title': 'Motif scanner',
'description': __doc__,
'path': ['Sequence analysis', 'Motif scanner'],
'output': MotifScanForm,
'in': in_parameters,
'out': out_parameters,
'meta': meta,
}
def __call__(self, **kw):
fasta_file = kw.get('fastafile')
background = kw.get('background') or None
assembly_id = kw.get('assembly') or None
regions_file = kw.get('regions')
motifs_list = kw.get('motifs')
motif_add = kw.get('customMotif')
threshold = float(kw.get('threshold') or 0)
if motifs_list is None: motifs_list = []
if isinstance(motifs_list, basestring): motifs_list = motifs_list.split("|")
if not isinstance(motifs_list, list): motifs_list = [motifs_list]
if background is None and assembly_id is None:
background = self.temporary_path(fname='background.txt')
stats = {'A': 0.25,'C': 0.25, 'G': 0.25, 'T': 0.25}
if fasta_file:
with execution(None) as ex:
stats = fasta_composition(ex,fasta_file,frequency=True)
with open(background,"w") as bgr:
bgr.write(" ".join(["1"]+[str(stats[n]) for n in ['A','C','G','T']]))
if assembly_id is not None:
assembly = genrep.Assembly(assembly_id)
else:
if regions_file is not None:
raise ValueError("Please specify an assembly if you specify regions.")
assembly = None
motifs = {}
if motif_add is not None:
mname = os.path.basename(os.path.splitext(motif_add)[0])
if mname: motifs[mname] = motif_add
for mot in motifs_list:
gid, mname = mot.split(' ')
pwmfile = self.temporary_path()
_ = g.get_motif_PWM(int(gid), mname, output=pwmfile)
motifs[mname] = pwmfile
if len(motifs) == 0:
raise ValueError("Please give at least one motif to scan for")
track_output = self.temporary_path(fname='motif_scan', ext="sql")
with execution(None) as ex:
_ = save_motif_profile( ex, motifs, assembly, regions_file, fasta_file,
background=background, threshold=threshold,
output = track_output,
description=None, via='local' )
self.new_file(track_output, 'motif_track')
return self.display_time()
