I'm pretty new to Perl and this is my most complex project yet. Apologies if any parts of my explanation don't make sense or I miss something out - I'll be happy to provide further clarification. It's only one line of code that's causing me an issue.
The Aim:
I have a text file that contains a single column of data. It reads like this:
0
a,a,b,a
b,b,b,a
1
a,b,b,a
b,b,b,a
It continues like this with a number in ascending order up to 15, and the following two lines after each number are a combination of four a's or b's separated by commas. I have tied this file to an array @diplo
so I can specify specific lines of it.
I also have got a file that contains two columns of data with headers that I have converted into a hash of arrays (with each of the two columns being an array). The name of the hash is $lookup and the array names are the names of the headings. The actual arrays only start from the first value in each column that isn't a heading. This file looks like this:
haplo frequency
"|5,a,b,a,a|" 0.202493719
"|2,b,b,b,a|" 0.161139191
"|3,b,b,b,a|" 0.132602458
This file contains all of the possible combinations of a or b at the four positions combined with all numbers 0-14 and their associated frequencies. In other words, it includes all possible combinations from "|0,a,a,a,a|" followed be "|1,a,a,a,a|" through to "|13,b,b,b,b|" and "|14,b,b,b,b|".
I want my Perl code to go through each of the combinations of letters in @diplo starting with a,a,b,a and record the frequency associated with the row of the haplo array containing each number from 0-14, e.g. first recording the frequency associated with "|0,a,a,b,a|" then "|1,a,a,b,a|" etc.
The output would hopefully look like this:
0 #this is the number in the @diplo file and they increase in order from 0 up to 15
0.011 0.0023 0.003 0.0532 0.163 0.3421 0.128 0.0972 0.0869 0.05514 0.0219 0.0172 0.00824 0.00886 0.00196 #these are the frequencies associated with x,a,a,b,a where x is any number from 0 to 14.
My code: And here is the Perl code I created to hopefully sort this out (there is more to create the arrays and such which I can post if required, but I didn't want to post a load of code if it isn't necessary):
my $irow=1; #this is the row/element number in @diplo
my $lrow=0; #this is the row/element in $lookup{'haplo'}
my $copynumber=0;
#print "$copynumber,$diplo[2]";
while ($irow<$diplolines-1) {
while ($copynumber<15) {
while ($lrow<$uplines-1) {
if ("|$copynumber,$diplo[$irow]|" = $lookup{'haplo'}[$lrow]) { ##this is the only line that causes errors
if ($copynumber==0) {
print "$diplo[$irow-1]\n";
#print "$lookup{'frequency'}[$lrow]\t";
}
print "$lookup{'frequency'}[$lrow]\t";
}
$lrow=$lrow+1;
}
$lrow=0;
$copynumber=$copynumber+1;
}
$lrow=0;
$copynumber=0;
$irow=$irow+1;
}
However, the line if ("|$copynumber,$diplo[$irow]|" = $lookup{'haplo'}[$lrow])
is causing an error Can't modify string in scalar assignment near "]) "
. I have tried adding in speech marks, rounded brackets and apostrophes around various elements in this line but I still get some sort of variant on this error. I'm not sure how to get around this error.
Apologies for the long question, any help would be appreciated.
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