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1 #!/usr/bin/env python
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2 #Greg Von Kuster
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3 """
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4 Calculate correlations between numeric columns in a tab delim file.
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5 usage: %prog infile output.txt columns method
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6 """
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7
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8 import sys
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9 #from rpy import *
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10 import rpy2.robjects as robjects
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11 r = robjects.r
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12
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13 def stop_err(msg):
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14 sys.stderr.write(msg)
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15 sys.exit()
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16
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17 def main():
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18 method = sys.argv[4]
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19 assert method in ( "pearson", "kendall", "spearman" )
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20
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21 try:
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22 columns = map( int, sys.argv[3].split( ',' ) )
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23 except:
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24 stop_err( "Problem determining columns, perhaps your query does not contain a column of numerical data." )
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25
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26 matrix = []
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27 skipped_lines = 0
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28 first_invalid_line = 0
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29 invalid_value = ''
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30 invalid_column = 0
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31
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32 for i, line in enumerate( file( sys.argv[1] ) ):
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33 valid = True
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34 line = line.rstrip('\n\r')
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35
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36 if line and not line.startswith( '#' ):
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37 # Extract values and convert to floats
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38 row = []
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39 for column in columns:
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40 column -= 1
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41 fields = line.split( "\t" )
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42 if len( fields ) <= column:
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43 valid = False
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44 else:
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45 val = fields[column]
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46 if val.lower() == "na":
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47 row.append( float( "nan" ) )
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48 else:
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49 try:
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50 row.append( float( fields[column] ) )
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51 except:
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52 valid = False
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53 skipped_lines += 1
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54 if not first_invalid_line:
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55 first_invalid_line = i+1
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56 invalid_value = fields[column]
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57 invalid_column = column+1
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58 else:
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59 valid = False
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60 skipped_lines += 1
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61 if not first_invalid_line:
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62 first_invalid_line = i+1
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63
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64 if valid:
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65 # matrix.append( row )
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66 matrix += row
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67
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68 if skipped_lines < i:
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69 try:
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70 out = open( sys.argv[2], "w" )
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71 except:
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72 stop_err( "Unable to open output file" )
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73
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74 # Run correlation
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75 # print >> sys.stderr, "matrix: %s" % matrix
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76 # print >> sys.stderr, "array: %s" % array( matrix )
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77 try:
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78 # value = r.cor( array( matrix ), use="pairwise.complete.obs", method=method )
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79 fv = robjects.FloatVector(matrix)
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80 m = r['matrix'](fv, ncol=len(columns),byrow=True)
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81 rslt_mat = r.cor(m, use="pairwise.complete.obs", method=method )
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82 value = []
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83 for ri in range(1, rslt_mat.nrow + 1):
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84 row = []
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85 for ci in range(1, rslt_mat.ncol + 1):
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86 row.append(rslt_mat.rx(ri,ci)[0])
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87 value.append(row)
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88 except Exception, exc:
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89 out.close()
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90 stop_err("%s" %str( exc ))
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91 for row in value:
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92 print >> out, "\t".join( map( str, row ) )
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93 out.close()
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94
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95 if skipped_lines > 0:
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96 msg = "..Skipped %d lines starting with line #%d. " %( skipped_lines, first_invalid_line )
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97 if invalid_value and invalid_column > 0:
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98 msg += "Value '%s' in column %d is not numeric." % ( invalid_value, invalid_column )
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99 print msg
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100
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101 if __name__ == "__main__":
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102 main()
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