Mercurial > repos > boris > hetbox

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hetbox.py	Thu Jun 13 15:09:48 2013 -0400
@@ -0,0 +1,160 @@
+#!/usr/bin/env python
+# Code by Boris Rebolledo-Jaramillo
+# (boris-at-bx.psu.edu)
+# Edited by Nick Stoler
+# (nick-at-bx.psu.edu)
+# New in this version:
+# - Add in proper header line if not present
+
+import os
+import sys
+import numpy
+from rpy2.robjects import Formula
+from rpy2.robjects.packages import importr
+from rpy2 import robjects
+
+def fail(message):
+  sys.stderr.write(message+'\n')
+  sys.exit(1)
+
+COLUMN_LABELS = ['SAMPLE', 'CHR',  'POS', 'A', 'C', 'G', 'T', 'CVRG',
+                 'ALLELES', 'MAJOR', 'MINOR', 'MINOR.FREQ.PERC.'] #, 'STRAND.BIAS']
+
+args = sys.argv[1:]
+if len(args) >= 1:
+  infile = args[0]
+else:
+  fail('Error: No input filename provided (as argument 1).')
+if len(args) >= 2:
+  outfile = args[1]
+else:
+  fail('Error: No output filename provided (as argument 2).')
+if len(args) >= 3:
+  report = args[2]
+else:
+  report = ''
+
+# Check input file
+add_header = False
+if not os.path.exists(infile):
+  fail('Error: Input file '+infile+' could not be found.')
+with open(infile, 'r') as lines:
+  line = lines.readline()
+  if not line:
+    fail('Error: Input file seems to be empty')
+  line = line.strip().lstrip('#') # rm whitespace, comment chars
+  labels = line.split("\t")
+  if 'SAMPLE' not in labels or labels[11] != 'MINOR.FREQ.PERC.':
+    sys.stderr.write("Error: Input file does not seem to have a proper header "
+      +"line.\nAdding an artificial header..")
+    add_header = True
+
+base = importr('base')
+utils = importr('utils')
+stats = importr('stats')
+rprint = robjects.globalenv.get("print")
+graphics = importr('graphics')
+grdevices = importr('grDevices')
+grdevices.png(file=outfile, width=1024, height=768)
+
+# Read file into a data frame
+if add_header:
+  # add header line manually if not present
+  DATA = utils.read_delim(infile, header=False)
+  labels = robjects.r.names(DATA)
+  for i in range(len(labels)):
+    try:
+      labels[i] = COLUMN_LABELS[i]
+    except IndexError, e:
+      fail("Error in input file: Too many columns (does not match hardcoded "
+        +"column labels).")
+else:
+  DATA = utils.read_delim(infile)
+  # Remove comment from header, if present
+  labels = robjects.r.names(DATA)
+  if labels[0][0:2] == 'X.':
+    labels[0] = labels[0][2:]
+
+# Multiply minor allele frequencies by 100 to get percentage
+#  .rx2() looks up a column by its label and returns it as a vector
+#  .ro turns the returned object into one that can be operated on per-element
+minor_freq = DATA.rx2('MINOR.FREQ.PERC.').ro * 100
+samples    = DATA.rx2('SAMPLE')
+
+# Formula() creates a Python object representing the R object returned by x ~ y
+formula = Formula('minor_freq ~ samples')
+# The "environment" in .getenvironment() is the entire R workspace in which the
+# Formula object exists. The R workspace meaning all the defined variables.
+# Here, the .getenvironment() method is being used to set some variables in the
+
+# R workspace
+formula.getenvironment()['minor_freq'] = minor_freq
+formula.getenvironment()['samples']    = samples
+
+# create boxplot - fill kwargs1 with the options for the boxplot function
+kwargs1 = {'ylab':"Minor allele frequency (%)", 'col':"gray", 'xaxt':"n",
+           'outpch':"*",'main':"Distribution of minor allele frequencies",
+           'cex.lab':"1.5"}
+p = graphics.boxplot(formula, **kwargs1)
+table  = base.table(DATA.rx2('SAMPLE'))
+graphics.text(0.5, 1, 'N:', font=2)
+for i in range(1, base.length(table)[0]+1, 1):
+    graphics.text(i, 1, table[i-1], font=2)
+
+graphlabels = base.names(table)
+kwargs3 = {'pos':"0", 'las':"2", 'cex.axis':"1"}
+graphics.axis(1, at=range(1, len(graphlabels)+1, 1), labels=graphlabels, **kwargs3)
+grdevices.dev_off()
+
+if not report:
+  sys.exit(0)
+
+
+####################################
+# GENERATE REPORT
+# report should be something like:
+# SAMPLE NoHET MEDIAN MAD TEST
+# s1     7      10%   n   p/w/f
+# n <= 5      pass
+# 6 <= n <=10 warn
+# n >= 11     fail
+# MAD <= 2.0  fail
+# MAD > 2.0    pass
+###################################
+
+SAMPLES=[]
+for i in range(len(table)):
+    SAMPLES.append(base.names(table)[i])
+
+def boxstats(data,sample):
+    VALUES = [100*float(x.strip().split('\t')[11]) for x in list(open(data)) if x.strip().split('\t')[0]==sample]
+    NoHET  = len(VALUES)
+    MEDIAN = numpy.median(VALUES)
+    MAD    = numpy.median([abs(i - MEDIAN) for i in VALUES]) # Median absolute distance (robust spread statistic)
+    return [NoHET,MEDIAN, MAD]
+
+boxreport = open(report, "w+")
+boxreport.write("SAMPLE\tTOTAL.SITES\tMEDIAN.FREQ.\tMAD.FREQ\tEVAL\n")
+for sample in SAMPLES:
+    ENTRY = [sample] + boxstats(infile,sample)
+    if ENTRY[1] <= 5:
+        ENTRY.append('pass')
+    elif 6 <= ENTRY[1] <=10:
+        ENTRY.append('warn')
+    elif ENTRY[1] >= 11:
+        ENTRY.append('fail')
+    if ENTRY[3] <=2.0:
+        ENTRY.append('fail')
+    elif ENTRY[3] >2.0:
+        ENTRY.append('pass')
+    if len(set(ENTRY[4:6])) == 2:
+        ENTRY.append('warn')
+    else:
+        ENTRY.append(list(set(ENTRY[4:6]))[0])
+    boxreport.write ('%s\t%d\t%.1f\t%.1f\t%s\n' % tuple([ENTRY[i] for i in [0,1,2,3,6]]))
+
+boxreport.close()
+
+
+
+