Question

我是一个Perl新手，坚持另一个需要一些帮助和输入的生物信息学问题。

问题简述：

我有一个文件，它有超过40,000个独特的 DNA序列。通过唯一，我的意思是唯一的序列ID。我在帖子的末尾附上了一部分，以帮助你展示它的样子。
我需要将40,000个序列中的每个分成3个部分。因此，如果特定序列长度为999个字符，则3个部分中的每个将具有333个字符。

我需要通过3个单独的部分来寻找以下模式：

$ gpat = [G] {3,5}; $ npat = [A-Z] {1,25};
$ pattern = $ gpat。$ npat。$ gpat。$ npat。$ gpat。$ npat。$ gpat;

如果$ pattern出现在3个部分的第一个中，则增加'开始'的计数器，如果3个部分中的第2个出现$ pattern，则增加'middle'的计数器，最后如果$ pattern出现在第3部分，增加'结束'的反击。

打印“开始”，“中间”和“结束”的计数器，即基本上每个序列的“开始”，“中间”，“结束”的总和。

在第一个序列中说，值分别为'2'，'5'，'3'，在第二个序列中，值为'4'，'1'，'6'，最终计数应为' 7,6,9' 。

我遇到的问题：

如果特定序列被分成3个部分，则潜在的$ pattern将丢失。例如，说出如下序列：

gggatgtcgatgcatggggatgcatcgatgcggggactagctagcgggatgctacgatggggatgatgataatatcgcggcgcatatatgctagtctatatatta

分为3个部分，产生以下3个子部分，每个部分长度为35个字符：

gggatgtcgatgcatggggatgcatcgatgcgggg
actagctagcgggatgctacgatggggatgatgat
aatatcgcggcgcatatatgctagtctatatatta

因此， $ pattern被拆分为前两部分。无论如何说“如果$ pattern从第1部分开始到第2部分结束”，增加“开始”的数量？

##更新## 由于Cupidvogel建议的代码，以下问题已得到解决

2.如果序列长度不能被3整除，我如何将序列分成3个部分？我尝试使用int，但最后一部分是1-2 人物简短。

以下是我到目前为止编写的代码。

它读入文件，显示标题名称和序列，每个序列将被分成的长度，最后序列分成3个部分，如果序列长度可以被3整除，则可以正常工作。 t，最后的第3部分是1-2个字符短。

#Take Filename from user print "Please enter file name : "; $in =<>; chomp $in; open (FASTA,"$in") or die ; while (<FASTA>) { $/=">"; @array = split '\n', $_; $header=shift @array; # Header of the fasta sequence print "\n\nNext sequence: \n"; print $header,"\n"; $seq= join '', @array; # sequence $seq=~s/\s//g; $seq=~s/\*//g; $seq=~s/>//g; print $seq,"\n\n"; $num = int(length($seq)/3); @arr = unpack("A$num A$num A*",$seq); print " New method gives this :", @arr; print "\nThe first element is :", $arr[0]; print "\nThe second element is :",$arr[1]; print "\nThe third element is :",$arr[2] ; #The following lines of code were originally written to split... #...the sequence into 3 parts, albeit unsuccessfully #my $split = (length $seq)/3; #print $split,"\n\n"; #my $int = int $split; #print $int,"\n\n"; #my @array2 = $seq =~ /(.{$int})/g; #print join (" ", @array2),"\n\n"; #print $array2[0],"\n",$array2[1],"\n",$array2[2]; } exit;

到目前为止，我一直在尝试使用以下示例文件编写的代码：sample.fa

>ABC_123 2 atgtcgatcgatcggcgggcatgcgcgcgcggatg atatatagcgcgcgctatatagcgcgactctacgc atgctgctgactagctatagtcgctgactgcgcgt gggaaaaagggcccgggccccgttttggggatcta ggggatagctgatgctagcatgcatgctgactgca >DEF_456 4 gggatgtcgatgcatggggatgcatcgatgcgggg actagctagcgggatgctacgatggggatgatgat aatatcgcggcgcatatatgctagtctatatatta >GHI_789 1 atagctgctagtcgatcggcgcgggtatcgatcgg ggatcgatcgatcggggatcgatcgggggatcgat

