from bsPlugins import *
from bbcflib.track import track,stats
from bbcflib import genrep
import os
output_list = ['txt','pdf']
class FileStatisticsForm(BaseForm):
child = twd.HidingTableLayout()
sample = twb.BsFileField(label='Input file: ',
help_text='Select the file to examine',
validator=twb.BsFileFieldValidator(required=True))
output = twf.SingleSelectField(label='Output: ',
options=output_list,
prompt_text=None,
help_text='Type of report')
by_chrom = twf.CheckBox(label='By chromosome: ',
value=False,
help_text='Split statistics by chromosome (default: whole genome)')
submit = twf.SubmitButton(id="submit", value="Submit")
meta = {'version': "1.0.0",
'author': "BBCF",
'contact': "webmaster-bbcf@epfl.ch"}
in_parameters = [
{'id':'sample', 'type':'track', 'required':True},
{'id':'output', 'type':'list', 'required':True},
{'id':'by_chrom', 'type':'boolean', 'required':True}]
out_parameters = [{'id':'stats', 'type':'file'},
{'id':'pdf', 'type':'file'}]
[docs]class FileStatisticsPlugin(BasePlugin):
"""Calculates diverse statistics from a track file,
such as a distribution of scores and feature lengths, and prints them to the output file."""
info = {
'title': 'Basic track statistics',
'description': __doc__,
'path': ['Analysis', 'File Statistics'],
'output': FileStatisticsForm,
'in': in_parameters,
'out': out_parameters,
'meta': meta,
}
def _plot_pdf(self,filename,stats,title=""):
import rpy2.robjects as robjects
import rpy2.robjects.numpy2ri as numpy2ri
robjects.r('pdf("%s",paper="a4",height=8,width=8)' %filename)
for chrom,st in stats.iteritems():
if chrom:
_title = title+":"+chrom
else:
_title = title
if 'feat_stats' in st:
fst = st['feat_stats']
robjects.r.assign('len',numpy2ri.numpy2ri(fst[1].keys()))
robjects.r.assign('num',numpy2ri.numpy2ri(fst[1].values()))
robjects.r.assign('ylim',max(10,fst[0]))
robjects.r.assign('med',fst[2][5])
robjects.r.assign('men',fst[2][3])
robjects.r.assign('sdv',fst[2][4])
robjects.r("""
ypos=1
len=as.numeric(len)
num=as.numeric(num)
par(lwd=2,cex=1.1,cex.main=1.5,cex.lab=1.3,cex.axis=.8,mar=c(5,5,1,1),las=1,pch=20)
plot(len,num,type='h',main='%s',xlab='Feature Length',ylab='Frequency',ylim=c(1,ylim),log='y')
abline(v=med,col='red')
text(med,ylim,paste("median",med,sep="="),col='red',pos=4)
abline(h=ylim[1],col='green')
mtext(paste(ylim[1],"features"),side=2,at=10,col='green',las=1)
arrows(men-sdv,ypos,men+sdv,ypos,angle=90,code=3,length=.15,col='blue')
points(men,ypos,pch=19,col='blue')
"""%_title)
if 'score_stats' in st:
sst = st['score_stats']
robjects.r.assign('score',numpy2ri.numpy2ri(sst[0].keys()))
robjects.r.assign('num',numpy2ri.numpy2ri(sst[0].values()))
robjects.r.assign('med',sst[1][5])
robjects.r.assign('men',sst[1][3])
robjects.r.assign('sdv',sst[1][4])
robjects.r("""
ypos=1
score=as.numeric(score)
num=as.numeric(num)
par(lwd=2,cex=1.1,cex.main=1.5,cex.lab=1.3,cex.axis=0.8,mar=c(5,5,1,1),las=1,pch=20)
plot(score,num,type='h',main='%s',xlab='Score',ylab='Frequency',log='y')
abline(v=med,col='red')
text(med,ylim[1],paste("median",med,sep="="),col='red',pos=4)
arrows(men-sdv,ypos,men+sdv,ypos,angle=90,code=3,length=.15,col='blue')
points(men,ypos,pch=19,col='blue')
"""%_title)
robjects.r("dev.off()")
return None
def __call__(self, **kw):
self.debug(**kw)
sample = track(kw['sample'],chrmeta="guess")
by_chrom = kw.get('by_chrom',False)
if isinstance(by_chrom, basestring):
by_chrom = (by_chrom.lower() in ['1', 'true', 't'])
outf = kw.get('output')
if outf not in output_list:
outf = output_list[0]
output = self.temporary_path(fname=sample.name+'_stats.'+outf)
if outf == 'txt':
out = open(output,"w")
else:
out = {}
if by_chrom:
chromlist = sample.chrmeta.keys()
else:
chromlist = [None]
for chrom in chromlist:
if outf == 'txt':
if chrom:
out.write("Chromosome %s\n--------------------\n"%chrom)
stats(sample,out=out,selection=chrom)
else:
out[chrom] = {}
stats(sample,out=out[chrom],selection=chrom)
if outf == 'txt' and chrom:
out.write("\n--------------------\n")
if outf == 'txt':
out.close()
self.new_file(output, 'stats')
else:
self._plot_pdf(output,out,sample.name)
self.new_file(output, 'pdf')
return self.display_time()
