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    cat input_file.fq | \ perl -ne '$s=<>;<>;<>;chomp($s);print length($s)."\n";' > output.txt

Just a stylistic note, but this can be restated as the following:

    perl -ne '$s=<>;<>;<>;chomp($s);print length($s)."\n";' \ <input_file.fq >output.txt

Unless I'm dumping the contents of a file to the console, I don't use cat that much .. head, tail and less are handier.

Alex / talexb / Toronto

"Groklaw is the open-source mentality applied to legal research" ~ Linus Torvalds


In reply to Re: command line perl reading from STDIN by talexb
in thread command line perl reading from STDIN by perlhappy

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