实际输入文件如下所示：

>NR_037701 1 aggagctatgaatattaatgaaagtggtcctgatgcatgcatattaaaca tgcatcttacatatgacacatgttcaccttggggtggagacttaatattt aaatattgcaatcaggccctatacatcaaaaggtctattcaggacatgaa ggcactcaagtatgcaatctctgtaaacccgctagaaccagtcatggtcg gtgggctccttaccaggagaaaattaccgaaatcactcttgtccaatcaa agctgtagttatggctggtggagttcagttagtcagcatctggtggagct gcaagtgttttagtattgtttatttagaggccagtgcttatttagctgct agagaaaaggaaaacttgtggcagttagaacatagtttattcttttaagt gtagggctgcatgacttaacccttgtttggcatggccttaggtcctgttt gtaatttggtatcttgttgccacaaagagtgtgtttggtcagtcttatga cctctattttgacattaatgctggttggttgtgtctaaaccataaaaggg aggggagtataatgaggtgtgtctgacctcttgtcctgtcatggctggga actcagtttctaaggtttttctggggtcctctttgccaagagcgtttcta ttcagttggtggaggggacttaggattttatttttagtttgcagccaggg tcagtacatttcagtcacccccgcccagccctcctgatcctcctgtcatt cctcacatcctgtcattgtcagagattttacagatatagagctgaatcat ttcctgccatctcttttaacacacaggcctcccagatctttctaacccag gacctacttggaaaggcatgctgggtctcttccacagactttaagctctc cctacaccagaatttaggtgagtgctttgaggacatgaagctattcctcc caccaccagtagccttgggctggcccacgccaactgtggagctggagcgg gagggaggagtacagacatggaattttaattctgtaatccagggcttcag ttatgtacaacatccatgccatttgatgattccaccactccttttccatc tcccagaagcctgctttttaatgcccgcttaatattatcagagccgagcc tggaatcaaactgcctctttcaaaacctgccactatatcctggctttgtg acctcagccaagttgcttgactattctcagtctcagtttctgcacctgtc aaatagggtttatgttaacctaactttcagggctgtcaggattaaatgag catgaaccacataaaatgtttggtgtatagtaagtgtacagtaaatactt ccattatcagtccctgcaattctatttttcttccttctctacacagcccc tgtctggctttaaaatgtcctgccctgctttttatgagtggataccccca gccctatgtggattagcaagttaagtaatgacactcagagacagttccat ctttgtccataacttgctctgtgatccagtgtgcatcactcaaacagact atctcttttctcctacaaaacagacagctgcctctcagataatgttgggg gcataggaggaatgggaagcccgctaagagaacagaagtcaaaaacagtt gggttctagatgggaggaggtgtgcgtgcacatgtatgtttgtgtttcag gtcttggaatctcagcaggtcagtcacattgcagtgtgtcgcttcacctg gctccctcttttaaagattttccttccctctttccaactccctgggtcct ggatcctccaacagtgtcagggttagatgccttttatgggccacttgcat tagtgtcctgatagaggcttaatcactgctcagaaactgccttctgccca ctggcaaagggaggcaggggaaatacatgattctaattaatggtccaggc agagaggacactcagaatttcaggactgaagagtatacatgtgtgtgatg gtaaatgggcaaaaatcatcccttggcttctcatgcataatgcatgggca cacagactcaaaccctctctcacacacatacacatatacattgttattcc acacacaaggcataatcccagtgtccagtgcacatgcatacacgcacaca ttcccttcctaggccactgtattgctttcctagggcatcttcttataaga caccagtcgtataaggagcccaccccactcatctgagcttatcaaccaat tacattaggaaagactgtatttcctagtaaggtcacattcagtagtactg agggttgggacttcaacacagctttttgggggatcataattcaacccatg acagccactgagattattatatctccagagaataaatgtgtggagttaaa aggaagatacatgtggtacaaggggtggtaaggcaagggtaaaaggggag ggaggggattgaactagacacagacacatgagcaggactttggggagtgt gttttatatctgtcagatgcctagaacagcacctgaaatatgggactcaa tcattttagtccccttctttctataagtgtgtgtgtgcggatatgtgtgc tagatgttcttgctgtgttaggaggtgataaacatttgtccatgttatat aggtggaaagggtcagactactaaattgtgaagacatcatctgtctgcat ttattgagaatgtgaatatgaaacaagctgcaagtattctataaatgttc actgttattagatattgtatgtctttgtgtccttttattcatgaattctt gcacattatgaagaaagagtccatgtggtcagtgtcttacccggtgtagg gtaaatgcacctgatagcaataacttaagcacacctttataatgacccta tatggcagatgctcctgaatgtgtgtttcgagctagaaaatccgggagtg gccaatcggagattcgtttcttatctataatagacatctgagcccctggc ccatcccatgaaacccaggctgtagagaggattgaggccttaagttttgg gttaaatgacagttgccaggtgtcgctcattagggaaaggggttaagtga