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1
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2 #!/usr/bin/env python
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3
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4 import sys
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5 import string
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6 import os
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7
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8 class convertitori:
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9 def __init__(self,input,inouttype,type,output):
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10 self.input = input
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11 self.inouttype = inouttype
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12 self.type = type
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13 self.output = output
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14
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15 def fp(self):
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16 count = 0
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17 cseq = 0
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18 fasta = []
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19 for riga in self.input:
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20 count += 1
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21 if ">" in riga:
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22 f = ""
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23 p = self.input.index(riga,count-1)
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24 c = 1
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25 y = riga[1:].replace(" ","_")
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26 if y >= 10:
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27 f = f + y[:10] + '\t'
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28 else:
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29 f = f + y + "_"*(10-len(y)) + '\t'
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30 try:
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31 while ">" not in self.input[p+c]:
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32 f = f + (self.input[p+c].strip())
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33 c += 1
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34 except:
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35 pass
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36 fasta.append(f)
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37 num = str(len(fasta))
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38 lun = str(len(fasta[0].split("\t")[1]))
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39 for sequence in fasta:
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40 if str(len(sequence.split("\t")[1])) != lun:
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41 sys.exit("The input file does not contains a multiple alignment in fasta format. Please ensure that all the sequences have the same length")
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42 self.output.write(num + '\t' + lun + '\n')
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43 for seq in fasta:
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44 self.output.write(seq + '\n')
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45
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46 def fn(self):
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47 count = 0
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48 fasta = []
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49 for riga in self.input:
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50 count += 1
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51 if ">" in riga:
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52 f = ""
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53 p = self.input.index(riga,count-1)
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54 c = 1
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55 y = riga[1:].replace(" ","_")
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56 if y >= 10:
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57 f = f + y[:10] + '\t'
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58 else:
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59 f = f + y + "_"*(10-len(y)) + '\t'
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60 try:
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61 while ">" not in self.input[p+c]:
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62 f = f + (self.input[p+c].strip())
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63 c += 1
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64 except:
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65 pass
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66 fasta.append(f)
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67 num = str(len(fasta))
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68 lun = str(len(fasta[0].split("\t")[1]))
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69 for sequence in fasta:
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70 if str(len(sequence.split("\t")[1])) != lun:
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71 sys.exit("The input file does not contains a multiple alignment in fasta format. Please ensure that all the sequences have the same length")
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72 self.output.write("#NEXUS\n\nBEGIN DATA;\nDIMENSIONS NTAX=%s NCHAR=%s;\nFORMAT DATATYPE=DNA INTERLEAVE MISSING=-;\n\nMATRIX\n"%(num,lun))
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73 porzioni = int(lun)/100
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74 for volte in range(porzioni):
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75 for seq in fasta:
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76 part = ""
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77 self.output.write(seq.split("\t")[0] + '\t')
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78 cont = 0
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79 for chara in seq.split("\t")[1][volte*100:(volte+1)*100]:
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80 cont += 1
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81 part = part + chara
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82 if cont%20.0 == 0:
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83 part = part + " "
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84 part = part + "\n"
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85 self.output.write(part)
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86 self.output.write("\n\n\n")
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87 for seq in fasta:
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88 part = ""
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89 cont = 0
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90 self.output.write(seq.split("\t")[0] + '\t')
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91 for chara in seq.split("\t")[1][(volte+1)*100:]:
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92 cont += 1
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93 part = part + chara
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94 if cont%20.0 == 0:
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95 part = part + " "
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96 part = part + "\n"
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97 self.output.write(part)
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98
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99 def pn(self):
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100 num = int(self.input[0].split()[0])
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101 lun = float(self.input[0].split()[1])
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102 lunf = float(len(self.input))
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103 self.output.write("#NEXUS\n\nBEGIN DATA;\nDIMENSIONS NTAX=%s NCHAR=%s;\nFORMAT DATATYPE=DNA INTERLEAVE MISSING=-;\n\nMATRIX\n"%(int(num),lun))
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104 spia = 0
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105 porzioni = int(lun)/100
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106 if (lunf-1)/num == 1.0:
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107 spia = 1
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108 if spia == 1:
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109 for volte in range(porzioni):
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110 for seq in self.input[1:]:
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111 part = ""
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112 self.output.write(seq.split("\t")[0] + '\t')
