Mercurial > repos > iuc > ngsutils_bam_filter

annotate ngsutils/bed/__init__.py @ 0:4e4e4093d65d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
author iuc
date Wed, 11 Nov 2015 13:04:07 -0500
parents
children 7a68005de299
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4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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1 import os
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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2 import ngsutils.support.ngs_utils
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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3 import pysam
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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4
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6 class BedStreamer(object):
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7 '''
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8 Streams BedRegions from a BED file
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9
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10 Note - this can only be used once! There is no mechanism to seek the stream.
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11 '''
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12
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13 def __init__(self, fname=None, fileobj=None, quiet=False):
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14 if not fname and not fileobj:
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15 raise ValueError("You must specify either fname or fileobj!")
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17 self.reader = ngsutils.support.gzip_reader(fname=fname, quiet=quiet, fileobj=fileobj)
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19 def __iter__(self):
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20 return self
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21
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22 def next(self):
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23 try:
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24 while True:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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25 line = self.reader.next().strip()
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26 if line and line[0] != '#':
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27 cols = line.split('\t')
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28 while len(cols) < 6:
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29 cols.append('')
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30
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31 return BedRegion(*cols)
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32 except:
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33 raise StopIteration
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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36
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37 class BedFile(object):
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38 '''
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39 BED files are read in their entirety memory, in a series of bins. Each bin
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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40 is ~100kb in size. Each bin can then be iterated over.
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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41
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42 This is less efficient than using a proper index, but in reality, this
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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43 usually isn't an issue. However, if the BED file has been Tabix indexed,
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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44 that index will be used for random access.
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45
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46 NOTE: This isn't very efficient, so perhaps this can be remodeled into a BedFile
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47 and a BedFileIndex where the file is indexed only if random access is requested.
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48 '''
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49
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50 _bin_const = 100000
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51
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52 def __init__(self, fname=None, fileobj=None, region=None):
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53 self._bins = {}
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54 self._bin_list = []
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55 self._cur_bin_idx = 0
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56 self._cur_bin_pos = 0
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57 self._tellpos = 0
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58 self._total = 0
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59 self._length = 0
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60 self.__tabix = None
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61
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62 self.filename = fname
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63
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64 if os.path.exists('%s.tbi' % fname):
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65 self.__tabix = pysam.Tabixfile(fname)
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66
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67 if fileobj:
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68 self.__readfile(fileobj)
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69 elif fname:
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70 with ngsutils.support.ngs_utils.gzip_opener(fname) as fobj:
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71 self.__readfile(fobj)
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72 elif region:
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73 chrom, startend = region.split(':')
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74 if '-' in startend:
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75 start, end = [int(x) for x in startend.split('-')]
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76 else:
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77 start = int(startend)
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78 end = start
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79 start -= 1
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80
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81 self.__add_region(BedRegion(chrom, start, end))
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82 else:
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83 raise ValueError("Must specify either filename, fileobj, or region")
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84
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85 def __readfile(self, fobj):
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86 for line in fobj:
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87 line = line.strip()
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88 if line and line[0] != '#':
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89 cols = line.split('\t')
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90 while len(cols) < 6:
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91 cols.append('')
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92
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93 region = BedRegion(*cols)
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94 self.__add_region(region)
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95
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96 self._bin_list.sort()
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97 for bin in self._bins:
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98 self._bins[bin].sort()
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99
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100 def __add_region(self, region):
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101 self._total += region.end - region.start
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102 self._length += 1
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103
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104 startbin = region.start / BedFile._bin_const
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105 endbin = region.end / BedFile._bin_const
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106
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107 for bin in xrange(startbin, endbin + 1):
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108 if not (region.chrom, bin) in self._bins:
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109 self._bin_list.append((region.chrom, bin))
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110 self._bins[(region.chrom, bin)] = []
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111 self._bins[(region.chrom, bin)].append(region)
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112
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113 def fetch(self, chrom, start, end, strand=None):
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114 '''
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115 For TABIX indexed BED files, find all regions w/in a range
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116
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117 For non-TABIX index BED files, use the calculated bins, and
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118 output matching regions
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119 '''
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120
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121 if self.__tabix:
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122 for match in self.__tabix.fetch(chrom, start, end):
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123 region = BedRegion(*match.split('\t'))
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124 if not strand or (strand and region.strand == strand):
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125 yield region
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126 else:
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127 startbin = start / BedFile._bin_const
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128 endbin = end / BedFile._bin_const
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129
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130 buf = set()
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131
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132 for bin in xrange(startbin, endbin + 1):
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133 if (chrom, bin) in self._bins:
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134 for region in self._bins[(chrom, bin)]:
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135 if strand and strand != region.strand:
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136 continue
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137 if start <= region.start <= end or start <= region.end <= end:
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138 if not region in buf:
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139 yield region
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140 buf.add(region)
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141 elif region.start < start and region.end > end:
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142 if not region in buf:
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143 yield region
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144 buf.add(region)
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145
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146 def tell(self):
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147 return self._tellpos
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148
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149 def close(self):
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150 pass
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151
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152 @property
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153 def length(self):
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154 return self._length
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155
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156 @property
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157 def total(self):
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158 return self._total
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159
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160 def __iter__(self):
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161 self._cur_bin_idx = 0
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162 self._cur_bin_pos = 0
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163 self._tellpos = 0