aaatgctgtataaactgcatgatgtttgcaggcagttgtggttttcctgc ccagcctgccaccaccgggccatgcggatatgttgtccagcccaacacca caggaccatttctgtatgtaagacaattctatccagcccgccacctctgg actccctcccctgtatgtaagccctcaataaaaccccacgtctcttttgc tggcaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa aaa >NM_198399 1 aacagattttaactctgaaaagccatttccagtgtctatagactattgtg agcctggagaagtagcatttagttgggatagcttcactagagctgcctgc caaagacttccttccacaggatcttgtcgcaccagcaactgacaggagct tgggagctcgggagcttgggagagggcttatgtttttaataatgtagctg tcagttcgaagcctggaaatgttgaccctcaaagggcataaaatcttgtt attttaatttgcatctgggagaatgtctgagcaaggagacctgaatcagg caatagcagaggaaggagggactgagcaggagacggccactccagagaac ggcattgttaaatcagaaagtctggatgaagaggagaaactggaactgca gaggcggctggaggctcagaatcaagaaagaagaaaatccaagtcaggag caggaaaaggtaaactgactcgcagccttgctgtctgtgaggaatcttct gccagaccaggaggtgaaagtcttcaggatcagactctctgaaaactgca aatggaaaggaattcaaaagaatttagattaaaagttaaataaaaagtag gcacagtagtgctgaattttcctcaaaggctctcttttgataaggctgaa ccaaatataatcccaagtatcctctctccttccttgttggagatgtctta cctctcagctccccaaaatgcacttgcctataagaaacacaattgctggt tcatatgaaacttaggaaatagtgaataaggtgcatttaactttggagaa atacttttatggctttggtggagatttctcaatactgcaaaagttgtcca gaaatgaatctgagctgatggtgactttaagttaatattattaatatatc actgcatatttttacccttatttttgctccttacagcaagattagtaggt tataaaaatttaaatttaaacaaaattatttcatgacaaaatgggaaact tcacatcatacttatttttgtttgcctttcaggcatcatattagctttta taaaaaatggtcttgctgctgaaattgtacttattttatcagaggctggg tgcagtcaagacaaaagtaaaatggtttacctgagcccaggggagggaaa attgattaagatatcattatttttgtttggtttggttttgcttttttcct cttactttaattgaaatactctgaattcccctcatggaaacagagagcat tgagagcactttctttaaaaggaccaaaaataaattcctaatagattttg tcctaagagagtgtttttttttctagcatcattttctttacatgccactc atgtcataaggcatggacaggctatctttcagtggccattactatgtttc gtacacatgctttattttacttgggctctgagaaatgtgtggctttcctt cagcattttatttgtgcttctctttttaatggagattgaaaagggagaat aatgtgaatatcacggcttatattattaaatgttgattgatggcttgtaa tgtactgcacacaatatatgttaactctgcagaatgacagaccctgggag aagtaatgccccagttgtcccccactcctaatgccaggcagagaaggaca gcctttatagacttaatctgctttttgtcccatttgacaaggtaccagga ggaaattttttaagggatcaactgtatcacagtgcccactctggacctaa gtctagtgtatccatacaattggtgcagagaaataaggtgtaaatggtgc tttgttcctgctggttccaagctcagaaaccaagactagctttgtaggag agaatgagagcctgcaagcctctctttggattggctgaggagtggtggga gcagggggttgatagaaaacatccagacacacatataagcaagtggccgt gctacctttttagagaataaagaaacagacttttgagtttatatgcaatg ccttcattaggtaccaccggcacttacaaaatgtgcggactgaatcccag agaacactggcagatgtatacagtatatggattgtatcgcttccccaatg tttgtaaattcacagtatttggaaaactgccttcattttccagtgtggga aaaactcttgctacctgtattacttgatctcagacccatacctgatggtt cagtctgtccttaagttaaaagaattttgcttttctaatgttatactatt tacctgtcagtgtattactgcaacttgaatcactcttttactgttgttgg atataaacttatcctgtaccaatgtatttattaacacttgtattttatta ttgagcatatcaataaaaatattaaaaaataacagattgttttttaccaa aaaaaaaaaaaaa >NR_026816 1 caacccactctctgtgctatgacttcattactctttcccagcccagccct gggcaagccccttacgaagtctcaggctacctggatgaccaccctttctt atgatgctgcaaggagggcaggtgggcagagccccgtgcatcctgggctc aggccagggacccaagagcttgggagaagctggttctcagactgaaggcc agagcccagcaccttgtcaccatcccggggagcatcatggcacacaacaa ccagagccaaggctacagctagagagttgactcctctatttgagattgac aggcctcggaagtcaaaataagtggtttcctagaccgggtcgagagcaag tctctattggtcccaactgagttttttcagctggtttttcaaccaaacag