Perl从输入文件中删除新行并写入输出文件(Perl to remove new lines from input file and write to output file)

我的输入是一个包含一系列字符串的文件，如下所示： ABCDEFGHIJKL XKGKASKGKD SGJKSKGS

我想删除新行并将输出写入新文件：ABCDEFGHIJKLXKGKASKGKDSGJKSKGS

到目前为止我有这个：

#! /usr/bin/perl use strict; use warnings; my $input = $ARGV[0]; my $output = "concatenated.txt"; #Output sequence #Open output file open >"$output"; or die "unable to open $output"; #Open input file open "<$input" or die "unable to open $input"; while (<INPUT>) { if( /^[AGCT]/) chomp; print $output; } close $input; close $output; print "Done!\n";

但它还没有奏效。在这种情况下，是否足够连接？如何将我创建的内容写入输出文件？

My input is a file with a series of strings, something like this: ABCDEFGHIJKL XKGKASKGKD SGJKSKGS

I want to remove the new lines and write the output to a new file: ABCDEFGHIJKLXKGKASKGKDSGJKSKGS

So far I have this:

#! /usr/bin/perl use strict; use warnings; my $input = $ARGV[0]; my $output = "concatenated.txt"; #Output sequence #Open output file open >"$output"; or die "unable to open $output"; #Open input file open "<$input" or die "unable to open $input"; while (<INPUT>) { if( /^[AGCT]/) chomp; print $output; } close $input; close $output; print "Done!\n";

But it doesn't work yet. Is chomp enough to concatenate in this instance? How do I write what I have created to the output file?

最满意答案

如果我猜对了:-)如果你的文件看起来像这样有多个序列，你需要在id行和序列的最后一行之后保留换行符。

perl 1衬里可能是这样的：

perl -0777 -pe 's/^[TAGC]+\K\n(?!>)//gm' fasta.txt > concatenated.txt

-0777表示将整个文件-0777成一个字符串。

这个替换表示匹配从行开头开始的所有[TAGC] ，（使用\K ，保留所有内容，不要擦除）。然后是换行符\n后面没有> ，（以下行的开头是id）。

这将删除新行，前提是它是一个序列行，而不是新的id行。 g开关表示全局执行此操作，并且m开关允许插入符号^在行的开头而不是通常的行为匹配，在字符串的开头匹配。

>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

更新如果您需要脚本中的解决方案，则以下内容将产生与命令行相同的结果。

命令行将是perl yourscript.pl fasta.txt请注意，我没有显式打开'fasta.txt'，而是使用了空文件句柄<> 。它读取命令行中指定的fasta文件。

#!/usr/bin/perl use strict; use warnings; # Output sequence my $output = "concatenated.txt"; open my $handle, '>', $output or die "unable to open $output"; my $current = <>; while (my $next = <>) { # if current line is seq characters (not a header) # AND the next line isn't a header if (substr($current, 0, 1) ne '>' && substr($next, 0, 1) ne '>') { chomp($current) } print $handle $current; $current = $next; # print last line if at the end of file print $handle $current if eof; }

If I am guessing right :-) If your file looks like this with more than 1 sequence, you would need to keep newlines after the id line and the last line of the sequence.

A perl 1 liner could be this:

perl -0777 -pe 's/^[TAGC]+\K\n(?!>)//gm' fasta.txt > concatenated.txt

The -0777 says to slurp the whole file into one string.

This substitution says to match all [TAGC] starting at the beginning of the line, (with \K, keep everything before, don't erase). Then a newline \n that is not followed by a >, (beginning of the following line is id).

This erases the new line provided it is a sequence line and not followed by a new id line. The g switch says to do this globally and the m switch allows the caret, ^, to match at the beginning of a line rather than its usual behavior, matching at the beginning of the string.

>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

Update If you need the solution in a script, then the following would produce the same results as the command line.

The command line would be perl yourscript.pl fasta.txt Note that instead of explicitly opening 'fasta.txt', I used the empty filehandle, <>. That reads in the fasta file specified on the command line.

#!/usr/bin/perl use strict; use warnings; # Output sequence my $output = "concatenated.txt"; open my $handle, '>', $output or die "unable to open $output"; my $current = <>; while (my $next = <>) { # if current line is seq characters (not a header) # AND the next line isn't a header if (substr($current, 0, 1) ne '>' && substr($next, 0, 1) ne '>') { chomp($current) } print $handle $current; $current = $next; # print last line if at the end of file print $handle $current if eof; }

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