annotate ChipSeqRatioAnalysis.py @ 6:f224513123a1 draft

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author petr-novak
date Mon, 02 Dec 2019 03:45:28 -0500
parents e320ef2d105a
children
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petr-novak
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1 #!/usr/bin/env python3
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petr-novak
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2 import re
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3 import argparse
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petr-novak
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4 import csv
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petr-novak
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5 import os
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petr-novak
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6 import sys
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petr-novak
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7 import os.path
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petr-novak
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8 import subprocess
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petr-novak
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9 import shlex
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petr-novak
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10 import multiprocessing as mp
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11 import tempfile
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12 import itertools as it
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13
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14
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15 def get_arguments():
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16
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17 parser = argparse.ArgumentParser()
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18 parser.add_argument('-m',
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19 '--max_cl',
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20 default=300,
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21 type=int,
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22 help='Sets the maximum cluster number. Default = 300')
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23 parser.add_argument('-b',
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24 '--bitscore',
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25 default=30,
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26 type=int,
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27 help='minimal bitscore to report')
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28 parser.add_argument(
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29 '-n',
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30 '--nproc',
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31 default=mp.cpu_count(),
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32 type=int,
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33 help='Sets the number of cpus to be used. Default = all available')
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34 parser.add_argument('-c',
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35 '--ChipSeq',
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36 required=True,
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37 help='Fasta file containing the Chip Sequences')
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38 parser.add_argument('-i',
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39 '--InputSeq',
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40 required=True,
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41 help='Fasta file containing the Input Sequences')
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42 parser.add_argument(
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43 '-o',
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44 '--output',
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45 required=False,
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46 default='ChipSeqRatio.csv',
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47 help=('Specify a name for the CSV file to which the'
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48 ' output will be save to. Default: ChipSeqRatio.csv'))
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49 parser.add_argument(
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50 '-ht',
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51 '--html',
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52 required=False,
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53 default='ChipSeqRatioReport',
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54 help='Specify a name for the html report. Default : ChipSeqRatioReport')
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55 parser.add_argument('-k',
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56 '--Contigs',
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57 required=True,
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58 help='Contig file for blast')
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59 args = parser.parse_args()
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60 return args
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61
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62
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63 def split(filename, num_chunks):
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64 # splits a files into nproc files
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65 files = []
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66 temp_files = []
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67
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68 # creating a list with nproc temporary files
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69 for f in range(num_chunks):
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70 temp_files.append(tempfile.NamedTemporaryFile('w', delete=False))
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71 with open(filename, 'r') as f:
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72 end = os.path.getsize(filename)
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73 for temp in it.cycle(temp_files):
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74 # cycling indefenitly through temp files
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75 ID = f.readline() # get sequence id
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76 if ID[0] == '>':
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77 temp.write(ID)
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78 SEQP = f.tell() # get file pointer location
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79 while f.readline()[0] is not '>':
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80 f.seek(SEQP) # jump to last saved file pointer
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81 temp.write(f.readline()) # write sequen
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82 SEQP = f.tell() # overwrite last file pointer location
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83 # break loop if file pointer reached the EOF
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84 if (SEQP == end):
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85 break
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86 if (SEQP == end): # break loop if file pointer reached the EOF
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87 break
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88 f.seek(SEQP)
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89
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90 for f in range(num_chunks):
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91 # save temp files names into list for further use
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92 files.append(temp_files[f].name)
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93 temp_files[f].close() # close temp files
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94 return files
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95
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96
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97 def blast(query, database, bitscore):
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98 # blast a file for given arguments and save result to a list
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99 print(query)
