Perl matching array across file - perl

Question

I have a file which looks like this.
In the Perl code, i am using an array #query = ('A+80', 'A+40', 'A+202', 'B+130', 'B+268', 'B+211', 'A+35');
What I want to do is: for each element of the array, scan the lines in the file shown below and print out something like this:
A+80 - HELIX
A+40 - SHEET
A+202 - HELIX
B+130 - HELIX
B+268 - SHEET
B+211 - SHEET
A+35 - LOOP
The logic behind this output is to extract for each entry in array, the first part i.e. A or B, and the second part, i.e. the number associated with the 1st part. Consider the first entry in the array: A+80. On the third line of the file the number 80 is lying between 78 (the 6th column) and 90 (the 9th column) and also first alphabet A is also matching in both cases. Hence the program prints HELIX for this query.
Consider 2nd element: A+40. The 2nd part i.e the number lies in the range as on this line
SHEET 2 B 3 ARG A 37 VAL A 43 1
i.e. between the numbers listed in columns 7 and 10, and the alphabet matches too. Hence for this entry the output is: SHEET
For other cases, like B+211. THe line given below matches the number and the alphabet associated with it.
SHEET 2 B 3 ARG A 37 VAL A 43 1
Hence the output for this entry is: SHEET
Also, for entries whose alphabet and number associated with it, do not match any of the lines in the file. the code outputs: A+35 - LOOP
What is an efficient way to do this in Perl?
Since I am a beginner with Perl, I am as of now splitting each entry in successive array elements, i.e. for #query, and matching/comparing the alphabet and number to each of the relevant columns in the lines. But somehow am unable to get the output desired.
Please help...
HELIX 1 1 GLY A 9 GLN A 30 1
HELIX 2 2 ASP A 47 ILE A 63 1
HELIX 3 3 GLU A 78 GLU A 90 1
HELIX 4 4 THR A 111 ALA A 117 1
HELIX 5 5 PRO A 120 LYS A 122 5
HELIX 6 6 SER A 129 ARG A 137 1
HELIX 7 7 CYS A 147 THR A 159 1
HELIX 8 8 GLY A 178 ASN A 188 1
HELIX 9 9 LEU A 202 LYS A 208 1
HELIX 10 10 GLY A 224 TRP A 226 5
HELIX 11 11 TYR A 258 GLU A 263 1
HELIX 12 12 VAL A 275 PHE A 294 1
HELIX 13 13 GLY B 9 GLN B 30 1
HELIX 14 14 ASP B 47 ILE B 63 1
HELIX 15 15 GLU B 78 GLU B 90 1
HELIX 16 16 THR B 111 ALA B 117 1
HELIX 17 17 PRO B 120 LYS B 122 5
HELIX 18 18 SER B 129 ARG B 137 1
HELIX 19 19 CYS B 147 THR B 159 1
HELIX 20 20 GLY B 178 TRP B 187 1
HELIX 21 21 LEU B 202 LYS B 208 1
HELIX 22 22 GLY B 224 TRP B 226 5
HELIX 23 23 TYR B 258 GLU B 263 1
HELIX 24 24 GLY B 276 PHE B 294 5
SHEET 1 A 2 GLU A 5 LEU A 7 0
SHEET 2 A 2 PHE A 267 THR A 269 1
SHEET 1 B 3 LYS A 66 LEU A 72 0
SHEET 2 B 3 ARG A 37 VAL A 43 1
SHEET 3 B 3 GLY A 96 VAL A 99 1
SHEET 1 C 4 THR A 191 CYS A 195 0
SHEET 2 C 4 HIS A 167 VAL A 171 1
SHEET 3 C 4 ILE A 211 VAL A 214 1
SHEET 4 C 4 ILE A 232 ASP A 235 1
SHEET 1 D 2 GLU B 5 LEU B 7 0
SHEET 2 D 2 PHE B 267 THR B 269 1
SHEET 1 E 3 LYS B 66 LEU B 72 0
SHEET 2 E 3 ARG B 37 VAL B 43 1
SHEET 3 E 3 GLY B 96 VAL B 99 1
SHEET 1 F 4 THR B 191 CYS B 195 0
SHEET 2 F 4 HIS B 167 VAL B 171 1
SHEET 3 F 4 ILE B 211 VAL B 214 1
SHEET 4 F 4 ILE B 232 ASP B 235 1
SHEET 1 G 2 ASN B 239 PRO B 242 0
SHEET 2 G 2 ARG B 250 VAL B 253 -1

