confused with interactions...

Anonymous Monk has asked for the wisdom of the Perl Monks concerning the following question:

Hello all, I have a school assignment in Biology but I seem to be unable to begin... What I was given is something like the following : This is my input file:

>2BL2A
H1-H2      MMDYLITQV       GMVFAVLAMATATIFSGIGSAKGVGMTGEAAAALTT  
 M--F #(aminoacids that interact)
L--V
H1-H6      MMDYLITQV    SVVQGLNFLGASLPIAFTGLFSGIAQGKVAAAGIQILAKK  
M--V
L--V
I--V
M--V
[download]

The output file i want to be sth like that

                                          
>2BL2A
H1  MMDYLITQV
H2  GMVFAVLAMATATIFSGIGSAKGVGMTGEAAAALTT 
D=1  I=1  L=1  M=2  Q=1  T=1  Y=1  V=1  The  total aa num =9
A=9  E=1  F=2  G=6  I=2  K=1  L=2  M=3  S=2  T=5  V=3    The  total aa
+ num =36
MF 1-->4  ## 1 is the number of how many times the aminoacids interact
+ and 4 is the number of how many times there is a possibility
LV 1-->5  ## these two aminoacids(MF) to interact. M=2 from H1 and  F=
+2 from H2 2x2=4  
                  ## L=1 from H1, V=3 from H2 1x3=3
                  ## L=2 form H2, V=1 from H1 2x1=2  the sum is 5   
H1  MMDYLITQV
H6  SVVQGLNFLGASLPIAFTGLFSGIAQGKVAAAGIQILAKK 
D=1  I=1  L=1  M=2  Q=1  T=1  Y=1  V=1 The  total aa num =9
A=7  F=3  G=6  I=4  K=3  L=5  N=1  P=1  Q=3  S=3  T=1  V=3    The  tot
+al aa num =40
MV 2-->6  ##M=2 from H1 V=3 from H6  2x3=6
LV 1-->8  ## L=1 from H1 V=3 from H6 1x3=3 L=5 from H6 V=1   from H1  
+5x1=5    3+5=8 possible interactions
IV 1-->7
[download]

Any help please?

Comment on confused with interactions... Select or Download Code

Replies are listed 'Best First'.
Re: confused with interactions... by davido (Cardinal) on Jul 04, 2007 at 17:37 UTC
We can explain the file parsing, if you can first explain the actual "rules" set. For example, I have no idea when amino acids interact, and when there is a possibility. Those of us who don't have a background in your subject would be better able to assist if we understand the basics of the puzzle. Dave	[reply]
Re: confused with interactions... by GrandFather (Saint) on Jul 04, 2007 at 21:10 UTC
Some tools that will help: using split as: `my @H1aAcids = split //, $H1` you get an array containing the individual letters (amino acids I presume) using a hash (see perldata) you can count the number of occurrences of each letter: `$H1count{$_}++ for @H1aAcids` If you want any more help you're going to have to tell us in terms of a recipe (algorithm) how the output relates to the input or wait for one of the biologically knowledgeable monks to stroll by. DWIM is Perl's answer to Gödel	[reply] [d/l] [select]