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100 arguments = (
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101 "blastn -task blastn -db {} -query {} "
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102 "-evalue 1e-2 -gapopen 5 -gapextend 2 -word_size 11 -num_alignments 1"
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103 " -penalty -3 -reward 2 -outfmt 6 -dust no").format(database, query)
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104 cmd = shlex.split(arguments)
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105 Blast_Output = [0 for x in range(max_cl + 1)]
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106 ma = re.compile('(\S+)\tCL(\d+)Contig') # expression to check for
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107 with subprocess.Popen(cmd,
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108 stdout=subprocess.PIPE,
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109 universal_newlines=True) as p:
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110 for line in p.stdout:
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111 if float(line.split()[11]) > bitscore:
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112 gr = ma.match(line)
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113 previous_query = ''
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114 if gr:
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115 if (gr.group(1) != previous_query):
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116 if (int(gr.group(2)) > max_cl):
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117 Blast_Output[0] = Blast_Output[0] + 1
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118 else:
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119 Blast_Output[int(gr.group(2))] = Blast_Output[
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120 int(gr.group(2))] + 1
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121 previous_query = gr.group(1)
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122 return Blast_Output
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123
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124
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125 def ReduceLists(x, y):
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126 ''' reduces two lists into a 2-dim matrix '''
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127 Matrix = [[0 for i in range(max_cl + 1)] for i in range(2)]
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128 for i in range(len(x)):
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129 for j in range(len(x[i])):
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130 Matrix[0][j] = Matrix[0][j] + x[i][j]
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131 for i in range(len(y)):
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132 for j in range(len(y[i])):
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133 Matrix[1][j] = Matrix[1][j] + y[i][j]
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134 return Matrix
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135
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136
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137 def fasta_size(fastafile):
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138 with open(fastafile, 'r') as f:
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139 s = 0
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140 for i in f:
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141 if i[0] == ">":
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142 s += 1
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143 return s
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144
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145
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146 def makeblastdb(filename):
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147 dbtmp = tempfile.NamedTemporaryFile()
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148 cmd = [
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149 'makeblastdb', '-in', filename, '-input_type', 'fasta', '-dbtype',
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150 'nucl', '-out', dbtmp.name
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151 ]
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152 subprocess.call(cmd)
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153 return dbtmp
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154
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155
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156 if __name__ == "__main__":
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157 args = get_arguments()
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158 max_cl = args.max_cl
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159 output = args.output
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160 HTMLreport = args.html
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161 contigs = args.Contigs
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162
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163 # Creation of database
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164 db = makeblastdb(contigs)
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165
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166 inputN = fasta_size(args.InputSeq)
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167 chipN = fasta_size(args.ChipSeq)
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168
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169 # Reading and distribution of data to temp files for multiprocessing
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170 filesC = split(args.ChipSeq, args.nproc)
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171 filesI = split(args.InputSeq, args.nproc)
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172
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173 # start of parallized blast
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174 pool = mp.Pool(processes=args.nproc)
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175 results = [pool.apply_async(blast, args=(f, db.name, args.bitscore)) for f in filesC]
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176 Cout = [p.get() for p in results]
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177 results = [pool.apply_async(blast, args=(f, db.name, args.bitscore)) for f in filesI]
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178 Iout = [p.get() for p in results]
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179
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180 # Merging of blast output into a 2-dim matrix
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181 Matrix = ReduceLists(Cout, Iout)
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182
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183 with open(args.output, 'w') as f:
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184 print("Cluster", "Chip_Hits", "Input_Hits", sep='\t', file=f)
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185 for hit in range(1, args.max_cl + 1):
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186 print(hit, Matrix[0][hit], Matrix[1][hit], sep='\t', file=f)
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187 Rarguments = "Rscript " + \
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188 os.path.dirname(__file__) + "/ChipSeqRatioAnalysis.R"
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189 # order is important - programmed by georg - this it realy ugly!
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190 args = shlex.split(Rarguments)
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191 args.append(output)
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192 args.append(HTMLreport)
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193 args.append(str(inputN))
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194 args.append(str(chipN))
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195 with subprocess.Popen(args, stderr=subprocess.PIPE) as p:
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196 print("Creating HTML report")
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197 stdout, stderr = p.communicate()
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198 if (len(stderr) > 0):
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199 print(stderr)
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200 # cleanup
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201 for i in filesC + filesI:
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202 os.unlink(i)