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1 #Florent Angly
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2 import sys
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3 from galaxy_utils.sequence.fastq import fastqReader, fastqWriter, fastqNamedReader, fastqJoiner
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4
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5 def main():
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6 input_filename = sys.argv[1]
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7 input_type = sys.argv[2] or 'sanger'
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8 mate1_filename = sys.argv[3]
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9 mate2_filename = sys.argv[4]
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10 single1_filename = sys.argv[5]
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11 single2_filename = sys.argv[6]
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12
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13 type = input_type
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14 input = fastqNamedReader( open( input_filename, 'rb' ), format = type )
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15 mate1_out = fastqWriter( open( mate1_filename, 'wb' ), format = type )
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16 mate2_out = fastqWriter( open( mate2_filename, 'wb' ), format = type )
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17 single1_out = fastqWriter( open( single1_filename, 'wb' ), format = type )
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18 single2_out = fastqWriter( open( single2_filename, 'wb' ), format = type )
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19 joiner = fastqJoiner( type )
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20
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21 i = None
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22 skip_count = 0
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23 found = {}
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24 for i, read in enumerate( fastqReader( open( input_filename, 'rb' ), format = type ) ):
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25
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26 if read.identifier in found:
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27 del found[read.identifier]
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28 continue
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29
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30 mate1 = input.get( read.identifier )
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31
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32 mate2 = input.get( joiner.get_paired_identifier( mate1 ) )
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33
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34 if mate2:
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35 # This is a mate pair
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36 found[mate2.identifier] = None
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37 if joiner.is_first_mate( mate1 ):
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38 mate1_out.write( mate1 )
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39 mate2_out.write( mate2 )
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40 else:
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41 mate1_out.write( mate2 )
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42 mate2_out.write( mate1 )
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43 else:
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44 # This is a single
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45 skip_count += 1
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46 if joiner.is_first_mate( mate1 ):
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47 single1_out.write( mate1 )
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48 else:
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49 single2_out.write( mate1 )
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50
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51 if i is None:
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52 print "Your input file contained no valid FASTQ sequences."
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53 else:
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54 if skip_count:
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55 print 'There were %i reads with no mate.' % skip_count
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56 print 'De-interlaced %s pairs of sequences.' % ( (i - skip_count + 1)/2 )
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57
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58 input.close()
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59 mate1_out.close()
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60 mate2_out.close()
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61 single1_out.close()
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62 single2_out.close()
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63
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64
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65 if __name__ == "__main__":
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66 main()
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