老师,这是在组学大讲堂找的三个物种做比较基因组学分析的一个脚本,运行显示Can't find string terminator " Usage End." anywhere before EOF at ../script/mcscan.filter.pl line 13.的错误,请老师看下这个脚本,谢谢老师

### mcscan.filter.pluse Getopt::Long;use strict;use Bio::SeqIO;use Bio::Seq;use File::Basename qw(basename dirname);use Cwd qw(abs_path);#get optsmy %opts;GetOptions(\%opts, "in=s", "out=s","id1=s","id2=s","h");if(!defined($opts{id2}) || !defined($opts{id1}) || !defined($opts{in}) || !defined($opts{out}) || defined($opts{h})){        print <<"       Usage End.";
Usage Forced parameter: -gff genoma gff file <infile> must be given -fa genoma fasta file <infile> must be given -o output gff file <outfile> must be given -out output fasta file <outfile> must be given Other parameter: -h Help document Usage End. exit;}open(IN,"$opts{id1}") || die "open $opts{id1} failed\n";my %gene1;while(<IN>){ next if(/^#/); chomp; my @line = split ("\t"); $gene1{$line[0]} = $line[0];}close(IN);open(IN,"$opts{id2}") || die "open $opts{id2} failed\n";my %gene2;while(<IN>){ next if(/^#/); chomp; my @line = split ("\t"); $gene2{$line[0]} = $line[0];}close(IN);open(IN,"$opts{in}") || die "open $opts{in} failed\n";open(OUT,">$opts{out}") || die "open $opts{out} failed\n";while(<IN>){ next if(/^#/); chomp; my @line = split ("\t"); if(exists $gene1{$line[0]} && exists $gene2{$line[1]}){ print OUT "#DC143C*$line[0]\t$line[0]\t$line[1]\t$line[1]\t100\t+\n"; }}close(IN);close(OUT);
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omicsgene - 生物信息
擅长:重测序,遗传进化,转录组,GWAS

这个 脚本已经不用了,你再看看新课程吧: https://bdtcd.xetslk.com/s/1BAqPp

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  • 提出于 2022-03-16 00:05

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