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113 cont = 0
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114 for chara in seq.split("\t")[1][volte*100:(volte+1)*100]:
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115 cont += 1
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116 part = part + chara
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117 if cont%20.0 == 0:
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118 part = part + " "
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119 part = part + "\n"
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120 self.output.write(part)
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121 self.output.write("\n\n\n")
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122 for seq in self.input[1:]:
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123 part = ""
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124 cont = 0
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125 self.output.write(seq.split("\t")[0] + '\t')
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126 for chara in seq.split("\t")[1][(volte+1)*100:]:
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127 cont += 1
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128 part = part + chara
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129 if cont%20.0 == 0:
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130 part = part + " "
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131 part = part + "\n"
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132 self.output.write(part)
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133 else:
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134 if len(self.input[1])<=11:
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135 for volte in range(porzioni):
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136 interm = 0
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137 for seq in self.input[1:]:
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138 if seq == "\n":
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139 interm += 1
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140 if (self.input.index(seq)+interm)%2 == 0 and seq != "\n":
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141 part = ""
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142 cont = 0
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143 for chara in seq[volte*100:(volte+1)*100]:
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144 cont += 1
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145 part = part + chara
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146 if cont%20.0 == 0:
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147 part = part + " "
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148 part = part + "\n"
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149 self.output.write(part)
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150 elif (self.input.index(seq)+interm)%2 != 0 and seq != "\n":
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151 self.output.write(seq[:10] + "\t")
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152 self.output.write("\n\n\n")
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153 interm = 0
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154 for seq in self.input[1:]:
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155 if seq == "\n":
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156 interm += 1
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157 if (self.input.index(seq)+interm)%2 == 0 and seq != "\n":
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158 part = ""
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159 cont = 0
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160 for chara in seq[(volte+1)*100:]:
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161 cont += 1
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162 part = part + chara
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163 if cont%20.0 == 0:
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164 part = part + " "
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165 part = part + "\n"
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166 self.output.write(part)
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167 elif (self.input.index(seq)+interm)%2 != 0 and seq != "\n":
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168 self.output.write(seq[:10] + "\t")
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169 else:
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170 try:
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171 diz = {}
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172 volta = 0
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173 for riga in self.input[1:]:
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174 if self.input.index(riga) in range(num+1):
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175 numriga = self.input.index(riga)
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176 diz[self.input.index(riga)] = [self.input[numriga][:10],self.input[numriga][10:].strip().replace(" ","")]
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177 else:
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178 if riga == "\n":
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179 volta += 1
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180 else:
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181 numriga = self.input.index(riga)
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182 prima = diz[numriga - ((num+1)*volta)][1] + self.input[self.input.index(riga)].strip().replace(" ","")
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183 diz[numriga - ((num+1)*volta)] = [diz[numriga - ((num+1)*volta)][0],prima]
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184 for volte in range(porzioni):
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185 for seq in diz.keys():
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186 cont = 0
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187 self.output.write(diz[seq][0] + "\t")
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188 for chara in diz[seq][1][volte*100:(volte+1)*100]:
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189 self.output.write(chara)
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190 cont += 1
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191 if cont%20.0 == 0:
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192 self.output.write(" ")
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193 self.output.write("\n")
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194 self.output.write("\n\n\n")
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195 for seq in diz.keys():
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196 cont = 0
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197 self.output.write(diz[seq][0] + "\t")
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198 for chara in diz[seq][1][(volte+1)*100:]:
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199 self.output.write(chara)
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200 cont += 1
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201 if cont%20.0 == 0:
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202 self.output.write(" ")
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203 self.output.write("\n")
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204 except:
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205 sys.exit("The input file is not in the proper format. Please check that your file is in Phylip standard interleaved (or sequential) format ")
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206
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207 def pf(self):
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208 num = int(self.input[0].split()[0])
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209 lun = float(len(self.input))
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210 spia = 0
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211 if (lun-1)/num == 1.0:
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212 spia = 1
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213 if spia == 1:
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214 for riga in self.input[1:]:
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215 for ele in range(int(lun-1)):
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216 cont = 0
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217 self.output.write(">" + self.input[ele+1][:10] + "\n")
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218 for char in self.input[ele+1][10:].strip().replace(" ",""):
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219 self.output.write(char)
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220 cont += 1
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221 if cont%80.0 == 0:
