changeset 4:1c21e9f3104b draft default tip

updated script comments and remove "evaluation" column of the report

--- a/hetbox.py	Tue Jun 25 00:50:46 2013 -0400
+++ b/hetbox.py	Tue Jun 25 00:51:35 2013 -0400
@@ -1,4 +1,5 @@
 #!/usr/bin/env python
+
 # Code by Boris Rebolledo-Jaramillo
 # (boris-at-bx.psu.edu)
 # Edited by Nick Stoler
@@ -6,6 +7,7 @@
 # New in this version:
 # - Add in proper header line if not present
 
+
 import os
 import sys
 import array
@@ -105,7 +107,7 @@
 p = graphics.boxplot(formula, axes=0,ylim=ylimit, lty=1,**kwargs1)
 
 table = base.table(DATA.rx2('SAMPLE'))
-#graphics.text(-1, 1, 'N:', font=2)
+graphics.text(0, -1, 'N:', font=2)
 for i in range(1, base.length(table)[0]+1, 1):
     graphics.text(i, -1, table[i-1], font=2)
 
@@ -116,20 +118,8 @@
 grdevices.dev_off()
 
 if not report:
-  sys.exit(0)
-
+    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)):
@@ -143,25 +133,11 @@
     return [NoHET,MEDIAN, MAD]
 
 boxreport = open(report, "w+")
-boxreport.write("SAMPLE\tTOTAL.SITES\tMEDIAN.FREQ.\tMAD.FREQ\tEVAL\n")
+boxreport.write("#sample\tNo.sites\tmedian.freq\tMAD.freq\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.write ('%s\t%d\t%.1f\t%.1f\n' % tuple([ENTRY[i] for i in [0,1,2,3]]))
 boxreport.close()