cacctcatctcccagtgaggggaagggaaggctgggctgagagcagcaag gctgctcatctcacctctccccacccagccatgccagccgcctcacctgg tggggagaggtgggcctcacctgggtcccctggcagtgctctgtgaaggg tcttgacattgcactgtaataataaaggtgtgtgtgaagtatcaaaaaaa >NR_027917 1 atgaagatgattgagcagcacaatcaggaatacagggaagggaaacacag cttcacaatggccatgaacgcctttggagaaatgaccagtgaagaattca ggcaggtggtgaatggctttcaaaaccagaagcacaggaaggggaaagtg ctccaggaacctctgcttcatgacatccgcaaatctgtggattggagaga gaaaggctacgtgactcctgtgaaggatcagtgcagctggggctctgtaa ggacagatgttaggaaaactgagaaactagtttcactgagtgtgcagacc tggtggactgctctaggcttcaaggcaatgttggctgcatttttggagaa ccattattttgcttccagtatgttgccgacaatggaggcctggactctga ggaatccttttcatatgaagaaaagctctggagactggaaagtccaaggt cacagaggtgcatctggtgagagccttcttgctagtggggaatctcagca gagtcctgaggtggcacagtattctgggaagcatcaagtgcagtgtcatc ttatcgaggaggctctgcagatgctaagtggtggggatgaggatcacgat gaagacaaatggccccatgacatgaggaatcatctggctggagaggccca ggtgtag >NR_002777 3 cttgtcctttcagaagatcagagacaagtgatatctgtgccaatttggcc ttttcagtgttataattatggtgtcttgggatcccaatatttctcctaat gtttccctgatgtgatactttgagagcccaggatgccagtacaataattg aaattcacaaatgtctggtatcttgtccctcgtgccccatatattatctg tggtttcggagagctcacttgtctcttatcttcagaaatgacagcacatg aaatgttgtttggagccactgtcacatcaactgtagaaaaattaacaggt cagctaagggatataatgtaactttatttgtgatatgagagaaatcttga taaagacttgagagaaaactgggaggaaccttgtttagaagttataagga ggggtaagttatgtgtgtcttggaaggagaatcataaatcttaaaacatg agcctaatagagaacataaaattctaaaagataaagataataataatgat aagccgcagggtggcttatgataatgtgacttctccttaccccagtagcg tcggacatctgtcagctctgaaatgataaaaatgcacaatattgaataca aacaaaggagtcagcactgaaattcattttctctccagattagggaaaga gtaggtatgccctatggtagggcagtaaattgctgaatgatgagatgaaa cagccacctagccatttcccattaaatataatcccatcagcagcagacaa tatctatcctcccctatcccctctatccatatttggaaactgcaccctct tccctatttagcaccctaacaccacttgaattccataaccctgttgttga tctagctctcctcacctctaaacacttctagcattcctttcagatcagga gctcgaaacactctcctttgattttttggaaaagtttctggcttcttcaa ggtcacgttctccgtcctaagaattaaaaaaaaaaaaaaaaacttccaaa cctttgaccttgtgtccgtggaacacccctgacttcctatcatttcaacc cattgaggcacttgaactctcttcttggggatcctgagaagggagagtgc aaactcttgaccctggaggcaaacaaaatgttctcatgtttgccttccca cttactttctgtgagaacgtgggaagatcttaacctctcagaagcacagt ttcttccttctaaaatgaaataattaacctctccctgtctacattcttaa actcataggacataaaaaaaaaaaaaa >NR_033769 1 ggcctctggcgggcctccagccagttagaccatttgactaggacgtgtgc agctcagccagccacagaactggaatttttcaggagcagggggagcatgg agtttggactttgctgagcaactgaagtggagcgcagagcttgctcgctt aggagagggcagcatggatggcaaacaagggggcatggatgggagcaagc ccacggggccaagagactctcctgacaccaggcttctttcaaacccattg atgggtgattctgtgtctgattggtctcctatgcctgaagctgcaatcta cggacatcagctgtctctgaggaacctcatcagccacgggtggcttgtga acatcatcatggcagatcatgtttccccactccatgaagcctgtctcaga ggtcatccctctcgtgtaaagattttattaaagcatggagctcaggtgaa tggcgtgacaacagactggcacactccactgtttaatgtttgtatcagca gcagctgggattatgcttctgcagcatggagccagcgttcaacctgagag tgatctggcatcccccgtccatgaagctgctaggagaggccacgtggagt gtgtcgactctcttacagcttataggggcaaaaatgaccataacatcagc cacgtgggcacttcactgtatttggcttgtgaaaaccagcagatagcctg tgtcaagaagcttctggagtcaggagcagacctgaacccagggagaggtt ccccacttcatgcagtggccttcatgaaggccctcatgaaggattcccca cttcatgcagtggccaggacagccagtgaagagctggcctgcctgctcat ggattttggagcagacacccaggccaagaatgctgaaggcaaatgtcatg tggagctggtgcctccagagagccctttgatccagctcttcttggagaga