Mercurial > repos > drosofff > blast_to_scaffold

annotate blast_to_scaffold.py @ 3:f7474298b40a draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit fb47b9859a0703f1fa4a1e76b75b9dae29ca8329
author drosofff
date Fri, 25 Mar 2016 19:22:25 -0400
parents 4be47f92e0f7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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a97704553a32 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 5ecc0c7c2e7a6c1dfff04a881e55aa4b6d6e60a9
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1 #!/usr/bin/env python
a97704553a32 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 5ecc0c7c2e7a6c1dfff04a881e55aa4b6d6e60a9
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2 import sys
a97704553a32 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 5ecc0c7c2e7a6c1dfff04a881e55aa4b6d6e60a9
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3 import argparse
a97704553a32 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 5ecc0c7c2e7a6c1dfff04a881e55aa4b6d6e60a9
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4
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5 def insert_newlines(string, every=60):
a97704553a32 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit 5ecc0c7c2e7a6c1dfff04a881e55aa4b6d6e60a9
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6 lines = []
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7 for i in xrange(0, len(string), every):
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8 lines.append(string[i:i+every])
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9 return '\n'.join(lines)
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10
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11 def getseq (fastadict, transcript, up, down, orientation="direct"):
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12 def reverse (seq):
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13 revdict = {"A":"T","T":"A","G":"C","C":"G","N":"N"}
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14 revseq = [revdict[i] for i in seq[::-1]]
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15 return "".join(revseq)
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16 pickseq = fastadict[transcript][up-1:down]
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17 if orientation == "direct":
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18 return pickseq
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19 else:
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20 return reverse(pickseq)
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21
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22 def Parser():
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23 the_parser = argparse.ArgumentParser(
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24 description="Generate DNA scaffold from blastn or tblastx alignment of Contigs")
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25 the_parser.add_argument(
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26 '--sequences', action="store", type=str, help="input sequence file in fasta format")
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27 the_parser.add_argument(
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28 '--guideSequence', action="store", type=str, help="the reference sequence to guide the scaffold assembly in fasta format")
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29 the_parser.add_argument(
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30 '--blast-tab', dest="blast_tab", action="store", type=str, help="13-columns tabular blastn or tblastx output")
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31 the_parser.add_argument(
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32 '--output', action="store", type=str, help="output file path, fasta format")
3
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33 the_parser.add_argument(
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34 '--scaffold_prefix', action="store", type=str, help="the prefix that will be used for the header of the fasta scaffold")
f7474298b40a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit fb47b9859a0703f1fa4a1e76b75b9dae29ca8329
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35 the_parser.add_argument(
f7474298b40a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/blast_to_scaffold commit fb47b9859a0703f1fa4a1e76b75b9dae29ca8329
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36 '--scaffold_suffix', action="store", type=str, help="the sufix that will be used for the header of the fasta scaffold")
0
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37 args = the_parser.parse_args()
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38 return args
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39
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40 def blatnInfo (file):
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41 blastlist = []
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42 with open(file, "r") as f:
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43 for line in f:
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44 minilist = []
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45 fields = line.rstrip().split()
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46 minilist.append(fields[0])
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47 minilist.extend(fields[6:10])
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48 blastlist.append(minilist)
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49 blastlist.sort(key=lambda x: x[3], reverse=True)
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50 return blastlist
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51
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52 def myContigs (file):
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53 Contigs = {}
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54 with open(file, "r") as f:
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55 for line in f:
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56 if line[0] == ">":
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57 header = line[1:-1]
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58 Contigs[header] = ""
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59 else:
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60 Contigs[header] += line[:-1]
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61 return Contigs
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62
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63 def myGuide (file):
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64 Guide = {}
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65 coordinate = 0
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66 with open(file, "r") as f:
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67 for line in f:
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68 if line[0] == ">":
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69 continue
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70 else:
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71 for nucleotide in line[:-1]:
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72 coordinate += 1
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73 Guide[coordinate] = nucleotide.lower()
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74 return Guide
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75
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76 def updateGuide (blastlist, GuideDict, ContigsDict):
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77 '''
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78 the blastlist object is a list of list with
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79 element [0] : name of the blasted Contig
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80 element [1] : queryStart of the alignment to the reference
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81 element [2] = queryStop of the alignment to the reference
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82 element [3] : subjectStart of the alignment to the reference
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83 element [4] = subjectStop of the alignment to the reference
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84 '''
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85 for fields in blastlist:
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86 seqHeader = fields[0]
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87 queryStart = int(fields[1])
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88 queryStop = int(fields[2])
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89 subjectStart = int(fields[3])
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90 subjectStop = int(fields[4])
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91 if subjectStart > subjectStop:
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92 subjectStart, subjectStop = subjectStop, subjectStart
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93 orientation = "reverse"
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94 else:
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95 orientation = "direct"
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96 sequence = getseq (ContigsDict, seqHeader, queryStart, queryStop, orientation)
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97 for i in range(subjectStart, subjectStop+1):
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98 try:
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99 del GuideDict[i]
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100 except KeyError:
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101 continue
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102 for i, nucleotide in enumerate(sequence):
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103 GuideDict[i+subjectStart] = nucleotide
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104
3
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105 def finalAssembly (GuideDict, outputfile, prefix, suffix):
0
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106 finalSeqList = []
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107 for keys in sorted(GuideDict):
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108 finalSeqList.append(GuideDict[keys])
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109 finalSequence = insert_newlines("".join(finalSeqList) )
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110 Out = open (outputfile, "w")
3
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111 print >> Out, ">Scaffold_from_%s_guided_by_%s" % (prefix, suffix)
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112 print >> Out, finalSequence
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113 Out.close()
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114
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115 def __main__():
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116 args = Parser()
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117 ContigsDict = myContigs (args.sequences)
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118 GuideDict = myGuide (args.guideSequence)
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119 blastlist = blatnInfo(args.blast_tab)
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120 updateGuide(blastlist, GuideDict, ContigsDict)
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121 finalAssembly(GuideDict, args.output, args.scaffold_prefix, args.scaffold_suffix)
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122
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123 if __name__ == "__main__":
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124 __main__()