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1 #!/usr/bin/perl
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2 use strict;
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3 use warnings;
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4 use Getopt::Std;
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5
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6 my %opt;
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7 getopts('S:I:O:',\%opt);
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8
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9 my @usage=qq(
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10 Version: 2016042201
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11 Usage: perl Converter_finished.pl [options]
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12
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13 Options:
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14
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15 -S String Input the strains nickname,
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16 If 2 or more, join them with '+',
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17 For example: CT18+NC_011834+SPA
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18 -I String Input file directory
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19 -O String Output file directory
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20 );
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21
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22 if (!scalar(keys %opt))
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23 {
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24 print join("\n",@usage)."\n";
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25 exit;
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26 }
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27
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28 my @sp;
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29 if (exists($opt{"S"}))
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30 {
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31 @sp=split(/\+/,$opt{"S"});
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32 }else
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33 {
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34 print "-S could not be empty!";
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35 print join("\n",@usage)."\n";
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36 exit;
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37 }
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38
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39 my $output;
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40 if (exists($opt{"O"}))
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41 {
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42 $output=$opt{"O"};
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43 }else
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44 {
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45 print "-O could not be empty!";
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46 print join("\n",@usage)."\n";
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47 exit;
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48 }
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49
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50 my $input;
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51 if (exists($opt{"I"}))
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52 {
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53 $input=$opt{"I"};
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54 }else
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55 {
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56 print "-I could not be empty!";
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57 print join("\n",@usage)."\n";
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58 exit;
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59 }
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60
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61 my $sp;
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62 my $line;
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63 my @row;
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64 my @tmp;
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65 my %hash;
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66 my $flag;
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67 my $file;
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68
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69
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70 if ((-e $output) and ((-d $output)))
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71 {
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72 }else
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73 {
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74 mkdir($output);
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75 }
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76
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77 if ($input!~/\/$/)
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78 {
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79 $input=$input."/";
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80 }
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81
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82
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83 if ($output!~/\/$/)
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84 {
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85 $output=$output."/";
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86 }
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87
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88
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89 foreach $sp (@sp)
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90 {
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91 %hash=();
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92 $file=$input.$sp.".faa";
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93 open(F,$file) or die "could not open $file";
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94 open(R,">$output$sp.pep");
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95 while ($line=<F>)
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96 {
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97 if ($line=~/^>/)
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98 {
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99 @row=split(/\|/,$line);
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100 print R ">$row[1]\n";
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101 }else
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102 {
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103 print R $line;
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104 }
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105 }
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106 close(F);
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107 close(R);
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108
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109 $file=$input.$sp.".ptt";
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110 open(F,"$file") or die "could not open $file";
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111 open(R,">$output$sp.function");
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112 $_=<F>;
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113 $_=<F>;
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114 $_=<F>;
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115 while ($line=<F>)
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116 {
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117 chomp($line);
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118 @row=split(/\t/,$line);
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119 print R $row[3]."\t".$row[7]."\t".$row[8]."\n";
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120 @tmp=split(/\.\./,$row[0]);
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121 if ($row[1] eq "+")
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122 {
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123 $hash{$tmp[0]."-".$tmp[@tmp-1]}=$row[3];
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124 }else
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125 {
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126 $hash{"c".$tmp[@tmp-1]."-".$tmp[0]}=$row[3];
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127 }
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128 }
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129 close(R);
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130 close(F);
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131
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132 $file=$input.$sp.".ffn";
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133 open(F,"$file") or die "could not open $file";;
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134 open(R,">$output/$sp.nuc");
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135 while ($line=<F>)
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136 {
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137 if ($line=~/^>/)
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138 {
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139 my $key=&getKey($line);
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140 if (exists($hash{$key}))
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141 {
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142 $flag=1;
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143 print R ">$hash{$key}\n";
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144 }else
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145 {
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146 $flag=0;
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147 }
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148 }else
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149 {
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150 if ($flag)
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151 {
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152 print R $line;
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153 }
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154 }
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155 }
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156 close(R);
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157 close(F);
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158 }
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159
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160 sub getKey()
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161 {
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162 (my $line)=@_;
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163 my @tmp;
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164 my $strand;
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165 chomp($line);
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166 @tmp=split(/ /,$line);
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167 @tmp=split(/\:/,$tmp[0]);
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168
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169 if($tmp[@tmp-1]=~/c/)
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170 {
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171 $strand="-";
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172 }else
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173 {
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174 $strand="+";
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175 }
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176 $_=$tmp[@tmp-1];
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177 s/c//g;
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178 s/ //g;
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179 @tmp=split(/\,|-/,$_);
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180 @tmp=sort{$a<=>$b} @tmp;
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181 if($strand eq "-")
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182 {
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183 return "c".$tmp[@tmp-1]."-".$tmp[0];
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184 }else
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185 {
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186 return $tmp[0]."-".$tmp[@tmp-1];
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187 }
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188 }
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