Mercurial > repos > devteam > weightedaverage

annotate WeightedAverage.py @ 2:efa2b391e887 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
author devteam
date Wed, 05 Oct 2016 13:39:38 -0400
parents 90611e86a998
children
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1 #!/usr/bin/env python
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2 """
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3 usage: %prog bed_file_1 bed_file_2 out_file
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4 -1, --cols1=N,N,N,N: Columns for chr, start, end, strand in first file
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5 -2, --cols2=N,N,N,N,N: Columns for chr, start, end, strand, name/value in second file
2
efa2b391e887 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
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6 -z, --allow_zeros: Include zeros in calculations
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7 """
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8
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9 import collections
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10 import sys
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11 from galaxy.tools.util.galaxyops import *
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12 from bx.cookbook import doc_optparse
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13
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14
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15 #export PYTHONPATH=~/galaxy/lib/
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16 #running command python WeightedAverage.py interval_interpolate.bed value_interpolate.bed interpolate_result.bed
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17
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18 def stop_err(msg):
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19 sys.stderr.write(msg)
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20 sys.exit()
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21
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22
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23 def FindRate(chromosome, start_stop, dictType):
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24 OverlapList = []
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25 for tempO in dictType[chromosome]:
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26 DatabaseInterval = [tempO[0], tempO[1]]
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27 Overlap = GetOverlap( start_stop, DatabaseInterval )
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28 if Overlap > 0:
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29 OverlapList.append([Overlap, tempO[2]])
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30
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31 if len(OverlapList) > 0:
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32 SumRecomb = 0
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33 SumOverlap = 0
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34 for member in OverlapList:
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35 SumRecomb += member[0]*member[1]
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36 SumOverlap += member[0]
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37 averageRate = SumRecomb/SumOverlap
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38 return averageRate
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39 else:
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40 return 'NA'
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41
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42
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43 def GetOverlap(a, b):
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44 return min(a[1], b[1])-max(a[0], b[0])
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45
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efa2b391e887 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
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46 def get_float_no_zero( field ):
efa2b391e887 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
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47 rval = float( field )
efa2b391e887 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
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48 assert rval
efa2b391e887 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
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49 return rval
efa2b391e887 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
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50
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51
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52 options, args = doc_optparse.parse( __doc__ )
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53
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54 try:
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55 chr_col_1, start_col_1, end_col_1, strand_col1 = parse_cols_arg( options.cols1 )
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56 chr_col_2, start_col_2, end_col_2, strand_col2, name_col_2 = parse_cols_arg( options.cols2 )
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57 input1, input2, input3 = args
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58 except Exception, eee:
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59 print eee
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60 stop_err( "Data issue: click the pencil icon in the history item to correct the metadata attributes." )
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61
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efa2b391e887 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
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62 if options.allow_zeros:
efa2b391e887 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
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63 get_value = float
efa2b391e887 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
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64 else:
efa2b391e887 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
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65 get_value = get_float_no_zero
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66 RecombChrDict = collections.defaultdict(list)
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67
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68 skipped = 0
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69 for line in open( input2 ):
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70 temp = line.strip().split()
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71 try:
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efa2b391e887 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
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72 value = get_value( temp[ name_col_2 ] )
efa2b391e887 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
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73 except Exception:
0
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74 skipped += 1
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75 continue
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76 tempIndex = [ int( temp[ start_col_2 ] ), int( temp[ end_col_2 ] ), value ]
efa2b391e887 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
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77 RecombChrDict[ temp[ chr_col_2 ] ].append( tempIndex )
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78
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79 print "Skipped %d features with invalid values" % (skipped)
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80
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81 fdd = open( input3, 'w' )
efa2b391e887 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
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82 for line in open( input1 ):
efa2b391e887 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
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83 line = line.strip()
efa2b391e887 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
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84 temp = line.split('\t')
efa2b391e887 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
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85 chromosome = temp[ chr_col_1 ]
efa2b391e887 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/weightedaverage commit f770c3c58f1e7e1fa5ed22d7f7aca856d36729e8
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86 start = int( temp[ start_col_1 ] )
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87 stop = int( temp[ end_col_1 ] )
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88 start_stop = [start, stop]
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89 RecombRate = FindRate( chromosome, start_stop, RecombChrDict )
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90 try:
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91 RecombRate = "%.4f" % (float(RecombRate))
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92 except:
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93 RecombRate = RecombRate
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94 fdd.write( "%s\t%s\n" % ( line, RecombRate ) )
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95 fdd.close()