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1 #!/usr/bin/env python
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2 #
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3 #Copyright (c) 2011, Pacific Biosciences of California, Inc.
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4 #
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5 #All rights reserved.
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6 #
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7 #Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
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8 # * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
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9 # * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
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10 # * Neither the name of Pacific Biosciences nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
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11 #
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12 #THIS SOFTWARE IS PROVIDED BY PACIFIC BIOSCIENCES AND ITS CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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13 #WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL PACIFIC BIOSCIENCES OR ITS CONTRIBUTORS BE LIABLE FOR ANY
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14 #DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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15 #LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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16 #(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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17 #
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18 import sys, os
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19 from optparse import OptionParser
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20 from galaxy import eggs
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21 import pkg_resources
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22 pkg_resources.require( 'bx-python' )
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23 from bx.seq.fasta import FastaReader
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24
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25 def getStats( fastaFile, genomeLength, minContigLength ):
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26 lengths = []
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27 stats = { "Num" : 0,
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28 "Sum" : 0,
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29 "Max" : 0,
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30 "Avg" : 0,
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31 "N50" : 0,
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32 "99%" : 0 }
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33 fasta_reader = FastaReader( open( fastaFile, 'rb' ) )
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34 while True:
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35 seq = fasta_reader.next()
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36 if not seq:
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37 break
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38 if seq.length < minContigLength:
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39 continue
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40 lengths.append( seq.length )
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41 if lengths:
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42 stats[ 'Num' ] = len( lengths )
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43 stats[ 'Sum' ] = sum( lengths )
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44 stats[ 'Max' ] = max( lengths )
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45 stats[ 'Avg' ] = int( sum( lengths ) / float( len( lengths ) ) )
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46 stats[ 'N50' ] = 0
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47 stats[ '99%' ] = 0
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48 if genomeLength == 0:
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49 genomeLength = sum( lengths )
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50 lengths.sort()
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51 lengths.reverse()
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52 lenSum = 0
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53 stats[ "99%" ] = len( lengths )
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54 for idx, length in enumerate( lengths ):
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55 lenSum += length
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56 if ( lenSum > genomeLength / 2 ):
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57 stats[ "N50" ] = length
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58 break
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59 lenSum = 0
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60 for idx, length in enumerate( lengths ):
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61 lenSum += length
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62 if lenSum > genomeLength * 0.99:
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63 stats[ "99%" ] = idx + 1
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64 break
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65 return stats
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66
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67 def __main__():
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68 #Parse Command Line
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69 usage = 'Usage: %prog input output --minContigLength'
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70 parser = OptionParser( usage=usage )
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71 parser.add_option( "--minContigLength", dest="minContigLength", help="Minimum length of contigs to analyze" )
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72 parser.add_option( "--genomeLength", dest="genomeLength", help="Length of genome for which to calculate N50s" )
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73 parser.set_defaults( minContigLength=0, genomeLength=0 )
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74 options, args = parser.parse_args()
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75 input_fasta_file = args[ 0 ]
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76 output_tabular_file = args[ 1 ]
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77 statKeys = "Num Sum Max Avg N50 99%".split( " " )
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78 stats = getStats( input_fasta_file, int( options.genomeLength ), int( options.minContigLength ) )
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79 fout = open( output_tabular_file, "w" )
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80 fout.write( "%s\n" % "\t".join( map( lambda key: str( stats[ key ] ), statKeys ) ) )
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81 fout.close()
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82
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83 if __name__=="__main__": __main__()
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