gaagggcccccttcttttgatgcagttatgcctagaaatcagaagggctt tggaatccagcagcatcataagataaccaaagtcgtcctcccagaggatc tgaaatggtttctcctacatctttgtatgtatcaatggaatggattcaca aacaatgtgaaaacattattgagtgttgtagccactagaattttaaaatc aagttaggtttatagagtttgactagttttttcgattagatttgtattag ttataaatttgttcatagagtttgactaattttttcgattagatttgtat ttgttaaactctgaagccagagtttaaacacactgcatacgtttgtatga ttagttagaaggcatgaagacttttttccctgcttggagactgtctaaaa taacagctattgttttgcatatccactgcaggccaagcactttcagcatc atctaattcagccctcacagcaactgggtcaatctgtccaatttcccagg gcaaggatagaggagtcagattcaaatacaggttttctgacgttaactta tgtgatgatttgatcaaagcaggattttccagcatcactatccttgttcc atctctgctatatgggaatgaaaataaagaaatgtatttcaaaaaaataa aaagaaaagaaaaacagagacggtc >NM_016326 3 atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag tgtgaaaggccacgtgaagatgctgcggctggtgtttgcacttgtgacag cagtatgctgtcttgccgacggggcccttatttaccggaagcttctgttc aatcccagcggtccttaccagaaaaagcctgtgcatgaaaaaaaagaagt tttgtaattttatattactttttagtttgatactaagtattaaacatatt tctgtattcttccacatattttctgcagttattttaactcagtataggag ctagaggaagagatttccgaagtctgcaccccgcgcagagcactactgta acttccaagggagcgctgggagcagcgggatcgggttttccggcacccgg gcctgggtggcagggaagaatgtgccgggatccgcctcagggatctttga atctctttactgcctggctggccggcagctccg >NM_181641 2 atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag tgtgaaaggccacgtgaagatgctgcggctggcactaactgtgacatcta tgaccttttttatcatcgcacaagcccctgaaccatatattgttatcact ggatttgaagtcaccgttatcttatttttcatacttttatatgtactcag acttgatcgattaatgaagtggttattttggcctttgcttgtgtttgcac ttgtgacagcagtatgctgtcttgccgacggggcccttatttaccggaag cttctgttcaatcccagcggtccttaccagaaaaagcctgtgcatgaaaa aaaagaagttttgtaattttatattactttttagtttgatactaagtatt aaacatatttctgtattcttccacatattttctgcagttattttaactca gtataggagctagaggaagagatttccgaagtctgcaccccgcgcagagc actactgtaacttccaagggagcgctgggagcagcgggatcgggttttcc ggcacccgggcctgggtggcagggaagaatgtgccgggatccgcctcagg gatctttgaatctctttactgcctggctggccggcagctccg >NM_001144931 1 gtttccgttcctctgcccgccatgccgttcctagagctgcacacgaattt ccccgccaaccgagtgcccgcggggctggagaaacggctgtgcgccgtcg ctgcctccatcttgggcaaacctgcagaccttgtgaacgtgacggtacgg ccgggcctggccagggcgctgagcgggtccaccgagccctgcgcgcagct gtccatctcctccatcggcgtagtgggcaccgccgaggacaaccgcagcc acagtgcccacttctttgagtttctcaccaaggagctagccctgggccag gaccggtgcgcaggggtagtaggcccggaatattattctaaaacacaatc agagtactccattcctgctaacagtttaaagccaaacacctaggcaggcc atttaggcttctgaatgactgggtcttgaccaggagagctgctgtctagg ttttctcttcctgaccagttcctcaagagaaatgcaaaactagtgattaa cagtaagagtcaggcagggcgcggtggctcacgcctgtaatcccagcact ttgggaggccgag >NR_029429 1 ggacaccaccccaaaatttcctagtcctctttgatacgggttcctccaat ctgtagctgccctccatctactgccagagccaagtctgctccaatcacaa caggttcaatcccagcctgtcctccaccttcagaaacgatggacaaacct atggactatcctatgggagtggcagcctgagtgtgttcctgggctatgac actgtgactgttcataacatcgttgtcaataaccaggagtttggcctgag tgagaatgagcccagcgaccccttttactattcagactttgacgggatcc tgggaatggcctacccaaacatggcagaggggaattcccctacagtaatg caggggatgctgcagcagagccagcttactcagcccgtcttcagcttcta cttcacctgccagccaacccgccagtattgtggagagctcatccttggag gtgtggaccccaactttattctggtcagatcatctggacccctgtcagcc cgtaactgtactggcagattgccatcgaggaatttgccatcggtaaccag gccactggcttgtgctctgagggttgccaggccattgtggataccgagac cttcctgc >NR_026551 1 tgtggcctgagaggacggccaggactggccagaaaagagagggacgtggc