How to code in perl using subroutines - perl

Question

I need to score my string patches following certain criteria:
Column 1: B for buried or E for Exposed - Threshold: 25%
Column 2: Amino acid
Column 3: Sequence name
Column 4: Amino acid number
Column 5: Relative Surface Accessibility - RSA
Column 6: Absolute Surface Accessibility
Column 7: Z-fit score for RSA prediction
Column 8: Probability for Alpha-Helix
Column 9: Probability for Beta-strand
Column 10: Probability for Coil
E K 132L_A_PDBID_CHAIN_SEQUENCE 1 0.716 147.261 1.150 0.016 0.005 0.979
E V 132L_A_PDBID_CHAIN_SEQUENCE 2 0.514 79.033 1.252 0.191 0.086 0.723
B F 132L_A_PDBID_CHAIN_SEQUENCE 3 0.134 26.793 -0.325 0.191 0.086 0.723
E G 132L_A_PDBID_CHAIN_SEQUENCE 4 0.570 44.835 1.012 0.354 0.048 0.598
Remember, the last three columns are the probabilities for either Helix/Sheet/Coil.......
So first we need to classify whether a certain residue falls under Helix/Sheet/Coil using some criterion function....based on the max. probability within the last 3 columns...
Then one we get the structural preferences, we need to score the sequences breaking into patches of 10......
My scoring criteria is this:
EXPOSED = 1; # +1 for letters that exposed
BURIED = 0; # 0 for letters that are buried
COIL = 3; # +3 for any coil
HELIX = 2; # +2 for any helix
SHEET = 1; # +1 for any sheet
The link below is for breaking a string into patches of 10~11
http://pastebin.com/GeW5AKF3
The problem I am facing is that I have splitted in string into horizontal patches as in the above link, but the file is vertically aligned......
Thanks for help....... Waiting for reply

Answer 1

This should get you going:
open my $fh, "<", "input.txt";
my #data;
while(my $line = <$fh>) # If we got line from file
{
chomp $line; # remove carraigereturn/linefeed
my #parts = split /\s+/, $line; # split based on values seperated by one or more spaces
push #data, [#parts] # Add array of split parts to data array
}
Thats puts everything into #data. You access it like this:
# now access whatever you want...
# example: line 3 column 6 (perl arrays start from 0 not 1):
print $data[2][5] . "\n"; #prints 26.793
# line 4 column 2:
print $data[3][1] . "\n"; #prints G
Then you can sort like this. (Example sort by Col1 then by Col5(RSA):)
#data = sort { if ( $a->[0] eq $b->[0] ) { $a->[4] <=> $b->[4] } else { $a->[0] cmp $b->[0] } } #data;
Then output data like this:
foreach my $line (#data)
{
foreach my $field (#$line)
{
print $field."\t";
}
print "\n";
}
Output is:
B F 132L_A_PDBID_CHAIN_SEQUENCE 3 0.134 26.793 -0.325 0.191 0.086 0.723
E V 132L_A_PDBID_CHAIN_SEQUENCE 2 0.514 79.033 1.252 0.191 0.086 0.723
E G 132L_A_PDBID_CHAIN_SEQUENCE 4 0.570 44.835 1.012 0.354 0.048 0.598
E K 132L_A_PDBID_CHAIN_SEQUENCE 1 0.716 147.261 1.150 0.016 0.005 0.979