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164 return self
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165
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166 def next(self):
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167 if self._cur_bin_idx >= len(self._bin_list):
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168 raise StopIteration
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169
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170 binvals = self._bins[self._bin_list[self._cur_bin_idx]]
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171 while self._cur_bin_pos < len(binvals):
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172 val = binvals[self._cur_bin_pos]
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173 self._cur_bin_pos += 1
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174
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175 startbin = (val.chrom, val.start / BedFile._bin_const)
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176 if startbin == self._bin_list[self._cur_bin_idx]:
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177 self._tellpos += 1
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178 return val
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179
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180 self._cur_bin_idx += 1
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181 self._cur_bin_pos = 0
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182 return self.next()
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183
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184
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185 class BedRegion(object):
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186 def __init__(self, chrom, start, end, name='', score='', strand='', thickStart='', thickEnd='', rgb='', *args):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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187 self.chrom = chrom
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iuc
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188 self.start = int(start)
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iuc
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189 self.end = int(end)
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190 self.name = name
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191
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iuc
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192 if score == '':
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iuc
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193 self.score = 0
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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194 else:
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iuc
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195 self.score = float(score)
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196
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iuc
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197 if strand == '':
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iuc
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198 self.strand = None
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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199 else:
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200 self.strand = strand
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201
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iuc
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202 if thickStart == '':
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iuc
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203 self.thickStart = None
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204 else:
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iuc
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205 self.thickStart = thickStart
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iuc
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206
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iuc
parents:
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207 if thickEnd == '':
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iuc
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208 self.thickEnd = None
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209 else:
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iuc
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210 self.thickEnd = thickEnd
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iuc
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211
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iuc
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212 if rgb == '':
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iuc
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213 self.rgb = None
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214 else:
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215 self.rgb = rgb
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216
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iuc
parents:
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217 self.extras = args
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218
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iuc
parents:
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219 def clone(self, chrom=None, start=None, end=None, name=None, score=None, strand=None, thickStart=None, thickEnd=None, rgb=None, *args):
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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220 cols = []
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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221 cols.append(self.chrom if chrom is None else chrom)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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222 cols.append(self.start if start is None else start)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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223 cols.append(self.end if end is None else end)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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224 cols.append(self.name if name is None else name)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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225 cols.append(self.score if score is None else score)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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226 cols.append(self.strand if strand is None else strand)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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227 cols.append(self.thickStart if thickStart is None else thickStart)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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228 cols.append(self.thickEnd if thickEnd is None else thickEnd)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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229 cols.append(self.rgb if rgb is None else rgb)
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230
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231 for i, val in enumerate(self.extras):
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232 if len(args) > i:
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iuc
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233 cols.append(args[i])
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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234 else:
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iuc
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235 cols.append(val)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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236
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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237 return BedRegion(*cols)
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238
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239 @property
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iuc
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240 def score_int(self):
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iuc
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241 score = str(self.score)
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iuc
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242 if score[-2:] == '.0':
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243 score = score[:-2]
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244
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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245 return score
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246
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iuc
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247 def __key(self):
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248 return (self.chrom, self.start, self.end, self.strand, self.name)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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249
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iuc
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250 def __lt__(self, other):
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iuc
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251 return self.__key() < other.__key()
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252
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iuc
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253 def __gt__(self, other):
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iuc
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254 return self.__key() > other.__key()
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255
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iuc
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256 def __eq__(self, other):
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iuc
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257 return self.__key() == other.__key()
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258
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iuc
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259 def write(self, out):
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260 out.write('%s\n' % self)
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261
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iuc
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diff changeset
262 def __repr__(self):
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iuc
parents:
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263 outcols = []
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264
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iuc
parents:
diff changeset
265 if self.rgb:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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266 outcols.append(self.rgb)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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267 if self.thickEnd or outcols:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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diff changeset
268 outcols.append(self.thickEnd if self.thickEnd else self.end)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
269 if self.thickStart or outcols:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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270 outcols.append(self.thickStart if self.thickStart else self.start)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
diff changeset
271 if self.strand or outcols:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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272 outcols.append(self.strand)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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273 if self.score_int != '' or outcols:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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274 outcols.append(self.score_int)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
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275 if self.name or outcols:
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
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276 outcols.append(self.name)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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277
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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278 outcols.append(self.end)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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279 outcols.append(self.start)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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280 outcols.append(self.chrom)
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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281
4e4e4093d65d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ngsutils commit 09194687c74a424732f8b0c017cbb942aad89068
iuc
parents:
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282 return '\t'. join([str(x) for x in outcols[::-1]])