Mercurial > repos > drosofff > msp_blastparser_and_hits

annotate BlastParser_and_hits.py @ 0:69ea2a13947f draft

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author drosofff
date Sun, 21 Jun 2015 14:31:29 -0400
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children 1964514aabde
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0
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1 #!/usr/bin/python
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2 # blastn blastx parser revised debugged: 3-4-2015. Commit issue.
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3 # drosofff@gmail.com
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4
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5 import sys
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6 import argparse
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7 from collections import defaultdict
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8
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9 def Parser():
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10 the_parser = argparse.ArgumentParser()
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11 the_parser.add_argument('--blast', action="store", type=str, help="Path to the blast output (tabular format, 12 column)")
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12 the_parser.add_argument('--sequences', action="store", type=str, help="Path to the fasta file with blasted sequences")
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13 the_parser.add_argument('--fastaOutput', action="store", type=str, help="fasta output file of blast hits")
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14 the_parser.add_argument('--tabularOutput', action="store", type=str, help="tabular output file of blast analysis")
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15 the_parser.add_argument('--flanking', action="store", type=int, help="number of flanking nucleotides added to the hit sequences")
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16 the_parser.add_argument('--mode', action="store", choices=["verbose", "short"], type=str, help="reporting (verbose) or not reporting (short) oases contigs")
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17 args = the_parser.parse_args()
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18 if not all ( (args.sequences, args.blast, args.fastaOutput, args.tabularOutput) ):
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19 the_parser.error('argument(s) missing, call the -h option of the script')
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20 if not args.flanking:
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21 args.flanking = 0
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22 return args
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23
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24 def median(lst):
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25 lst = sorted(lst)
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26 if len(lst) < 1:
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27 return None
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28 if len(lst) %2 == 1:
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29 return lst[((len(lst)+1)/2)-1]
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30 if len(lst) %2 == 0:
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31 return float(sum(lst[(len(lst)/2)-1:(len(lst)/2)+1]))/2.0
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32
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33 def mean(lst):
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34 if len(lst) < 1:
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35 return 0
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36 return sum(lst) / float(len(lst))
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37
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38 def getfasta (fastafile):
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39 fastadic = {}
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40 for line in open (fastafile):
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41 if line[0] == ">":
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42 header = line[1:-1]
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43 fastadic[header] = ""
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44 else:
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45 fastadic[header] += line
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46 for header in fastadic:
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47 fastadic[header] = "".join(fastadic[header].split("\n"))
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48 return fastadic
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49
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50 def insert_newlines(string, every=60):
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51 lines = []
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52 for i in xrange(0, len(string), every):
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53 lines.append(string[i:i+every])
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54 return '\n'.join(lines)
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55
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56 def getblast (blastfile):
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57 '''blastinfo [0] Percentage of identical matches
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58 blastinfo [1] Alignment length
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59 blastinfo [2] Number of mismatches
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60 blastinfo [3] Number of gap openings
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61 blastinfo [4] Start of alignment in query
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62 blastinfo [5] End of alignment in query
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63 blastinfo [6] Start of alignment in subject (database hit)
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64 blastinfo [7] End of alignment in subject (database hit)
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65 blastinfo [8] Expectation value (E-value)
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66 blastinfo [9] Bit score
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67 blastinfo [10] Subject length (NEED TO BE SPECIFIED WHEN RUNNING BLAST) '''
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68 blastdic = defaultdict (dict)
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69 for line in open (blastfile):
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70 fields = line[:-1].split("\t")
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71 transcript = fields[0]
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72 subject = fields[1]
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73 blastinfo = [float(fields[2]) ] # blastinfo[0]
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74 blastinfo = blastinfo + [int(i) for i in fields[3:10] ] # blastinfo[1:8] insets 1 to 7
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75 blastinfo.append(fields[10]) # blastinfo[8] E-value remains as a string type
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76 blastinfo.append(float(fields[11])) # blastinfo[9] Bit score
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77 blastinfo.append(int(fields[12])) # blastinfo[10] Subject length MUST BE RETRIEVED THROUGH A 13 COLUMN BLAST OUTPUT
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78 try:
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79 blastdic[subject][transcript].append(blastinfo)
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80 except:
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81 blastdic[subject][transcript] = [ blastinfo ]
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82 return blastdic
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83
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84 def getseq (fastadict, transcript, up, down, orientation="direct"):
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85 def reverse (seq):
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86 revdict = {"A":"T","T":"A","G":"C","C":"G","N":"N"}
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87 revseq = [revdict[i] for i in seq[::-1]]
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88 return "".join(revseq)
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89 pickseq = fastadict[transcript][up-1:down]
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90 if orientation == "direct":
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91 return pickseq
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92 else:
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93 return reverse(pickseq)
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94
