in reply to Re^4: mismatching characters in dna sequence
in thread mismatching characters in dna sequence

Hm. The first and most obvious problem is you've forgotten my here:

    my( $ref, $matches, $query ) = $read->padded_alignment;
#...^^

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A more subtle potential problem is not having the shebang line as the first line of the file:

# V5: Inline::C
#!/opt/local/bin/perl

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I don't know what that first line is meant to do, but either delete it or move it below the Inline C code.

Make those two corrections and then see what happens.

You do have a C compiler correctly installed don't you?

With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'
Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
"Science is about questioning the status quo. Questioning authority".
In the absence of evidence, opinion is indistinguishable from prejudice.

The start of some sanity?

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Re^6: mismatching characters in dna sequence
by prbndr (Acolyte) on Dec 30, 2011 at 20:58 UTC
    thanks...this is really quick! it was really the missing "my" that did me in. is there a quick way to tabulate all the respective transitions? e.g. 
    A:T = 234
A:G = 492
A:C = 273
T:A = 400
...

    [download]
    and so on... basically output the total number of each type of transition?
[reply]
[d/l]
      basically output the total number of each type of transition?

      Per sequence compared, or for all the sequences?

      With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'
      Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
      "Science is about questioning the status quo. Questioning authority".
      In the absence of evidence, opinion is indistinguishable from prejudice.

      The start of some sanity?
[reply]
        for all the sequences
[reply]

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