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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: 2009-05-06
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6 #Modified:
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7 #Description: ɾ³ýmatched reads
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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","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{'i'};
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20 my $fileout=$opts{'o'};
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21
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22 open IN,"<$filein"; #input file
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23 open OUT,">$fileout"; #output file
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24
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25 my ($name,$seq);
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26 while (my $aline=<IN>) {
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27 chomp $aline;
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28 if ($aline=~/^>(\S+)/) {
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29 $name=$1;
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30 while (my $new=<IN>) {
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31 chomp $new;
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32 if ($new=~/^>(\S+)/) {
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33 print OUT $name,"\t",length($seq),"\n";
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34 $seq ="";
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35 $name=$1;
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36 next;
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37 }
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38 else{$seq .=$new;}
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39 }
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40 }
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41 print OUT $name,"\t",length($seq),"\n";
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42 }
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43
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44 close IN;
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45 close OUT;
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46 sub usage{
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47 print <<"USAGE";
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48 Version $version
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49 Usage:
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50 $0 -i -o
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51 options:
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52 -i input file
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53 -o output file
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54 -h help
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55 USAGE
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56 exit(1);
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57 }
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