Update:
You say " "last;" is also not working here..". I don't see any "last;" statement in the code, should be fine if put in the right place. Step 1: get your code to compile.
I suggest your read chomp doc to understand what chomp() does. If you insist on splitting on \t, chomp the input line first as the doc's suggest.
Update2: Some code:
I can tell that you are beginner at Perl and because this doesn't look like
homework, I wrote some code for you that incorporates my advice
above. I hope some actual code is easier to understand than general advice. Please
play with this and adapt it to your needs.
It is possible to make an "in memory" data structure of either file1 or file2. In this case, I picked file 1 and generated a hash table from it. The keys of this "file 1 hash table" are like "chr17:69112551" and the value of each key like that is set to "1" although that "1" value is never used in my code.
From looking at your code, it appears that the desired output is one line for each
line in file 2.
In your code, if ($ary[0] eq $any[0] and $ary[1] == $any[1])
has been transformed into: if ( exists ($file1_hash{"$any[0]:$any[1]"})). Using
a combined hash key like this expresses the "and" function. Then there is another
condition for the "or" function.
The net effect of code like this is that each line in file 1 or file 2 is only read once. File I/O is "expensive" in terms of CPU power. Every line in file 1 is read and a hash table created. Then for each line in file 2, the line is read, parsed and a decision is reached based upon the result of 2 look-up statements into the file 1 hash. These hash look-ups are very efficient and scale to very big files.
I couldn't see any way to get an "E" with your test data, so I added some extra data to my test cases. In the future, it is best if you can provide an example "desired output" that demo's the basic decisions which need to be made.
Have fun. Ask questions if you don't understand. If I made a mistake and didn't understand something, asking about that is fine too. Oops, just had a thought that you wanted an output line per line of file 1 instead of file 2? In that case, code changes, possibly make a HoA, Hash of Array out of file 2 to start off.
#!/usr/bin/perl use warnings; use strict; use Data::Dumper; my $file1 = <<END; chr17 69112551 chr1 67058869 chr7 151046672 chr7 151047369 chr1 66953654 END my $file2 = <<END; chr1 66953622 66953654 chr1 67200451 67200472 chr1 67200475 67200478 chr1 67058869 67058880 chr1 67058881 67058885 chr1 67058887 67058895 END open my $infile1, '<', \$file1 or die "unable to open first file $!"; open my $infile2, '<', \$file2 or die "unable to open 2nd file $!"; ### create memory structure of file 1: ### so that we only have to read file1 once! # my %file1_hash; while (my $line = <$infile1>) { next if $line =~ /^\s*$/; #skip blank lines (a common infile goof +) my ($key, $value) = split /\s+/, $line; # use better "names" I have # no idea of what a chr col + means $file1_hash{"$key:$value"} = 1; } close $infile1; # file handle closure is optional, but I'd do it. ### process each line in file2: ### If a line "matches" with any line in file1, then "E", else "M" ### I don't know that these numbers mean, come up with better comment +. while (my $line = <$infile2>) { chomp $line; #so that output with E or M can be on same line next if $line =~ /^\s*$/; #skip blank lines (a common infile goof +) my ($chr, $val1, $val2) = split /\s+/,$line; if ( exists $file1_hash{"$chr:$val1"} or exists $file1_hash{"$chr:$val2"} ) { print "$line\tE\n"; # match exists with file 1 } else { print "$line\tM\n"; # match does NOT exist with file 1 } } __END__ Prints the following: chr1 66953622 66953654 E chr1 67200451 67200472 M chr1 67200475 67200478 M chr1 67058869 67058880 E chr1 67058881 67058885 M chr1 67058887 67058895 M
In reply to Re: compare two files on the basis of Two IDs
by Marshall
in thread compare two files on the basis of Two IDs
by genome
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