| 1 | #!/usr/bin/env python
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| 2 | #
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| 3 | # Rick van der Zwet
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| 4 | import sys
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| 5 | import csv
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| 6 | import string
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| 7 |
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| 8 | from MultiReplace import MultiReplace
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| 9 |
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| 10 | DEBUG = False
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| 11 |
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| 12 | # gtg is small chance
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| 13 | start_codons = ['atg', 'gtg']
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| 14 | stop_codons = ['taa', 'tga', 'tag']
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| 15 |
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| 16 | dna_flip = string.maketrans('atgc','tacg')
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| 17 | def get_codon(seq, position, order):
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| 18 | codon = seq[position:position+3]
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| 19 | if not order:
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| 20 | # When living on the other side of the string make sure to flip
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| 21 | # around before comparison
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| 22 | codon = codon[::-1].translate(dna_flip)
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| 23 | return(codon)
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| 24 |
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| 25 | def gene_detect():
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| 26 |
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| 27 | # Training and testing
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| 28 | # A -- T, G -- C
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| 29 | # lend = Left End
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| 30 | # rend = Right End
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| 31 | edl_file = 'data/edl_genes.csv'
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| 32 |
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| 33 | # Counter limit of how many 'hard' errors are allowed before bailing out
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| 34 | stop_limit = 100
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| 35 |
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| 36 | # Current shifting offset
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| 37 | base_shift = 0
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| 38 | stop_counter = 0
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| 39 |
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| 40 | # Sequences of contig, XXX: Make it a FASTA / BioPython Parser
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| 41 | contig_seq = {}
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| 42 | abstract_contig = {}
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| 43 |
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| 44 | try:
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| 45 | reader = csv.reader(open(edl_file,"rU"))
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| 46 | reader.next()
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| 47 | for row in reader:
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| 48 | finished = False
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| 49 | while not finished:
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| 50 | (featureType, zNumber, contig, lend, rend, orientation,
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| 51 | segmentType, oIslandNumber, geneName, note, function, product,
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| 52 | translationNotes) = row
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| 53 | lend = int(lend)
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| 54 | rend = int(rend)
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| 55 | if not contig_seq.has_key(contig):
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| 56 | # Load data
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| 57 | try:
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| 58 | handle = open(contig + ".raw","rU")
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| 59 | contig_seq[contig] = handle.read()
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| 60 | abstract_contig[contig] = list('.' * len(contig_seq[contig]))
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| 61 | handle.close()
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| 62 | except IOError:
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| 63 | print "Unable to open '%s'" % (sys.argv[1])
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| 64 | sys.exit(64)
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| 65 | seq = contig_seq[contig]
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| 66 |
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| 67 | # Make a forward orientation mark as positive
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| 68 | if orientation == '>':
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| 69 | order = True
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| 70 | else:
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| 71 | order = False
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| 72 |
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| 73 | # Living the world upside down to order is off
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| 74 | if order:
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| 75 | start_pos = base_shift + lend - 1
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| 76 | stop_pos = base_shift + rend - 3
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| 77 | else:
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| 78 | start_pos = base_shift + rend -3
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| 79 | stop_pos = base_shift + lend - 1
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| 80 |
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| 81 | start_codon = get_codon(seq,start_pos,order)
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| 82 | stop_codon = get_codon(seq,stop_pos,order)
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| 83 | start_match = start_codon in start_codons
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| 84 | stop_match = stop_codon in stop_codons
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| 85 |
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| 86 | if DEBUG: print "%6s, %s, %s, %s, %s, %s, %s, %s, %s, %s," % \
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| 87 | (geneName,lend,rend,start_pos, stop_pos, contig,
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| 88 | start_codon, stop_codon, orientation, base_shift),
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| 89 | if DEBUG: print "%s, %s" % (start_match, stop_match)
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| 90 |
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| 91 | if start_match and stop_match:
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| 92 | # Used for training DNA sequences and overlaps
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| 93 | print "Gene found %s, %s" % (start_pos, stop_pos)
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| 94 | if start_pos < stop_pos:
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| 95 | abstract_contig[contig][start_pos:start_pos+3] = ['<'] * 3
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| 96 | abstract_contig[contig][start_pos+3:stop_pos] = ['|'] * (stop_pos - (start_pos + 3))
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| 97 | abstract_contig[contig][stop_pos:stop_pos+3] = ['>'] * 3
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| 98 | break
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| 99 |
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| 100 | if not start_match or not stop_match:
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| 101 | if DEBUG: print "### Function (comment):", function
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| 102 |
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| 103 | # Check for fucked up offsets, shifts
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| 104 | start_shift = []
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| 105 | stop_shift = []
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| 106 | # Technically speaking should the cope only the reading frames,
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| 107 | # but what the heck looking if 'free', but make sure to include
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| 108 | # the original frames as well
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| 109 | search_range = abs(base_shift) + 3
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| 110 | if not start_match:
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| 111 | # Somewhere else in the reading frame?
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| 112 | matches = []
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| 113 | for r in range(-search_range,search_range+1):
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| 114 | l = start_pos + r
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| 115 | t = get_codon(seq,l,order)
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| 116 | new_match = t in start_codons
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| 117 | if new_match:
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| 118 | matches.append("%i:%s" % (r, t))
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| 119 | start_shift.append(r)
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| 120 | if start_shift:
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| 121 | if DEBUG: print "# Start codon reading frame matches: ", ",".join(matches)
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| 122 | if not stop_match:
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| 123 | # Somewhere else in the reading frame?
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| 124 | matches = []
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| 125 | for r in range(-search_range,search_range+1):
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| 126 | l = stop_pos + r
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| 127 | t = get_codon(seq,l,order)
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| 128 | new_match = t in stop_codons
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| 129 | if new_match:
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| 130 | stop_shift.append(r)
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| 131 | matches.append("%i:%s" % (r, t))
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| 132 | if stop_shift:
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| 133 | if DEBUG: print "# Stop codon reading frame matches: ", ",".join(matches)
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| 134 |
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| 135 |
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| 136 | # Both wrong is something screwy in the data, check offset fix
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| 137 | if not start_match and not stop_match:
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| 138 | common_shift = list(set(start_shift) & set(stop_shift))
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| 139 | if common_shift:
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| 140 | if DEBUG: print "# Matching shifts: " + ",".join(map(str,common_shift))
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| 141 | # Get the value closest to 0 for shifting purposes
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| 142 | # Currently asume no negative shifts
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| 143 | base_shift += min(common_shift)
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| 144 | finished = False
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| 145 | continue
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| 146 | # Exercise left to the reader
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| 147 | if (stop_counter > stop_limit):
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| 148 | return
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| 149 | else:
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| 150 | stop_counter += 1
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| 151 | finished = True
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| 152 | else:
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| 153 | stop_counter = 0
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| 154 | finished = True
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| 155 |
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| 156 | except csv.Error, e:
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| 157 | sys.exit('file %s, line %d: %s' % (filename, reader.line_num, e))
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| 158 |
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| 159 | for contig in abstract_contig.keys():
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| 160 | handle = open(contig + "-gene.raw", "w")
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| 161 | handle.write(''.join(abstract_contig[contig]))
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| 162 | handle.close()
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| 163 |
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| 164 | if __name__ == "__main__":
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| 165 | gene_detect()
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