Mercurial > repos > dfornika > artic_align_trim

annotate align_trim.py @ 0:defebd1f95b9 draft

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"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
author dfornika
date Tue, 10 Mar 2020 22:03:49 +0000
parents
children 26516cf26444
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defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
1 #!/usr/bin/env python
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
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2
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
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3 # Written by Nick Loman
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
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4 # Originally part of the ZiBRA pipeline (zibraproject.org)
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
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5 # This file adapted from ARTICnetwork 'fieldbioinformatics' pipeline:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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6 # https://github.com/artic-network/fieldbioinformatics
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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7
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
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8 import sys
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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9
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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10 from collections import defaultdict
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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11 from copy import copy
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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12
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
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13 import pysam
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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14
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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15 def read_bed_file(fn):
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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16 bedfile = []
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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17 with open(fn) as csvfile:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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18 reader = csv.reader(csvfile, dialect='excel-tab')
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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19 for row in reader:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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20 bedrow = {}
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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21 bedrow['Primer_ID'] = row[3]
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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22
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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23 if len(row) >= 6:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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24 # new style bed
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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25 bedrow['direction'] = row[5]
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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26 elif len(row) == 5:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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27 # old style without directory
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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28 if 'LEFT' in row[3]:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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29 bedrow['direction'] = '+'
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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30 elif 'RIGHT' in row[3]:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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31 bedrow['direction'] = '-'
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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32 else:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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33 print("Malformed BED file!", file=sys.stderr)
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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34 raise SystemExit
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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35
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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36 if bedrow['direction'] == '+':
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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37 bedrow['end'] = int(row[2])
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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38 bedrow['start'] = int(row[1])
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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39 else:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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40 bedrow['end'] = int(row[1])
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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41 bedrow['start'] = int(row[2])
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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42 bedfile.append(bedrow)
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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43 return bedfile
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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44
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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45
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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46 def check_still_matching_bases(s):
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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47 for flag, length in s.cigartuples:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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48 if flag == 0:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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49 return True
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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50 return False
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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51
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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52 def trim(args, cigar, s, start_pos, end):
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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53 if not end:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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54 pos = s.pos
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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55 else:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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56 pos = s.reference_end
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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57
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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58 eaten = 0
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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59 while 1:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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60 ## chomp stuff off until we reach pos
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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61 if end:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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62 flag, length = cigar.pop()
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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63 else:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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64 flag, length = cigar.pop(0)
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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65
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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66 if args.verbose:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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67 print("Chomped a %s, %s" % (flag, length), file=sys.stderr)
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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68
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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69 if flag == 0:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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70 ## match
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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71 #to_trim -= length
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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72 eaten += length
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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73 if not end:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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74 pos += length
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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75 else:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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76 pos -= length
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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77 if flag == 1:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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78 ## insertion to the ref
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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79 #to_trim -= length
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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80 eaten += length
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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81 if flag == 2:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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82 ## deletion to the ref
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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83 #eaten += length
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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84 if not end:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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diff changeset
85 pos += length
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
86 else:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
87 pos -= length
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
88 pass
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
89 if flag == 4:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
90 eaten += length
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
91 if not end and pos >= start_pos and flag == 0:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
92 break
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
93 if end and pos <= start_pos and flag == 0:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
94 break
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
95
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
96 #print >>sys.stderr, "pos:%s %s" % (pos, start_pos)
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
97