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222 self.output.write('\n')
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223 self.output.write('\n')
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224 else:
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225 if len(self.input[1])<=11:
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226 interm = 0
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227 for riga in self.input[1:]:
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228 if riga == "\n":
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229 interm += 1
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230 if (self.input.index(riga)+interm)%2 == 0 and riga != "\n":
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231 cont = 0
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232 for char in riga.strip().replace(" ",""):
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233 self.output.write(char)
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234 cont += 1
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235 if cont%80.0 == 0:
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236 self.output.write('\n')
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237 self.output.write('\n')
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238 elif (self.input.index(riga)+interm)%2 != 0 and riga != "\n":
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239 self.output.write(">" + riga[:10] + "\n")
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240 else:
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241 try:
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242 diz = {}
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243 volta = 0
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244 for riga in self.input[1:]:
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245 if self.input.index(riga) in range(num+1):
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246 numriga = self.input.index(riga)
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247 diz[self.input.index(riga)] = [self.input[numriga][:10],self.input[numriga][10:].strip().replace(" ","")]
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248 else:
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249 if riga == "\n":
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250 volta += 1
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251 else:
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252 numriga = self.input.index(riga)
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253 prima = diz[numriga - ((num+1)*volta)][1] + self.input[self.input.index(riga)].strip().replace(" ","")
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254 diz[numriga - ((num+1)*volta)] = [diz[numriga - ((num+1)*volta)][0],prima]
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255 for elemento in diz.keys():
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256 self.output.write(">" + diz[elemento][0] + '\n')
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257 con = 0
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258 for char in diz[elemento][1]:
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259 self.output.write(char)
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260 con += 1
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261 if con%80 == 0:
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262 self.output.write('\n')
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263 self.output.write('\n')
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264 except:
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265 sys.exit("The input file is not in the proper format. Please check that your file is in Phylip standard interleaved (or sequential) format ")
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266
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267 def nf(self):
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268 try:
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269 diz = {}
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270 spia = 0
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271 for riga in self.input:
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272 if "MATRIX" in riga:
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273 spia = 1
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274 if spia == 1 and "MATRIX" not in riga and riga != "\n":
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275 if riga.split()[0] not in diz.keys():
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276 diz[riga.split()[0]] = ""
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277 else:
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278 for ele in riga.split()[1:]:
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279 diz[riga.split()[0]] = diz[riga.split()[0]] + ele.strip()
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280 for elemento in diz.keys():
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281 self.output.write(">" + elemento + '\n')
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282 con = 0
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283 for char in diz[elemento]:
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284 self.output.write(char)
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285 con += 1
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286 if con%80 == 0:
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287 self.output.write('\n')
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288 self.output.write('\n')
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289 except:
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290 sys.exit("The input file is not in Nexus format. ")
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291
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292 def np(self):
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293 try:
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294 diz = {}
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295 spia = 0
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296 for riga in self.input:
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297 if "MATRIX" in riga:
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298 spia = 1
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299 if spia == 1 and "MATRIX" not in riga and riga != "\n":
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300 if riga.split()[0] not in diz.keys():
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301 diz[riga.split()[0]] = ""
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302 else:
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303 for ele in riga.split()[1:]:
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304 diz[riga.split()[0]] = diz[riga.split()[0]] + ele.strip()
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305 num = str(len(diz.keys()))
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306 lun = str(len(diz.values()[0]))
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307 self.output.write(num + '\t' + lun + '\n')
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308 for elemento in diz.keys():
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309 if elemento >= 10:
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310 nome = elemento[:10] + '\t'
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311 else:
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312 nome = elemento + "_"*(10-len(elemento)) + '\t'
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313 self.output.write(nome + diz[elemento] + '\n')
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314 except:
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315 sys.exit("The input file is not in Nexus format. ")
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316
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317
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318 def fg(self):
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319 count = 0
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320 fasta = []
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321 for riga in self.input:
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322 count += 1
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323 if ">" in riga:
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324 f = ""
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325 p = self.input.index(riga,count-1)
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326 c = 1
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327 y = riga[1:-1].replace(" ","_")
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328 f = f + y + '\t'
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329 try:
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330 while ">" not in self.input[p+c]:
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331 f = f + (self.input[p+c].strip())
