Mercurial > repos > bgruening > bionano_scaffold

annotate remove_fake_cut_sites.py @ 4:8cc3862f8b8e draft

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"planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
author bgruening
date Tue, 25 May 2021 20:12:52 +0000
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4
8cc3862f8b8e "planemo upload for repository https://bionanogenomics.com/support/software-downloads/ commit a3d75aba3a21d88adb3706fbcefcaed4fbcb80fe"
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1 import re
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2 import sys
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3
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4 from Bio import SeqIO
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5 from Bio.Seq import Seq
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6
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7
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8 def main():
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9
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10 fasta_file = sys.argv[1]
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11 output_file = sys.argv[2]
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12 log_file = sys.argv[3]
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13
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14 output_handle = open(output_file, "w")
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15 log_handle = open(log_file, "w")
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16
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17 with open(fasta_file, "r") as fasta_input_handle:
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18 for record in SeqIO.parse(fasta_input_handle, "fasta"):
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19
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20 change_count = 0
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21 cut_sites = [
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22 Seq("CTTAAG"),
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23 Seq("CTTCTCG"),
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24 Seq("GCTCTTC"),
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25 Seq("CCTCAGC"),
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26 Seq("GAATGC"),
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27 Seq("GCAATG"),
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28 Seq("ATCGAT"),
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29 Seq("CACGAG"),
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30 ]
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31
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32 for cut_site in cut_sites:
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33 cut_site_both_orientations = (cut_site, cut_site.reverse_complement())
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34
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35 for cut_site_for_orientation in cut_site_both_orientations:
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36
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37 n_flank_length = 1
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38 search_pattern = (
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39 "N" * n_flank_length
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40 + str(cut_site_for_orientation)
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41 + "N" * n_flank_length
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42 )
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43 replacement = "N" * (
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44 n_flank_length * 2 + len(cut_site_for_orientation)
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45 )
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46
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47 (new_string, changes) = re.subn(
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48 search_pattern,
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49 replacement,
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50 str(record.seq.upper()),
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51 flags=re.IGNORECASE,
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52 )
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53 change_count += changes
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54
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55 record.seq = Seq(new_string)
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56
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57 if change_count > 0:
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58 log_handle.write(
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59 " ".join([record.id, ":", str(change_count), "changes\n"])
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60 )
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61 SeqIO.write([record], output_handle, "fasta")
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62
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63 # Finally, count the matches
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64 possible_fake_cut_sites = re.findall(
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65 "N[^N]{1,10}N", str(record.seq.upper())
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66 )
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67 if len(possible_fake_cut_sites) > 0:
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68 log_handle.write(
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69 " ".join(
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70 [
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71 record.id,
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72 ":",
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73 str(len(possible_fake_cut_sites)),
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74 "possible non-standard fake cut sites\n",
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75 ]
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76 )
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77 )
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78
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79 output_handle.close()
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80 log_handle.close()
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81
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82
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83 if __name__ == "__main__":
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84 main()