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
98 extra = abs(pos - start_pos)
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
99 if args.verbose:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
100 print("extra %s" % (extra), file=sys.stderr)
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
101 if extra:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
102 if flag == 0:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
103 if args.verbose:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
104 print("Inserted a %s, %s" % (0, extra), file=sys.stderr)
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
105
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
106 if end:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
107 cigar.append((0, extra))
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
108 else:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
109 cigar.insert(0, (0, extra))
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
110 eaten -= extra
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
111
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
112 if not end:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
113 s.pos = pos - extra
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
114
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
115 if args.verbose:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
116 print("New pos: %s" % (s.pos), file=sys.stderr)
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
117
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
118 if end:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
119 cigar.append((4, eaten))
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
120 else:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
121 cigar.insert(0, (4, eaten))
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
122 oldcigarstring = s.cigarstring
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
123 s.cigartuples = cigar
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
124
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
125 #print >>sys.stderr, s.query_name, oldcigarstring[0:50], s.cigarstring[0:50]
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
126
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
127 def find_primer(bed, pos, direction):
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
128 from operator import itemgetter
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
129
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
130 closest = min([(abs(p['start'] - pos), p['start'] - pos, p) for p in bed if p['direction'] == direction], key=itemgetter(0))
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
131 return closest
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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parents:
diff changeset
132
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
133 def is_correctly_paired(p1, p2):
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
134 name1 = p1[2]['Primer_ID']
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
135 name2 = p2[2]['Primer_ID']
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
136
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
137 name1 = name1.replace('_LEFT', '')
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
138 name2 = name2.replace('_RIGHT', '')
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
139
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
140 return name1 == name2
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
141
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
142 def go(args):
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
143 if args.report:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
144 reportfh = open(args.report, "w")
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
145 print("QueryName\tReferenceStart\tReferenceEnd\tPrimerPair\tPrimer1\tPrimer1Start\tPrimer2\tPrimer2Start\tIsSecondary\tIsSupplementary\tStart\tEnd\tCorrectlyPaired", file=reportfh)
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
146
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
147 bed = read_bed_file(args.bedfile)
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
148
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
149 counter = defaultdict(int)
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
150
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
151 infile = pysam.AlignmentFile("-", "rb")
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
152 outfile = pysam.AlignmentFile("-", "wh", template=infile)
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
153 for s in infile:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
154 cigar = copy(s.cigartuples)
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
155
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
156 ## logic - if alignment start site is _before_ but within X bases of
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
157 ## a primer site, trim it off
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
158
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
159 if s.is_unmapped:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
160 print("%s skipped as unmapped" % (s.query_name), file=sys.stderr)
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
161 continue
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
162
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
163 if s.is_supplementary:
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
164 print("%s skipped as supplementary" % (s.query_name), file=sys.stderr)
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
165 continue
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
166
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
167 p1 = find_primer(bed, s.reference_start, '+')
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
168 p2 = find_primer(bed, s.reference_end, '-')
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
parents:
diff changeset
169
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
dfornika
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170 correctly_paired = is_correctly_paired(p1, p2)
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171
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172 report = "%s\t%s\t%s\t%s_%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%d" % (s.query_name, s.reference_start, s.reference_end, p1[2]['Primer_ID'], p2[2]['Primer_ID'], p1[2]['Primer_ID'], abs(p1[1]), p2[2]['Primer_ID'], abs(p2[1]), s.is_secondary, s.is_supplementary, p1[2]['start'], p2[2]['end'], correctly_paired)
defebd1f95b9 "planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/artic_align_trim commit 374121821497c96c8450afda266951c2f431ba11-dirty"
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173 if args.report:
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174 print(report, file=reportfh)
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175
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176 if args.verbose:
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177 print(report, file=sys.stderr)
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178
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179 ## if the alignment starts before the end of the primer, trim to that position
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180
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181 try:
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182 if args.start:
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183 primer_position = p1[2]['start']
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184 else:
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185 primer_position = p1[2]['end']
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186
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187 if s.reference_start < primer_position:
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188 trim(args, cigar, s, primer_position, 0)
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189 else:
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190 if args.verbose:
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191 print("ref start %s >= primer_position %s" % (s.reference_start, primer_position), file=sys.stderr)
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192
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193 if args.start:
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194 primer_position = p2[2]['start']
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195 else:
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196 primer_position = p2[2]['end']
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197
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198 if s.reference_end > primer_position:
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199 trim(args, cigar, s, primer_position, 1)
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200 else:
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201 if args.verbose:
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202 print("ref end %s >= primer_position %s" % (s.reference_end, primer_position), file=sys.stderr)
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203 except Exception as e:
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204 print("problem %s" % (e,), file=sys.stderr)
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205 pass
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206
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207 if args.normalise:
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208 pair = "%s-%s-%d" % (p1[2]['Primer_ID'], p2[2]['Primer_ID'], s.is_reverse)
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209 counter[pair] += 1
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210
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211 if counter[pair] > args.normalise:
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212 continue
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213
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214 if not check_still_matching_bases(s):
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215 continue
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216
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217 outfile.write(s)
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218
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219 reportfh.close()
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220
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221 def main():
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222 import argparse
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223
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224 parser = argparse.ArgumentParser(description='Trim alignments from an amplicon scheme.')
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225 parser.add_argument('bedfile', help='BED file containing the amplicon scheme')
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226 parser.add_argument('--normalise', type=int, help='Subsample to n coverage per strand')
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227 parser.add_argument('--report', type=str, help='Output report to file')
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228 parser.add_argument('--start', action='store_true', help='Trim to start of primers instead of ends')
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229 parser.add_argument('--verbose', action='store_true', help='Debug mode')
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230
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231 args = parser.parse_args()
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232 go(args)
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233
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234
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235 if __name__ == "__main__":
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236 main()