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332 c += 1
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333 except:
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334 pass
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335 fasta.append(f)
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336 for seq in fasta:
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337 lun = str(len(seq.split("\t")[1]))
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338 self.output.write("LOCUS\t%s\t%s bp\nORIGIN\n"%(seq.split("\t")[0],lun))
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339 porzioni = int(lun)/60
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340 cont = 0
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341 for volte in range(porzioni):
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342 part = ""
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343 self.output.write(str(cont+1) + "\t")
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344 for chara in seq.split("\t")[1][volte*60:(volte+1)*60]:
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345 cont += 1
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346 part = part + chara
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347 if cont%10.0 == 0:
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348 part = part + " "
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349 self.output.write(part)
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350 self.output.write("\n")
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351 self.output.write(str(cont+1) + "\t")
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352 part = ""
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353 for chara in seq.split("\t")[1][(volte+1)*60:]:
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354 cont += 1
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355 part = part + chara
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356 if cont%10.0 == 0:
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357 part = part + " "
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358 self.output.write(part)
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359 self.output.write("\n")
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360 self.output.write("//\n\n")
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361
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362 def gf(self):
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363 for riga in self.input:
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364 if "LOCUS" in riga:
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365 nome = ""
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366 spia = 0
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367 len = ""
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368 seq = ""
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369 part = riga.split()
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370 for ele in part:
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371 if "bp" in ele:
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372 len = str(riga.index(ele)-1)
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373 nome = part[1] + '\t'
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374 if "DEFINITION" in riga:
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375 part = riga.split()
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376 for ele in part[1:]:
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377 nome = nome + ele + ' '
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378 if "ORIGIN" in riga:
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379 spia = 1
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380 if spia == 1 and "ORIGIN" not in riga:
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381 part = riga.split()
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382 for ele in part[1:]:
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383 seq = seq + ele.strip()
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384 if "//" in riga:
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385 self.output.write(">" + nome + '\n')
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386 con = 0
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387 for char in seq:
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388 self.output.write(char)
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389 con += 1
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390 if con%80 == 0:
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391 self.output.write('\n')
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392 self.output.write('\n')
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393 spia = 0
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394
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395 class check_fileformat:
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396 def __init__(self,inouttype,input):
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397 self.intype = inouttype[0]
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398 self.infile = input
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399 def single(self):
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400 if self.intype == "f":
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401 count = 0
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402 for riga in self.infile:
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403 if riga[0] == ">":
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404 count += 1
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405 if count == 1:
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406 if len(self.infile) < 2:
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407 sys.exit("The input file is not in fasta format. Please check that the first row starts with > and that the sequence starts from the second line")
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408 else:
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409 return "ok"
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410 else:
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411 if count >1:
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412 sys.exit("The input file is a multi-fasta file. Please resubmit the job using the 'multi sequence' option")
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413 if count == 0:
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414 sys.exit("The input file is not in fasta format. Please check that the first row starts with > and that the sequence starts from the second line")
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415 if self.intype == "g":
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416 locus = 0
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417 origin = 0
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418 end = 0
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419 lun = 1
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420 for riga in self.infile:
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421 if "LOCUS" in riga:
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422 locus = 1
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423 if "ORIGIN" in riga:
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424 origin = 1
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425 elif origin == 1 and len(riga.split()) >= 7:
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426 lun = 0
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427 if "//" in riga:
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428 end = 1
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429 if locus == 0 or origin == 0 or end == 0 or lun == 1:
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430 sys.exit("The input file is not in GenBank format. Please make sure that the file contains at least the LOCUS and ORIGIN fields. The file must also ends with //")
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431 else:
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432 return "ok"
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433 def multi(self):
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434 if self.intype == "p":
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435 if len(self.infile[0].split()) == 2 or len(self.infile[0].split()) == 3:
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436 if int(self.infile[0].split()[0]) > 1:
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437 return "ok"
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438 else:
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439 sys.exit("There is only one sequence in the file")
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440 else:
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441 sys.exit("the input file is not in phylip format.")