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95 def subjectCoverage (fastadict, blastdict, subject, QueriesFlankingNucleotides=0):
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96 SubjectCoverageList = []
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97 HitDic = {}
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98 bitScores = []
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99 for transcript in blastdict[subject]:
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100 prefix = "%s--%s_" % (subject, transcript)
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101 hitNumber = 0
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102 for hit in blastdict[subject][transcript]:
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103 hitNumber += 1
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104 suffix = "hit%s_IdMatch=%s,AligLength=%s,E-val=%s" % (hitNumber, hit[0], hit[1], hit[8])
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105 HitDic[prefix+suffix] = GetHitSequence (fastadict, transcript, hit[4], hit[5], QueriesFlankingNucleotides) #query coverage by a hit is in hit[4:6]
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106 SubjectCoverageList += range (min([hit[6], hit[7]]), max([hit[6], hit[7]]) + 1) # subject coverage by a hit is in hit[6:8]
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107 bitScores.append(hit[9])
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108 subjectLength = hit [10] # always the same value for a given subject. Stupid but simple
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109 TotalSubjectCoverage = len ( set (SubjectCoverageList) )
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110 RelativeSubjectCoverage = TotalSubjectCoverage/float(subjectLength)
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111 return HitDic, subjectLength, TotalSubjectCoverage, RelativeSubjectCoverage, max(bitScores), mean(bitScores)
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112
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113 def GetHitSequence (fastadict, FastaHeader, leftCoordinate, rightCoordinate, FlankingValue):
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114 if rightCoordinate > leftCoordinate:
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115 polarity = "direct"
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116 else:
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117 polarity = "reverse"
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118 leftCoordinate, rightCoordinate = rightCoordinate, leftCoordinate
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119 if leftCoordinate - FlankingValue > 0:
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120 leftCoordinate -= FlankingValue
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121 else:
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122 leftCoordinate = 1
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123 return getseq (fastadict, FastaHeader, leftCoordinate, rightCoordinate, polarity)
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124
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125 def outputParsing (F, Fasta, results, Xblastdict, fastadict, mode="verbose"):
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126 F= open(F, "w")
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127 Fasta=open(Fasta, "w")
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128 if mode == "verbose":
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129 print >>F, "# SeqId\t%Identity\tAlignLength\tStartSubject\tEndSubject\t%QueryHitCov\tE-value\tBitScore\n"
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130 for subject in sorted (results, key=lambda x: results[x]["meanBitScores"], reverse=True):
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131 print >> F, "#\n# %s" % subject
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132 print >> F, "# Suject Length: %s" % (results[subject]["subjectLength"])
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133 print >> F, "# Total Subject Coverage: %s" % (results[subject]["TotalCoverage"])
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134 print >> F, "# Relative Subject Coverage: %s" % (results[subject]["RelativeSubjectCoverage"])
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135 print >> F, "# Maximum Bit Score: %s" % (results[subject]["maxBitScores"])
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136 print >> F, "# Mean Bit Score: %s" % (results[subject]["meanBitScores"])
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137 for header in results[subject]["HitDic"]:
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138 print >> Fasta, ">%s\n%s" % (header, insert_newlines(results[subject]["HitDic"][header]) )
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139 print >> Fasta, "" # final carriage return for the sequence
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140 for transcript in Xblastdict[subject]:
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141 transcriptSize = float(len(fastadict[transcript]))
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142 for hit in Xblastdict[subject][transcript]:
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143 percentIdentity, alignLenght, subjectStart, subjectEnd, queryCov = hit[0], hit[1], hit[6], hit[7], "%.1f" % (abs(hit[5]-hit[4])/transcriptSize*100)
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144 Eval, BitScore = hit[8], hit[9]
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145 info = [transcript] + [percentIdentity, alignLenght, subjectStart, subjectEnd, queryCov, Eval, BitScore]
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146 info = [str(i) for i in info]
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147 info = "\t".join(info)
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148 print >> F, info
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149 else:
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150 print >>F, "# subject\tsubject length\tTotal Subject Coverage\tRelative Subject Coverage\tMaximum Bit Score\tMean Bit Score"
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151 for subject in sorted (results, key=lambda x: results[x]["meanBitScores"], reverse=True):
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152 line = []
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153 line.append(subject)
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154 line.append(results[subject]["subjectLength"])
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155 line.append(results[subject]["TotalCoverage"])
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156 line.append(results[subject]["RelativeSubjectCoverage"])
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157 line.append(results[subject]["maxBitScores"])
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158 line.append(results[subject]["meanBitScores"])
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159 line = [str(i) for i in line]
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160 print >> F, "\t".join(line)
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161 for header in results[subject]["HitDic"]:
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162 print >> Fasta, ">%s\n%s" % (header, insert_newlines(results[subject]["HitDic"][header]) )
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163 print >> Fasta, "" # final carriage return for the sequence
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164 F.close()
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165 Fasta.close()
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166
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167
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168
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169 def __main__ ():
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170 args = Parser()
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171 fastadict = getfasta (args.sequences)
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172 Xblastdict = getblast (args.blast)
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173 results = defaultdict(dict)
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174 for subject in Xblastdict:
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175 results[subject]["HitDic"], results[subject]["subjectLength"], results[subject]["TotalCoverage"], results[subject]["RelativeSubjectCoverage"], results[subject]["maxBitScores"], results[subject]["meanBitScores"] = subjectCoverage(fastadict, Xblastdict, subject, args.flanking)
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176 outputParsing (args.tabularOutput, args.fastaOutput, results, Xblastdict, fastadict, args.mode)
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177 if __name__=="__main__": __main__()