perl中SNP2CAPS怎么用

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SNP2CAPS可将SNP转换为CAPS标记，其具体用法： perl SNP2CAPS.pl chr5D:9950377.fa_1 link_gcg AanI,AarI,AasI,AatII,Aba6411II,AbaB8342IV,AbaCIII > chr5D:9950377.txt 其中...

SNP2CAPS可将SNP转换为CAPS标记，其具体用法：

perl SNP2CAPS.pl   chr5D:9950377.fa_1    link_gcg    AanI,AarI,AasI,AatII,Aba6411II,AbaB8342IV,AbaCIII   > chr5D:9950377.txt

其中chr5D:9950377.fa_1为SNP两端各150bp的序列；link_gcg限制性内切酶数据库；之后为分析用到的限制性内切酶列表 ；chr5D:9950377.txt为输出文件

chr5D:9950377.fa_1示例：>chr5D:9950377_RefACAACTTTATCTCGTATTTCATAGCAGTAGCCAACCAATCTTATGATATTTTGATGTTGGGCCCTCATAAGATTCAGAAGCTCATTCTTAAAACCAGCTTCGACTAGTCCGGGCTGGTTGTACAGTTTCTTCACGGCAATCACTTCCCCGTTATCAAGTACTCCCTGTTCAAAATCCCATGTTTAAAAGTAATAATGCAAGGGTTCAGGTAGCTAGTGTAGTGGTGGCATCTGTTTAAAAGTATTATTTTTTTCGTAAAATGCGCTTAATTTTCCTCCCAGCAACCTTTCCACCAACTGAT>chr5D:9950377_AltACAACTTTATCTCGTATTTCATAGCAGTAGCCAACCAATCTTATGATATTTTGATGTTGGGCCCTCATAAGATTCAGAAGCTCATTCTTAAAACCAGCTTCGACTAGTCCGGGCTGGTTGTACAGTTTCTTCACGGCAATCACTTCCCCGCTATCAAGTACTCCCTGTTCAAAATCCCATGTTTAAAAGTAATAATGCAAGGGTTCAGGTAGCTAGTGTAGTGGTGGCATCTGTTTAAAAGTATTATTTTTTTCGTAAAATGCGCTTAATTTTCCTCCCAGCAACCTTTCCACCAACTGAT

link_gcg文件如果找不到，可在这下载：

链接：https://pan.baidu.com/s/1eJGIOs2O8cULYbAbc83JCA 密码：ru01

输出文件chr5D:9950377.txt示例：#Marker Enzyme  Total size      Restriction Sites       Expected Fragments      MembersPredicted CAPS candidates-------------------------chr5D:9950377   AbaCIII 301     153     153,148 Altchr5D:9950377   AbaCIII 301             301     Refchr5D:9950377   AciI    301     148     153,148 Altchr5D:9950377   AciI    301             301     Refchr5D:9950377   BscGI   301             301     Altchr5D:9950377   BscGI   301     148     153,148 Refchr5D:9950377   BspACI  301     148     153,148 Altchr5D:9950377   BspACI  301             301     Refchr5D:9950377   FauI    301     155     155,146 Altchr5D:9950377   FauI    301             301     Refchr5D:9950377   LlaG50I 301     133     168,133 Altchr5D:9950377   LlaG50I 301     133,150 151,133,17      Refchr5D:9950377   SsiI    301     148     153,148 Altchr5D:9950377   SsiI    301             301     RefFollowing markers could not be converted into CAPS--------------------------------------------------

如果输出文件很多，这里有脚本可以批量提取酶信息，脚本如下。

#!/usr/bin/perl -wuse strict;use warnings;use Getopt::Long;use Config::General;use Cwd qw(abs_path getcwd);use FindBin qw($Bin $Script);use File::Basename qw(basename dirname);use Bio::SeqIO;use Bio::Seq;my $version = "1.3";## prepare parameters ######################################################################### -------------------------------------------------------------------------------------------## GetOptionsmy %opts;GetOptions(\%opts, "id=s", "od=s", "h");my $od = $opts{od};$od = abs_path($od);my $id = $opts{id};$id = abs_path($id);open(OUT,">$od/caps_out.txt") || die "open $od/caps_out.txt failed\n";my @sample = glob ("$id/*.txt");foreach my $i (@sample){my $basename = basename ($i);open(IN,"$i") || die "open $i failed\n";while(){next if(/^S2C#Format:/);next if(/^#/);next if(/^Predicted CAPS candidates/);next if(/^-/);next if(/^Following markers could not be converted into CAPS/);next if(/^$/);next if(!/\t/);print OUT $_;}close(IN);}close(OUT);

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