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442 if self.intype == "n":
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443 begin = 0
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444 matrix = 0
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445 ntax = 0
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446 if "#NEXUS" in self.infile[0]:
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447 for riga in self.infile:
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448 if "begin data;" in riga.lower():
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449 begin = 1
|
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450 if "matrix" in riga.lower():
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451 matrix = 1
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|
|
452 if "ntax" in riga.lower():
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|
453 r = riga.split()
|
|
|
454 ntax = int(r[1][5:])
|
|
|
455 if begin==1 and matrix == 1:
|
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|
456 return "ok"
|
|
|
457 else:
|
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|
458 sys.exit("the input file is not in nexus format.")
|
|
|
459 if ntax <= 1:
|
|
|
460 sys.exit("There is only one sequence in the file")
|
|
|
461 else:
|
|
|
462 sys.exit("the input file is not in nexus format.")
|
|
|
463 if self.intype == "f":
|
|
|
464 count = 0
|
|
|
465 for riga in self.infile:
|
|
|
466 if riga[0] == ">":
|
|
|
467 count += 1
|
|
|
468 if count > 1:
|
|
|
469 if len(self.infile) < 4:
|
|
|
470 sys.exit("The input file is not in fasta format. Please check that the first row starts with > and that the sequence starts from the second line")
|
|
|
471 else:
|
|
|
472 return "ok"
|
|
|
473 else:
|
|
|
474 if count == 1:
|
|
|
475 sys.exit("The input file is a single-fasta file. Please resubmit the job using the 'single sequence' option")
|
|
|
476 if count == 0:
|
|
|
477 sys.exit("The input file is not in fasta format. Please check that the first row starts with > and that the sequence starts from the second line")
|
|
|
478 if self.intype == "g":
|
|
|
479 locus = 0
|
|
|
480 origin = 0
|
|
|
481 end = 0
|
|
|
482 lun = 1
|
|
|
483 for riga in self.infile:
|
|
|
484 if "LOCUS" in riga:
|
|
|
485 locus = 1
|
|
|
486 if "ORIGIN" in riga:
|
|
|
487 origin = 1
|
|
|
488 if origin == 1 and len(riga.split()) >= 7:
|
|
|
489 lun = 0
|
|
|
490 if "//" in riga:
|
|
|
491 end = 1
|
|
|
492 if locus == 0 or origin == 0 or end == 0 or lun == 1:
|
|
|
493 sys.exit("The input file is not in GenBank format. Please make sure that the file contains at least the LOCUS and ORIGIN fields. The file must also ends with //")
|
|
|
494 else:
|
|
|
495 return "ok"
|
|
|
496
|
|
|
497
|
|
|
498 def main(input,output,inouttype,type):
|
|
|
499 check = check_fileformat(inouttype,input)
|
|
|
500 if type == "single":
|
|
|
501 c = check.single()
|
|
|
502 if c == "ok":
|
|
|
503 conv = convertitori(input,inouttype,type,output)
|
|
|
504 if inouttype == "f-g":
|
|
|
505 conv.fg()
|
|
|
506 if inouttype == "g-f":
|
|
|
507 conv.gf()
|
|
|
508 if type == "multi":
|
|
|
509 c = check.multi()
|
|
|
510 if c == "ok":
|
|
|
511 conv = convertitori(input,inouttype,type,output)
|
|
|
512 if inouttype == "f-g":
|
|
|
513 conv.fg()
|
|
|
514 if inouttype == "g-f":
|
|
|
515 conv.gf()
|
|
|
516 if inouttype == "f-p":
|
|
|
517 conv.fp()
|
|
|
518 if inouttype == "f-n":
|
|
|
519 conv.fn()
|
|
|
520 if inouttype == "p-f":
|
|
|
521 conv.pf()
|
|
|
522 if inouttype == "p-n":
|
|
|
523 conv.pn()
|
|
|
524 if inouttype == "n-p":
|
|
|
525 conv.np()
|
|
|
526 if inouttype == "n-f":
|
|
|
527 conv.nf()
|
|
|
528 output.close()
|
|
|
529
|
|
|
530 if __name__ == "__main__" :
|
|
|
531 input = open(sys.argv[1],"r").readlines()
|
|
|
532 output = open(sys.argv[2],"a")
|
|
|
533 inouttype = sys.argv[3]
|
|
|
534 type = sys.argv[4]
|
|
|
535 main(input,output,inouttype,type)
|