taaacgtgagggggcgtggccaagatggccgcgtgcgggatcctcgggta ccgggagcgaacgaggaggttctggctcagtgcatccactctgggagagc gtggacctggttcctgggggcgatcgccagtcacccatcaacattcggtg gagggacagtgtttatgatcccggcttaaaaccactgaccatctcttatg acccagccacctgcctccacgtctggaataatgggtactctttcctcgtg gaatttgaagattctacagataaatcagctgcacttagtgcattggaacg cagtcaaatttgaaaactttgaggatgcagcactggaagaaaatggtttg gctgtgataggagtatttttaaagatttcggaaacttctggcagcccagt gtctactggaaggcccaagccgcttgccagaaagctgcgccccgcccaaa agcactgggttctgcagtccaggcccttcctcagctcccaggtccaggag aactgcaaggtcacctacttccacaggaagcactgggtccgcatccggcc cctccgcaccactcctcccagctgggactacacccgcatctgcatccaga gagagatggtccccgcccgcatccgcgtcctgagagagatggtccccgag gcctggaggtgctttcccaacaggctgccgctgctgagcaacatcaggcc tgatttctccaaggctcccctggcctacgtgaagcggtggctttggaccg cccgccacccccacagcctgtccgcagcctggtgaccgtgaaaatcgccc cgccagagagcagaggaagcccgacgcccaggccatctgccttcaggtct gtgatgagaaacggagtggcctgttccgttgtgcccaggtctaggccgct gagcagagccctcactcccaggcagagttgtctgaatccttcct >NM_181640 2 atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag tgtgaaaggccacgtgaagatgctgcggctggatattatcaactcactgg taacaacagtattcatgctcatcgtatctgtgttggcactgataccagaa accacaacattgacagttggtggaggggtgtttgcacttgtgacagcagt atgctgtcttgccgacggggcccttatttaccggaagcttctgttcaatc ccagcggtccttaccagaaaaagcctgtgcatgaaaaaaaagaagttttg taattttatattactttttagtttgatactaagtattaaacatatttctg tattcttccacatattttctgcagttattttaactcagtataggagctag aggaagagatttccgaagtctgcaccccgcgcagagcactactgtaactt ccaagggagcgctgggagcagcgggatcgggttttccggcacccgggcct gggtggcagggaagaatgtgccgggatccgcctcagggatctttgaatct ctttactgcctggctggccggcagctccg >NM_016951 3 atgcgcgcaagagagcgggaagccgagctgggcgagaagtaggggagggc ggtgctccgccgcggtggcggttgctatcgcttcgcagaacctactcagg cagccagctgagaagagttgagggaaagtgctgctgctgggtctgcagac gcgatggataacgtgcagccgaaaataaaacatcgccccttctgcttcag tgtgaaaggccacgtgaagatgctgcggctggcactaactgtgacatcta tgaccttttttatcatcgcacaagcccctgaaccatatattgttatcact ggatttgaagtcaccgttatcttatttttcatacttttatatgtactcag acttgatcgattaatgaagtggttattttggcctttgcttgatattatca actcactggtaacaacagtattcatgctcatcgtatctgtgttggcactg ataccagaaaccacaacattgacagttggtggaggggtgtttgcacttgt gacagcagtatgctgtcttgccgacggggcccttatttaccggaagcttc tgttcaatcccagcggtccttaccagaaaaagcctgtgcatgaaaaaaaa gaagttttgtaattttatattactttttagtttgatactaagtattaaac atatttctgtattcttccacatattttctgcagttattttaactcagtat aggagctagaggaagagatttccgaagtctgcaccccgcgcagagcacta ctgtaacttccaagggagcgctgggagcagcgggatcgggttttccggca cccgggcctgggtggcagggaagaatgtgccgggatccgcctcagggatc tttgaatctctttactgcctggctggccggcagctccg >NR_002773 1 cagcaccacaccaggaccctccagaggctgtgagaaacatcctgcaccca ggtcctctctatctgtttatcattgtctattttgtattctgcattcagaa ccaagagcctgaagacgacccaggagctttagctatggctgtcttcatta ttttgtccctgtttagtgttctggtgacaggcatgggtgaaggtggggct gggagtgagaaaggaggtgagagggaatgtaagctgaaccagcttcccca ttgcccctccgtatctcccagtgcccagccttggacacaccctggccaga gccagctgtttgcagacctgagccgagaggagctgacggctgtgatgcgc tttctgacccagcagctggggccagggctggtggatgcagcccaggccca gccctcggacaactgtgtcttctcagtggagttgcagctgcctcccaagg ctgcagccctggctcacttggacagggggagccccccacctgcccgggag gcactggccatcgtcttctttggcaggcaaccccagcccaacgtgagtga gctggtggtggggccactgcctcacccctcctacatgcgggacgtgactg tggagcgtcatggaggccccctgccctatcaccgacgccccatgttgttc