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1 #!/usr/bin/perl -w
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2 #Filename:
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3 #Author: Tian Dongmei
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4 #Email: tiandm@big.ac.cn
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5 #Date: 2013/7/19
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6 #Modified:
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7 #Description:
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8 my $version=1.00;
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9
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10 use strict;
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11 use Getopt::Long;
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12
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13 my %opts;
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14 GetOptions(\%opts,"i=s","fa=s","o=s","h");
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15 if (!(defined $opts{i} and defined $opts{o} ) || defined $opts{h}) { #necessary arguments
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16 &usage;
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17 }
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18
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19 my $filein=$opts{'fa'};
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20 my $fileout=$opts{'o'};
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21
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22 open IN,"<$filein"; #input file
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23 my (%fa,%seq);
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24 while (my $aline=<IN>){
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25 chomp $aline;
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26 $aline=~s/^>//;
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27 my $seq=<IN>;
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28 chomp $seq;
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29 #$seq{$seq}=$aline;
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30 $fa{$aline}=$seq;
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31 }
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32 close IN;
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33
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34 open IN,"<$opts{i}";
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35 while(my $aline=<IN>){
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36 chomp $aline;
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37 if($aline=~/^\S+_x\d+/){
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38 $aline=~/^(\S+_x\d+)/;
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39 my $name=$1;
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40 delete($fa{$name});
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41 }
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42 }
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43 close IN;
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44
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45 open OUT,">$fileout"; #output file
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46 foreach my $key (keys %fa) {
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47 print OUT ">$key\n$fa{$key}\n";
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48 }
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49 close OUT;
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50 sub usage{
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51 print <<"USAGE";
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52 Version $version
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53 Usage:
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54 $0 -i -o
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55 options:
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56 -i input file
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57 -o output file
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58 -h help
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59 USAGE
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60 exit(1);
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61 }
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62
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