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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('N: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_draft.pl [options]
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12
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13 Options:
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14
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15 -N String Input the strain nickname
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16 -I String Input file directory
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17 -O String Output file directory
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18 );
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19
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20 if (!scalar(keys %opt))
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21 {
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22 print join("\n",@usage)."\n";
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23 exit;
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24 }
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25
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26 my $prefix;
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27 if (exists($opt{"N"}))
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28 {
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29 $prefix=$opt{"N"}
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30 }else
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31 {
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32 print "-N could not be empty!";
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33 print join("\n",@usage)."\n";
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34 exit;
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35 }
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36
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37 my $output;
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38 if (exists($opt{"O"}))
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39 {
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40 $output=$opt{"O"};
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41 }else
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42 {
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43 print "-O could not be empty!";
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44 print join("\n",@usage)."\n";
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45 exit;
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46 }
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47
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48 my $input;
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49 if (exists($opt{"I"}))
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50 {
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51 $input=$opt{"I"};
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52 }else
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53 {
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54 print "-I could not be empty!";
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55 print join("\n",@usage)."\n";
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56 exit;
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57 }
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58
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59 my $sp;
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60 my $line;
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61 my @row;
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62 my @tmp;
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63 my %hash;
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64 my $flag;
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65 my $file;
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66 my $list;
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67 my @list;
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68 my $pttlost;
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69 my $gi;
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70
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71 if ((-e $output) and ((-d $output)))
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72 {
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73 }else
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74 {
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75 mkdir($output);
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76 }
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77
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78 if ($input!~/\/$/)
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79 {
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80 $input=$input."/";
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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 opendir(DIR,"$input") || die "The input directory ( $input ) is not exists!\n";
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89 @list=grep(/faa$/,readdir(DIR));
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90 closedir(DIR);
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91 $_=join("\t",@list);
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92 s/.faa//g;
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93 @list=split(/\t/,$_);
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94
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95 open(PEP,">$output$prefix.pep");
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96 open(NUC,">$output$prefix.nuc");
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97 open(FUN,">$output$prefix.function");
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98
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99 foreach $list (@list)
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100 {
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101 %hash=();
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102 if (!(-e $input.$list.".faa"))
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103 {
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104 print $input.$list.".faa is not exists!\n$list.faa, $list.ffn and $list.ptt are skipped!\n";
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105 next;
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106 }
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107
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108 if (!(-e $input.$list.".ffn"))
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109 {
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110 print $input.$list.".ffn is not exists!\n$list.faa, $list.ffn and $list.ptt are skipped!\n";
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111 next;
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112 }
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113
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114 if (!(-e $input.$list.".ptt"))
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115 {
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116 open(F,$input.$list.".faa");
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117 @_=<F>;
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118 close(F);
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119 @_=grep(/^>/,@_);
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120 if (scalar(@_)>1)
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121 {
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122 print $input.$list.".ptt is not exists!\n";
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123 print "There are more than 1 sequence in $list.faa and $list.ffn, So $list.faa, $list.ffn and $list.ptt are skipped!\n";
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124 next;
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125 }
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126 $pttlost=1;
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127 }else
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128 {
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129 $pttlost=0;
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130 }
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131
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132 $file=$input.$list.".faa";
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133 open(F,$file) or die "could not open $file";
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134 while ($line=<F>)
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135 {
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136 if ($line=~/^>/)
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137 {
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138 @row=split(/\|/,$line);
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139 print PEP ">$row[1]\n";
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140 if ($pttlost ==1)
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141 {
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142 $gi=$row[1];
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143 }
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144 }else
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145 {
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146 print PEP $line;
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147 }
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148 }
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149 close(F);
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150
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151 if ($pttlost ==1)
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152 {
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153 print FUN "$gi\t-\thypothetical protein\n";
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154 }else
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155 {
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156 $file=$input.$list.".ptt";
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157 open(F,"$file") or die "could not open $file";
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158 $_=<F>;
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159 $_=<F>;
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160 $_=<F>;
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161 while ($line=<F>)
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162 {
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163 chomp($line);
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164 @row=split(/\t/,$line);
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165 print FUN $row[3]."\t".$row[7]."\t".$row[8]."\n";
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166 @tmp=split(/\.\./,$row[0]);
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167 if ($row[1] eq "+")
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168 {
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169 $hash{$tmp[0]."-".$tmp[@tmp-1]}=$row[3];
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170 }else
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171 {
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172 $hash{"c".$tmp[@tmp-1]."-".$tmp[0]}=$row[3];
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173 }
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174 }
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175 close(F);
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176 }
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177
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178
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179
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180 $file=$input.$list.".ffn";
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181 open(F,"$file") or die "could not open $file";;
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182 while ($line=<F>)
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183 {
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184 if ($line=~/^>/)
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185 {
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186 if ($pttlost==1)
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187 {
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188 print NUC ">$gi\n";
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189 $flag=1;
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190 }else
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191 {
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192 my $key=&getKey($line);
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193 if (exists($hash{$key}))
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194 {
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195 $flag=1;
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196 print NUC ">$hash{$key}\n";
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197 }else
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198 {
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199 $flag=0;
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200 }
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201 }
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202 }else
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203 {
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204 if ($flag)
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205 {
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206 print NUC $line;
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207 }
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208 }
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209 }
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210 close(F);
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211 }
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212
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213 close(PEP);
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214 close(NUC);
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215 close(FUN);
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216
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217 sub getKey()
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218 {
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219 (my $line)=@_;
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220 my @tmp;
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221 my $strand;
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222 chomp($line);
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223 @tmp=split(/ /,$line);
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224 @tmp=split(/\:/,$tmp[0]);
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225
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226 if($tmp[@tmp-1]=~/c/)
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227 {
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228 $strand="-";
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229 }else
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230 {
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231 $strand="+";
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232 }
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233 $_=$tmp[@tmp-1];
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234 s/c//g;
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235 s/ //g;
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236 @tmp=split(/\,|-/,$_);
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237 @tmp=sort{$a<=>$b} @tmp;
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238 if($strand eq "-")
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239 {
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240 return "c".$tmp[@tmp-1]."-".$tmp[0];
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241 }else
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242 {
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243 return $tmp[0]."-".$tmp[@tmp-1];
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244 }
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245 } |