caagagtacctggacatagaccagatgatcttcgacagagagctgcccca ggcttctgggcttctccatcactgttgcttctacaagcgccggggacgga acctggtgacaatgaccacggctccccgtggtctgcaatcaggggaccgg gccacctagtttggcctctactacaacatctcgggcgctgggttcttcct gcaccacgtgggcttggagctgctagtgaaccacaaggcccttgaccctg cccgctggactatccagaaggtgttctatcaaggccgctactatgacagc ctggcccagctggaggcccagtttgaggccggcctggtgaatgtggtgct gatcccagacaatggcacaggtgggtcctggtccctgaagtcccctgtgc ccccgggtccagctccccctctgcagttccatccccaaggcccccgcttc agtgtccagggaagtcgagtggcctcctcactgtggactttctcctttgg cctcggagcattcagtggcccaaggatctttgacgttcccttccaagggg agagggtggcctatgaagtcagtgtccaggcggccttggccatctatgga ggcaattctccttctgctctacgaagccggtacatagatagtggctttgg cttgggccacttctccacgcccctgacccatggggtggactgcccctacc tggccacctacgtggactggcacttcctttttgagtcccaggccgccaag acaatacgcgatgccttttgtatatttgaacagaaccagggcctccccct gcggcgacaccactcagatctctactcccactactttgggggccttgcgg aaacggtgctggtcatcagatctgtgtctactatgctcaactatgactat gtgtgggatatggtcttccaccctaatggggccatagaaatcagactcca caccaccggctacatcagctcagcattcccctttggtgctgcccagaggt atggaaacaaagtttcagagcacaccctgggcacggtccacacccacagc gcccacttcaaggtggacctggatgtagcaggtaaggcatcctggcagag gcaaaagtgctggaggggtgagctgaagtctccatgcctagctttaaaag ttttcgttgggctgggagcagtagcttatgcctgtaagcccaacactttg ggagactgaggggggtggatcacttgaggtcaggagttcaaaaccagcct ggccaacatggcgaaatcctgtctgtactaaaaatacaaaaattagctgg gcatgggtatgctgtaatcctagctactcgggaggctgaggcaggagaat cacttgaatctgggagtcagaggttgcagtgagctgagattgagccactg cactccatcctgcgtgactgaac >NR_037806 1 attcccagtcacccactcactcagaaagccgggagtcatcggacaccttg ctggtcagaggtcctgggggtggttttgaaccatcagagcttggactttt ctgacttccccagcaaggatcttcccacttcctgctccctgtgttcccac cctccagtgttggcacaggcccacccctggctccaccagagccagaagca gaggtagaatcaggcgggccccgggctgcactccgagcagtgttcctggc catctttgctactttcctagagaacccggctgttgccttaaatgtgtgag agggacttggccaaggcaaaagctggggagatgccagtgacaacatacag ttcatgactaggtttaggaattgggcactgagaaaattctcaatatttca gagagtccttcccttatttgggactcttaacacggtatcctcgctagttg gttttaagggaaacactctgctcctgggtgtgagcagaggctctggtctt gccctgtggtttgactctccttagaaccaccgcccaccagaaacataaag gattaaaatcacactaataacccctggatggtcaatctgataataggatc agatttacgtctaccctaattcttaacattgcagctttctctccatctgc agattattcccagtctcccagtaacacgtttctacccagatcctttttca tttccttaagttttgatctccgtcttcctgatgaagcaggcagagctcag aggatcttggcatcacccaccaaagttagctgaaagcagggcactcctgg ataaagcagcttcactcaactctggggaatgctaccattttttttccaaa gtagaaaggaagcacttctgagccagtgaccactgaaagatgaacactct tcctgatcctctcctctagaattcatctcctcctgctagcagccgcgtcc tggaggagcagcggatggggaatccattctgtttcttcctggtgtttagg aagttgccccacacacagattgccccgatgtccaaccagaagaagtgaaa ctgctgctgggtctggagaggtgaagacccgtggccagcttctgttgttg ccatcggccattgctttttgttcgcttgcttttggttttgcaagaagagc ggcctctgtctctgatctgcttcaaatcatcattccatcagtgacagaag tggctgttccatcagtggtcgcagccagttcagctcctgcatccatcccc aagtgttctgagtggaatttgaggcctccccaaccacctaccaaaaaagg agggtgaaatgaaaggaagaagaaaaactcagcattctttcctctgacaa agagtaaaacgacaaggaatatcggcctgaattctcttcccaagaagaaa gaaagcacaccaacgcaggcatttgtcttctgtccatggtgctgaagttt attcactttcaaaccactttcagtaacagcaaattctttagaaaaggaaa atacagggaaagggataaacctcactgacttggaggaaatcaagaggagt gagcacagcatcagaaagccccctggccccagactgcacccgctttcctg gccctaccttgaaatccatcaggtctgcgttggacacggcattgtacatg ggattagctctg

