Thanks for the reply basically the problem is that I do not need most of the fields contained in file 1 and most of the fields in file 2
Few lines of file1:
169: rs60465173 has merged into rs8057341 Homo sapiensCAGCTGACTGAGGCAGCGGGAGTTGAA/GAAGAAACGATATTAGTTCATGGTGA
ABI, AFFY, ILLUMINA-UK, ILLUMINA, ILLUMINA, ILLUMINA, ILLUMINA, ILLUMINA, ILLUMINA170: rs17312781 has merged into rs8057341 Homo sapiensCAGCTGACTGAGGCAGCGGGAGTTGAA/GAAGAAACGATATTAGTTCATGGTGA
ABI, AFFY, ILLUMINA-UK, ILLUMINA, ILLUMINA, ILLUMINA, ILLUMINA, ILLUMINA, ILLUMINA171: rs8057341 Homo sapiensCAGCTGACTGAGGCAGCGGGAGTTGAA/GAAGAAACGATATTAGTTCATGGTGA
ABI, AFFY, ILLUMINA-UK, ILLUMINA, ILLUMINA, ILLUMINA, ILLUMINA, ILLUMINA, ILLUMINA172: rs60162986 has merged into rs8046608 Homo sapiensCCCTACTTACTTGTGGCCTGTCCCCTC/TGTGAATGTGTCTCATGTCCCCAGTG
AFFY173: rs8046608 Homo sapiensCCCTACTTACTTGTGGCCTGTCCCCTC/TGTGAATGTGTCTCATGTCCCCAGTG
From there I need the rs value. And for this I made the code I wrote about. Now I have rs values in an array and I need to grab only the lines which contain the rsnumbers from a second huge txt file (1 GB)
The second file looks like
First row XXX XXX XXX XXX XXX XXX XXX XXX (1050 cells)
rsnumber AA AG AG AG AA AG AG AG (1050 times)
rsnumber TT AT AA AT AT .....
500 times more
I need to get from this file the rsnumbers stored in the array from file 1 toghether with the 1050 values on the string | [reply] |
Maybe I was not enough clear
Form file1 (you can see few lines) i need only the rs with 5-8 numbers field. The same field is the first column of file 2
Here we are
| [reply] |
Thanks every body for the help
Basically my output file 1 at the moment is a file with 1 column with rs values like
rs3547689
rs325678912
rs36789012
etc
I need now to find these value in file 2 and print out the line or in a separated file
The file 2 looks like
XXX XXX XXX XXX XXX XXX (1050 times)
rs3507865 AA AT AT AT TT AA (1050 values)
rs3456189 GG GC GG CC CC .....
more than 700 rows
Can you gimme a suggestion for keys for the hash? Can be row number even if I can not write on file 2? Cheers again
| [reply] |
Only 700 (even if long) rows? Then you don't need any disc-based hash. Just create a hash with the rs value (i.e. for example the 'rs3507865') of a row in file2 as key and the position in the file as data. The position in the file you can find with tell() (before reading the line).
Then just read the numbers in file1 and look up their position in the hash and use seek() in file2 to go there
open(FILE2,...
my $position=tell(FILE2);
my %rs;
while ($line=<FILE2>) {
my ($key)= $line=~/^(rs\d{5,})\b/;
if (defined $key) {
$rs{$key}= $position;
}
$position=tell(FILE2);
}
...
while (defined ($line= <FILE>)) {
...
foreach (@output) {
if (exists $rs{$_}) {
seek(FILE2,$rs{$_},0);
my $line= <FILE2>;
print FD $line;
}
}
UPDATE: Added a '^' to the regex in the script
| [reply]
[d/l] |