Perl oneliners for Bioinformatics

2017-02-09T00:00:00+00:00

To use most of one-liners in this post, you should:

If you’re working on Windows, download and install ActiveState Perl</a>.</li>
Replace variable $file</code> at the end of scripts by the real file name.</li>

Run the script as a command in CMD</code>.</li> </ol>Extract a reference sequence from a single-query FASTA file</a></li> Find plain-text files with same appendix in multiple directories recursively and merge them into one file</a></li> Filter FASTQ by length of query</a></li> To “flare out” FASTA queries</a></li> To calculate the proportion of gaps (“N” or “n”) in a genome</a></li> To get reads in FASTQ with specific length and count in descending order</a></li> To calculate positive and negtive read counts separately</a></li> To print file names in current directory</a></li> To remove all patches and scaffolds etc., but leave only chromosomes in a genome reference file.</a></li> To convert FASTQ into FASTA</a></li> </ul> Extract a reference sequence from a single-query FASTA file</h2> Replace the scalar $start and $end with two number indicating location then execute. perl -ne 'next if /^>/; $_ =~ s/[\r\n]+//g; @a = split //, $_; for (@a) {$i ++; if(($i >= $start) && ($i <= $end)) {print}}' $file</code></pre>Find plain-text files with same appendix in multiple directories recursively and merge them into one file</h2> Replace the scalar $append with the suffix (e.g. .seq) then execute. perl -MFile::Find -le "sub search{if (/\$append$/){($id) = map{/.+_(\(.+).seq$/} $_; open(SEQ, qq{<}, $File::Find::name) or die qq{Processing:$File::Find::name\n$!\n}; while(<SEQ>) {print MERGE qq{>$id}; print MERGE $_} }} open MERGE, qq{>}, qq{sanger.fa}; find({ wanted => \&search, no_chdir => 1 }, qq{.})" $file</code></pre>Filter FASTQ by length of query</h2> Replace the scalar $minlen and $maxlen with the number representing interval then execute. perl -lane "if ($. % 4 == 1) {$id = $_ =~ s/[\r\n]+//r} elsif ($. % 4 == 2) {$seq = $_ =~ s/[\r\n]+//r} elsif ($. % 4 == 3) {$name = $_ =~ s/[\r\n]+//r} else {$qual = $_ =~ s/[\r\n]+//r; print qq{$id\n$seq\n$name\n$qual} if ((length($seq) >= $minlen) && (length($seq) <= $maxlen))}" $file</code></pre>To “flare out” FASTA queries</h2> FASTA is a file format and is recommended that all lines of text be shorter than 80 characters. However, when we need to grep continuous strings in it, the line break such as [\r\n]</code> usually cause troubles. Use this command can remove newline characters in sequences. perl -pe '$. == 1 ? 23333333 : /^>/ ? $_ = qq{\n} . $_ : s/[\r\n]+//' $file</code></pre>To calculate the proportion of gaps (“N” or “n”) in a genome</h2> perl -lne 'next if /^>/; $_ =~ s/[\r\n]+//; $total_len += length($_); $n_count += map{/[nN]/g} $_ }{ END{print qq{Total length: $total_len}; print qq{N count: $n_count}; $n_ratio = $n_count / $total_len; print qq{N ratio: $n_ratio}}' $file</code></pre>To get reads in FASTQ with specific length and count in descending order</h2> Replace the scalar $length</code> with the length you’re interested in (without unit such as “bp”) then execute. perl -lne 'next unless (($. % 4 == 2)&&(length($_) == $length)); $count{$_}++; }{ for (sort {$count{$b} <=> $count{$a}} keys %count) {print qq{$_\t$count{$_}}}' $file</code></pre>To calculate positive and negtive read counts separately</h2> perl -lane 'next if /^@/; next if $F[1]&0x4; $len = eval join q{+}, map {/(\d+)[MID]/g} $F[5]; $pos{$len} ++ if $F[1] == 0; $neg{$len} ++ if $F[1] == 16 }{ print qq{$_\t$pos{$_}} for (keys %pos); print qq{$_\t-$neg{$_}} for (keys %neg)' $file</code></pre>To print file names in current directory</h2> perl -le "print for (glob qq{*})"</code></pre>To remove all patches and scaffolds etc., but leave only chromosomes in a genome reference file.</h2> perl -lpe '/^>/ && !/REF$/ ? last : /^>/ ? $_ =~ s/>(\w+)/>chr$1/ : 23333333' $file</code></pre>To convert FASTQ into FASTA</h2> perl -F'@' -lanE'$. % 4 == 1 ? say qq{>$F[1]} : $. % 4 == 2 ? say $_ : $. % 4 == 3 ? qq{Yu Sun is handsome} : 233333333' $file</code></pre>

Yu Sun - Perl

Perl oneliners for Bioinformatics

To convert FASTQ</em> into FASTA</em></h2>
`perl -F</span>'@'</span> -lanE</span>'$. % 4 == 1 ? say qq{>$F[1]} : $. % 4 == 2 ? say $_ : $. % 4 == 3 ? qq{Yu Sun is handsome} : 233333333'</span> $file</span></span></code></pre>`

Yu Sun - Perl

Perl oneliners for Bioinformatics

To convert FASTQ</em> into FASTA</em></h2> perl -F</span>'@'</span> -lanE</span>'$. % 4 == 1 ? say qq{>$F[1]} : $. % 4 == 2 ? say $_ : $. % 4 == 3 ? qq{Yu Sun is handsome} : 233333333'</span> $file</span></span></code></pre>

To convert FASTQ</em> into FASTA</em></h2>
`perl -F</span>'@'</span> -lanE</span>'$. % 4 == 1 ? say qq{>$F[1]} : $. % 4 == 2 ? say $_ : $. % 4 == 3 ? qq{Yu Sun is handsome} : 233333333'</span> $file</span></span></code></pre>`