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1 #!/usr/bin/env python
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2 from Bio import SeqIO
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3 import argparse
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4 import sys
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5
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6 def generate_windows(seq, window, step):
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7 '''
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8 Generates windows of a sequence, with the distance of windows
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9 defined by *step*.
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10
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11 seq -- string to split into windows.
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12 window -- integer specifying the size the generated fragments.
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13 step -- integer specifiying the distance between adjacent fragments.
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14 '''
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15 stop = window
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16 end = len(seq)
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17 for i in range(stop, end, step):
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18 start = stop-window
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19 fragment = seq[start:stop]
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20 stop_coordinate = stop #to return real stop coordinate
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21 stop = stop+step
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22 yield (fragment, start+1, stop_coordinate) #start+1 to adjust 0-based range
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23
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24
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25 def write_fragment(description, output_handle, fragment, start, stop):
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26 '''Write out fragments as fasta with description and start/stop coordinates as fasta header'''
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27 output_string = ">{0}_start:{1}_stop:{2}\n{3}\n".format(description, start, stop, fragment)
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28 output_handle.write(output_string)
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29
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30
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31 def handle_io(input, output, window = 21, step= 21):
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32 '''
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33 Keyword arguments:
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34 input -- file handle for fasta file containing sequences for which you wish to generate fragments.
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35 output -- file handle for the multi-fasta that will contain the generated fragments.
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36 window -- integer specifying the size of the fragments.
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37 step -- integer specifiying the distance between adjacent fragments.
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38 '''
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39 record_iterator = SeqIO.parse(input, "fasta")
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40 for entry in record_iterator:
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41 seq = str(entry.seq)
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42 description = str(entry.description)
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43 windows = generate_windows(seq, window, step)
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44 [write_fragment(description, output, *fragment) for fragment in windows]
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45 output.close()
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46 input.close()
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47
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48 def positive_int(val):
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49 try:
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50 assert(int(val) > 0)
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51 except:
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52 raise ArgumentTypeError("'%s' is not a valid positive int" % val)
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53 return int(val)
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54
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55 if __name__ == "__main__":
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56
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57 parser = argparse.ArgumentParser(description='Generate fixed size windows in fasta format from multi-fasta sequence.')
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58 parser.add_argument('--input', type=argparse.FileType('r'), required=True,
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59 help='supply an input multi-fasta file.')
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60 parser.add_argument('--output', type=argparse.FileType('w'), default=sys.stdout,
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61 help='supply an output multi-fasta file. If not specified use stdout.')
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62 parser.add_argument('--window', type=positive_int, default=21,
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63 help='Set the size of the generated windows')
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64 parser.add_argument('--step', type=positive_int, default=21,
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65 help='Set distance between the windows')
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66 args = parser.parse_args()
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67
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68 handle_io(args.input, args.output, args.window, args.step)
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