Answer 1

The program below seems to do what you need. It reads data from within the source file using the DATA file handle for convenience: you must arrange to open and read the appropriate data file.
The entirety of the file is read into memory for straightforward access. If the file is enormous (say, hundreds of megabytes) then this approach may be inappropriate and you will have to come back for more help.
The records vary in length, so the algorithm locates the relevant fields relative to the first three-letter field found.
The hash %categories contains all of the required file data. It is indexed by the key letter - A or B here - and the value of each element is an array of anonymous hashes containing the label (column 1), the letter, and the start and end of the range covered by each record.
Building the output is straightforward, and uses map and grep to find the 'label' of all the relevant entries in the hash. If none are found the text "LOOP" is added as a default.
use strict;
use warnings;
my #query = qw/ A+80 A+40 A+202 B+130 B+268 B+211 A+35 /;
my %categories;
while (<DATA>) {
next unless /\S/;
my #data = split;
my #indices = grep $data[$_] =~ /^[A-Z]{3}$/, 0 .. $#data;
my %info;
#info{qw/ label letter start end /} = #data[ 0, $indices[0]+1, $indices[0]+2, $indices[1]+2 ];
push #{ $categories{$info{letter}} }, \%info;
}
for my $item (#query) {
my ($letter, $value) = split /\+/, $item;
my #matches = map $_->{label},
grep { $value >= $_->{start} and $value <= $_->{end} }
#{ $categories{$letter} };
#matches = ('LOOP') unless #matches;
warn qq(Multiple categories for query "$item") unless #matches == 1;
printf "%s - %s\n", $item, $_ for #matches
}
__DATA__
HELIX 1 1 GLY A 9 GLN A 30 1
HELIX 2 2 ASP A 47 ILE A 63 1
HELIX 3 3 GLU A 78 GLU A 90 1
HELIX 4 4 THR A 111 ALA A 117 1
HELIX 5 5 PRO A 120 LYS A 122 5
HELIX 6 6 SER A 129 ARG A 137 1
HELIX 7 7 CYS A 147 THR A 159 1
HELIX 8 8 GLY A 178 ASN A 188 1
HELIX 9 9 LEU A 202 LYS A 208 1
HELIX 10 10 GLY A 224 TRP A 226 5
HELIX 11 11 TYR A 258 GLU A 263 1
HELIX 12 12 VAL A 275 PHE A 294 1
HELIX 13 13 GLY B 9 GLN B 30 1
HELIX 14 14 ASP B 47 ILE B 63 1
HELIX 15 15 GLU B 78 GLU B 90 1
HELIX 16 16 THR B 111 ALA B 117 1
HELIX 17 17 PRO B 120 LYS B 122 5
HELIX 18 18 SER B 129 ARG B 137 1
HELIX 19 19 CYS B 147 THR B 159 1
HELIX 20 20 GLY B 178 TRP B 187 1
HELIX 21 21 LEU B 202 LYS B 208 1
HELIX 22 22 GLY B 224 TRP B 226 5
HELIX 23 23 TYR B 258 GLU B 263 1
HELIX 24 24 GLY B 276 PHE B 294 5
SHEET 1 A 2 GLU A 5 LEU A 7 0
SHEET 2 A 2 PHE A 267 THR A 269 1
SHEET 1 B 3 LYS A 66 LEU A 72 0
SHEET 2 B 3 ARG A 37 VAL A 43 1
SHEET 3 B 3 GLY A 96 VAL A 99 1
SHEET 1 C 4 THR A 191 CYS A 195 0
SHEET 2 C 4 HIS A 167 VAL A 171 1
SHEET 3 C 4 ILE A 211 VAL A 214 1
SHEET 4 C 4 ILE A 232 ASP A 235 1
SHEET 1 D 2 GLU B 5 LEU B 7 0
SHEET 2 D 2 PHE B 267 THR B 269 1
SHEET 1 E 3 LYS B 66 LEU B 72 0
SHEET 2 E 3 ARG B 37 VAL B 43 1
SHEET 3 E 3 GLY B 96 VAL B 99 1
SHEET 1 F 4 THR B 191 CYS B 195 0
SHEET 2 F 4 HIS B 167 VAL B 171 1
SHEET 3 F 4 ILE B 211 VAL B 214 1
SHEET 4 F 4 ILE B 232 ASP B 235 1
SHEET 1 G 2 ASN B 239 PRO B 242 0
SHEET 2 G 2 ARG B 250 VAL B 253 -1
output
A+80 - HELIX
A+40 - SHEET
A+202 - HELIX
B+130 - HELIX
B+268 - SHEET
B+211 - SHEET
A+35 - LOOP