1. if letters are same it has to be 1 or 3 [ A/A or T/T or G/G or C/C ]
2. if same ID has 2 same letters first one has to be 1 and other has to be 3 [ see the ID S1 has T/T(bold) as 1 and G/G as 3.:::Red bold ]
3. if letters are different it has to be 2 [ A/G or T/A or T/C or others ]
Well, in this case, you'll have to generate the key-value pairs in the three hashes - %chartonum, %numtochar and %mainhash as you iterate through "input1", based on the 3 conditions mentioned.
Code:
$
$
$ cat input1
"aphab" "S1" "S2" "S3"
"a" "T/T" "A/A" "A/A"
"b" "A/G" "A/G" "A/A"
"c" "T/T" "G/G" "A/A"
"d" "G/G" "A/G" "A/G"
"e" "A/G" "G/G" "A/G"
"f" "T/T" "G/G" "A/G"
"g" "T/T" "G/G" "G/G"
"h" "T/T" "G/G" "G/G"
"I" "T/T" "G/G" "G/G"
$
$ cat input2
"ID" "Label" "log"
"S1" "xxx" 2.8
"S1" "xxx" 3
"S1" "xxx" 4
"S2" "yyy" 6.8
"S2" "yyy" 7
"S2" "yyy" 7.4
"S2" "yyy" 8
"S3" "zzz" 12
"S3" "zzz" 14
"S3" "zzz" 16
"S3" "zzz" 18
"S3" "zzz" 20
$
$ cat -n combine_2.pl
1 #!/usr/bin/perl -w
2
3 my %chartonum;
4 my %numtochar;
5 my %mainhash;
6
7 # first process all "input1" files i.e. all elements of the array @infile1
8 $file1 = "input1";
9
10 open(INFILE, $file1) or die "Can't open $file1: $!";
11 while (<INFILE>) {
12 chomp;
13 s/"//g;
14 s/[ ]+/ /g;
15 if ($. == 1) {
16 @x = split/ /;
17 } else {
18 @y = split/ /;
19 foreach $i (1..$#y) {
20 @t = split (/\//, $y[$i]);
21 if ($t[0] eq $t[1]) {
22 if (not defined $chartonum{$x[$i].",".$y[$i]} and
23 not defined $numtochar{$x[$i].",1"} and
24 not defined $numtochar{$x[$i].",3"}) {
25 $numtochar{$x[$i].",1"} = $y[$i];
26 $chartonum{$x[$i].",".$y[$i]} = 1;
27 }
28 elsif (not defined $chartonum{$x[$i].",".$y[$i]} and
29 not defined $numtochar{$x[$i].",3"}) {
30 $numtochar{$x[$i].",3"} = $y[$i];
31 $chartonum{$x[$i].",".$y[$i]} = 3;
32 }
33 } else {
34 if (not defined $chartonum{$x[$i].",".$y[$i]} and
35 not defined $numtochar{$x[$i].",2"}) {
36 $numtochar{$x[$i].",2"} = $y[$i];
37 $chartonum{$x[$i].",".$y[$i]} = 2;
38 } # end of if not defined
39 } # end of else i.e. t[0] ne t[1]
40 $mainhash{$x[$i].",".$chartonum{$x[$i].",".$y[$i]}}++;
41 } # end of foreach
42 } # end of $. > 1
43 }
44 close(INFILE) or die "Can't close $file1: $!";
45
46 # print the header
47 printf("%-12s%-12s%-12s%-12s%-12s%-s\n","\"ID\"","\"Label\"","\"StYPE\"","\"Ntype\"","\"Stype_No\"","\"log\"");
48 # now start processing the "input2" file
49 $infile2 = "input2";
50 open(INFILE, $infile2) or die "Can't open $infile2: $!";
51 while (<INFILE>) {
52 if ($. > 1) {
53 chomp;
54 s/"//g;
55 s/[ ]+/ /g;
56 # print $_,"\n";
57 @z = split/ /;
58 if (!defined $prev or $z[0] ne $prev) {$num = 1} else {$num++};
59 $prev = $z[0];
60 printf("%-12s%-12s%-12s%-12s%-12s%-s\n",
61 "\"$z[0]\"",
62 "\"$z[1]\"",
63 defined $numtochar{$z[0].",".$num} ? "\"".$numtochar{$z[0].",".$num}."\"" : "\"NULL\"",
64 exists $numtochar{$z[0].",".$num} ? $num : "\"null\"",
65 defined $mainhash{$z[0].",".$num} ? $mainhash{$z[0].",".$num} : "\"null\"",
66 $z[2]
67 );
68 }
69 }
70 close(INFILE) or die "Can't close $infile2: $!";
71
$
$ perl combine_2.pl
"ID" "Label" "StYPE" "Ntype" "Stype_No" "log"
"S1" "xxx" "T/T" 1 6 2.8
"S1" "xxx" "A/G" 2 2 3
"S1" "xxx" "G/G" 3 1 4
"S2" "yyy" "A/A" 1 1 6.8
"S2" "yyy" "A/G" 2 2 7
"S2" "yyy" "G/G" 3 6 7.4
"S2" "yyy" "NULL" "null" "null" 8
"S3" "zzz" "A/A" 1 3 12
"S3" "zzz" "A/G" 2 3 14
"S3" "zzz" "G/G" 3 3 16
"S3" "zzz" "NULL" "null" "null" 18
"S3" "zzz" "NULL" "null" "null" 20
$
$
Use the Data :: Dumper module to check the values of the 3 hashes right after "input1" is done processing at line 45.
But frankly, given the complexity of calculations involved, I'd rather look for some Perl Bioinformatics modules that have subroutines to do this.
Or check BioPerl, or books like "Beginning/Mastering Perl for Bioinformatics" at amazon.com.
HTH,
tyler_durden
PS - I'm assuming those A, C, G, T are the nucleotide bases of a DNA strand, and these files are related to Bioinformatics.
Last edited by durden_tyler; 03-16-2010 at 02:50 PM..
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03-16-2010