from bsPlugins import *
from bbcflib.track import track
from bbcflib import genrep
import os, shutil
from maplot import MAplot
__requires__ = ["numpy"]
ftypes = [(0, 'genes bodies'), (1, 'gene promoters'), (2, 'exons'), (3, 'custom upload')]
prom_up_def = 1000
prom_down_def = 100
class MaplotForm(BaseForm):
child = twd.HidingTableLayout()
input_type = twd.HidingRadioButtonList(label='Input type: ',
options=('Table', 'Signals'),
mapping={'Table': ['table'],
'Signals': ['Group1','Group2','feature_type','assembly'],},
help_text='Select input type (Formatted table, or signal tracks)')
table = twb.BsFileField(label='Table: ',
help_text='Select scores table',
validator=twb.BsFileFieldValidator(required=True))
class Group1(twb.BsMultiple):
label = "Signals group 1: "
signals1 = twb.BsFileField(label=' ',
help_text='Select signal files (position and score, e.g. bedgraph)',
validator=twb.BsFileFieldValidator(required=True))
class Group2(twb.BsMultiple):
label = "Signals group 2: "
signals2 = twb.BsFileField(label=' ',
help_text='Select signal files (position and score, e.g. bedgraph)',
validator=twb.BsFileFieldValidator(required=True))
feature_type = twd.HidingSingleSelectField(label='Feature type: ',
options=ftypes, prompt_text=None,
mapping={ftypes[-1][0]: ['features'],
1: ['upstream', 'downstream']},
help_text='Choose a feature set or upload your own',
validator=twc.Validator(required=True))
features = twb.BsFileField(label='Custom feature set: ',
help_text='Select a feature file (e.g. bed)',
validator=twb.BsFileFieldValidator())
upstream = twf.TextField(label='Promoter upstream distance: ',
validator=twc.IntValidator(required=True),
value=prom_up_def,
help_text='Size of promoter upstream of TSS')
downstream = twf.TextField(label='Promoter downstream distance: ',
validator=twc.IntValidator(required=True),
value=prom_down_def,
help_text='Size of promoter downstream of TSS')
assembly = twf.SingleSelectField(label='Assembly: ',
options=genrep.GenRep().assemblies_available(),
validator=twc.Validator(required=True),
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': 'input_type', 'type': 'radio'},
{'id': 'signals1', 'type': 'track', 'required': True, 'multiple':'Group1'},
{'id': 'signals2', 'type': 'track', 'required': True, 'multiple':'Group2'},
{'id': 'table', 'type': 'txt', 'required': True, 'multiple': True},
{'id': 'feature_type', 'type': 'int'},
{'id': 'upstream', 'type': 'int'},
{'id': 'downstream', 'type': 'int'},
{'id': 'assembly', 'type': 'assembly'},
{'id': 'features', 'type': 'track'},
]
out_parameters = [{'id': 'MA-plot', 'type': 'file'}]
[docs]class MaplotPlugin(BasePlugin):
"""Creates an MA-plot to compare levels of expression of genomic features
across two samples.
The input can be of two different types:
* Two 'signal' files, i.e. bedGraph-type text files,
and a list of genomic features - either from a pre-defined list such as Ensembl genes,
or a custom bed-like file. The name of each sample is the one given in the track
definition line ("track name=... description=... etc."), if specified, otherwise the name of
the file (without extension). </li>
* A tab-delimited table with feature names in the first column, then one column of respective
scores per sample. The first line is a header of the type "id sample1 sample2 ...".
"""
info = {
'title': 'MA-plot',
'description': __doc__,
'path': ['Graphics', 'MA-plot'],
'output': MaplotForm,
'in': in_parameters,
'out': out_parameters,
'meta': meta,
}
def __call__(self, **kw):
if kw.get('input_type') == 'Table':
table = kw.get('table')
assert os.path.exists(str(table)), "File not found: '%s'" % table
with open(table) as t:
colnames = t.readline()
_f = colnames.strip().split()
nscores = len(_f)-1
groups = len(list(set([x.split('.')[0] for x in _f])))
if nscores == 2: # 3 columns, cols 2 and 3 contain the scores
sample1 = [2]
sample2 = [3]
elif len(groups) == 2: # more columns, look if there are two groups of prefixes
sample1 = [_f.index(x) for x in _f if x.split('.')==groups[0]]
sample2 = [_f.index(x) for x in _f if x.split('.')==groups[1]]
else: # not implemented yet, ask the user to choose the columns he wants? Checkboxes...
raise ValueError("For the moment, either have only 2 columns of scores, \
or use names of the form <group_name>.<run_id>")
else:
# Use QuantifyTablePlugin to build a table from score tracks
from QuantifyTable import QuantifyTablePlugin
# Set QuantifyTablePlugin options
kw['score_op'] = 'sum'
kw['format'] = 'txt'
signals1 = kw['Group1']['signals1']
signals2 = kw['Group2']['signals2']
if not isinstance(signals1,(list,tuple)): signals1 = [signals1]
if not isinstance(signals2,(list,tuple)): signals2 = [signals2]
kw['signals'] = signals1 + signals2
signals = kw['signals']
nscores = len(signals)
qtable = QuantifyTablePlugin().quantify(**kw)
# Remove useless fields and add header based on file names
qtable = track(qtable, format='txt', fields=['chr','start','end','name']+ \
['score'+str(i) for i in range(nscores)])
table = self.temporary_path('scores_table.txt')
_f = ['score'+str(i) for i in range(nscores)]
strack = track(table, fields=['name']+_f)
signal_tracks = [track(s) for s in signals]
signames = [s.info.get('name',os.path.splitext(os.path.basename(s.path))[0]) for s in signal_tracks]
strack.write([('Name',signames[0],signames[1])])
strack.write(qtable.read(fields=strack.fields))
sample1 = range(len(signals1))
sample2 = range(nscores-len(signals1))
output_filename = MAplot(table, cols={1:sample1, 2:sample2})
output = self.temporary_path(fname='maplot.png')
shutil.move(output_filename,output)
self.new_file(output, 'MA-plot')
return self.display_time()
# nosetests --logging-filter=-tw2 test_Maplot.py
