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Re^2: Count the sequence length of each entry in the file

by davi54 (Sexton)
on Oct 02, 2020 at 16:54 UTC ( #11122486=note: print w/replies, xml ) Need Help??


in reply to Re: Count the sequence length of each entry in the file
in thread Count the sequence length of each entry in the file

Thank you for your help. Actually, the input file is formatted to have only 60 characters in each line and then it moves to the new line. So, that's the input file format when you see just a single S on the last line of the second entry.

On a different note, for the first entry, the sequence length value you get in your output (110) is one less than the actual sequence length which is 111. However, my output gives me a sequence length of 115, which is even worse. Do you know where the error might be?

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Re^3: Count the sequence length of each entry in the file
by kcott (Bishop) on Oct 03, 2020 at 04:47 UTC
    "for the first entry, the sequence length value you get in your output (110) is one less than the actual sequence length which is 111."
    $ perl -E 'say length "VQLQESGGGLVQAGGSLRLSCAASGRAVSMYNMGWFRQAPGQERELV +AAISRGGSIYYA"' 59 $ perl -E 'say length "DSVKGRFTISRDNAKNTLYLQMNNLKPEDTGVYQCRQGSTLGQGTQV +TVSS"' 51 $ perl -E 'say 59+51' 110

    If you add the newline between those two strings you'll get 111 for \n or 112 for \r\n. There's also whitespace after those strings which will further increase the length of the line. As I already stated, you posted your data as paragraph text: I can't tell what the original data was.

    I removed all whitespace in my code:

    $record =~ s/\s//gm;

    The correct length, after removing white space, is 110.

    — Ken

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