任何帮助和意见都将深表感谢。

感谢您抽出宝贵时间解决我的问题！

Answer 1

我没有将序列分成三个部分，而是看到这个工作的方式是在整个序列中找到所有出现的$pattern并确定模式从哪个开始。

内置变量$-[0]包含最近成功匹配开头的偏移量。

以下代码执行我认为您想要的内容。它的工作原理是累积每个序列（在找到新的序列ID或到达文件末尾时结束）并将其传递给process_seq子例程。

子程序获取序列的长度，并计算字符串每三分之一结束的偏移量。惯用sprintf '%.0f', $value用于将小数值舍入到最近的字符位置。

针对序列中每次出现的@counts调整$regex数组。通过比较@counts中匹配的起始位置和序列的三个段中每个段的结束偏移来建立要增加的$-[0]元素。

处理完每个序列后，@counts中的值会累积到@totals中，以显示所有序列的总体数据。

显示使用样本数据时程序的输出。总计为(9, 1, 6)。

use strict;
use warnings;

my $gpat = '[G]{3,5}';
my $npat = '[A-Z]{1,25}';
my $pattern = $gpat.$npat.$gpat.$npat.$gpat.$npat.$gpat; 
my $regex = qr/$pattern/i;

open my $fh, '<', 'sequences.txt' or die $!;

my ($id, $seq);
my @totals = (0, 0, 0);

while (<$fh>) {

  chomp;

  if (/^>(\w+)/) {
    process_seq($seq) if $id;
    $id = $1;
    $seq = '';
    print "$id\n";
  }
  elsif ($id) {
    $seq .= $_;
    process_seq($seq) if eof;
  }
}

print "Total: @totals\n";



sub process_seq {

  my $sequence = shift;
  my $length = length $sequence;

  my @offsets = map {sprintf '%.0f', $length * $_ / 3} 1..3;

  my @counts = (0, 0, 0);

  while ($sequence =~ /$regex/g) {
    my $place = $-[0];
    for my $i (0..2) {
      next if $place >= $offsets[$i];
      $counts[$i]++;
      last;
    }
  }

  print "@counts\n\n";
  $totals[$_] += $counts[$_] for 0..2;
}

<强>输出

NR_037701
0 0 1

NM_198399
1 0 0

NR_026816
1 0 1

NR_027917
0 0 0

NR_002777
0 0 0

NR_033769
1 0 0

NM_016326
1 0 1

NM_181641
1 0 1

NM_001144931
0 0 0

NR_029429
0 1 0

NR_026551
1 0 0

NM_181640
1 0 1

NM_016951
1 0 1

NR_002773
1 0 0

NR_037806
0 0 0

Total: 9 1 6

Answer 2

我解除了Borodin的process_seq功能，但使用了Bio：SeqIO按顺序读取文件序列，这比逐行手动读取和确定各种处理的逻辑更有优势。我相信这些优点是：

由许多其他人开发和测试的代码
如果可以通过Bio :: SeqIO模块完成输出，则可以使用Bio :: SeqIO读取（next_seq）方法读取结果文件。
我现在想不起的其他原因： - ）

我认为生物遗传密码模块的BioPerl软件包对于开始编程的生物学家来说必定是压倒性的。他可能不愿意尝试挖掘开始构建程序所需的信息。 BioPerl wiki是一个很好的起点，特别是Howto部分，然后有一个如何为初学者和其他人。你会发现大多数（？）有用的代码示例。 Bio::Seq在开头有一些很好的代码示例，并且是大多数通用序列函数的地方。此外，对于输入/输出，使用了Bio::SeqIO模块，并在其手册的开头有示例。

#!/usr/bin/perl
use strict;
use warnings;
use Bio::SeqIO;

my $gpat = '[G]{3,5}'; 
my $npat = '[A-Z]{1,25}'; 
my $pattern = $gpat.$npat.$gpat.$npat.$gpat.$npat.$gpat;  
my $regex = qr/$pattern/i; 

my $in = Bio::SeqIO->new ( -file   => "fasta_dat.txt",
                           -format => 'fasta');
my @totals;
while ( my $seq = $in->next_seq() ) {
    process($seq);
}

print "Totals:   ";
print "@totals\n";

sub process {
    my $seq = shift;
    my @offset = map {sprintf '%.0f', $seq->length * $_ / 3} 1..3;
    my $sequence = $seq->seq;

    my @count = (0,0,0);
    while ($sequence =~ /$regex/g) {
        my $place = $-[0];
        for my $i (0 .. 2) {
            next if $place >= $offset[$i];
            $count[$i]++;
            last;
        }
    }
    print $seq->id, "\n@count\n";
    $totals[$_] += $count[$_] for 0 .. $#count; 
}

Perl：在数组元素中搜索模式

2 个答案: