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akreibich07 you should look in the NCBI FTP folder (ftp://ftp.ncbi.nih.gov/genomes/). GenBank provides the information you are looking for, as ready to use files. alternately, if you know the accession numbers for all your sequences, use the batch download feature...

Learning one thing at a time. Now it works. Thanks a lot prex1.

Hi! I have a problem running this subroutine on arrays. I have 4 arrays @arr1, @arr2, @arr3, @arr4. I am trying to use the T-test subroutine to compare the statistical significance of these arrays. select FILEW2; &t_test(@arr1, @arr2), &t_test(@arr1, @arr3), &t_test(@arr1, @arr4)...

Hi! prex1, it much faster now. i can live with that. thanks so much. Steve, point well taken. I need to put more effort into programming.

Hi! i have a program that is working fine except that i have huge data sets to work with and the script that i wrote is slow. is there are way to make it work faster. thanks while (<FILE1>) { my ($a,$s,$p,$c) = $_ =~ /^(.+)\t(\d+)\t(\d+)\t(.+)/; $n=$a."\t".$s."\t".$c; $hash1{$n} = $p; }...

charming rharsh. done!

Hi! I am trying to use the Perl module on t-test http://backpan.perl.org/authors/id/Y/YU/YUNFANG/Statistics-TTest-1.0.html in a subroutine for working on my genetics data sets (not class work though) and am not able to direct the output to the OUTFILE. it prints to the console. Here are my two...

Prex1, i indeed had a typo in the code. Thanks a lot for straightening the error. For future reference, how do i use code tags. This is a plain text file and not a HTML code and i am using windows DOS.

prex1 thanks for the advice. print FILEW1"%$tmpvar[$count-1]\t$tmpvar[$count]\t$tmpvar[$count+1]\n"; is the line that is printing that single value. I also checked , there are no spaces at the end of the line.

Prex1 my apologies and thanks for the advice. I modified the line as push(@tmpvar, $tmpvar); rest of the code us same as above. now there are no error messages but it prints only the below to the out file. SCA_1.913347

Hi! Prex1/Kevin, thanks for posting the code. here is the sample data and the full script. I used Prex1 core, but still code returns errors. Please see if there is obvious error in my script. input.txt SCA_1.546604 SCA_1.608602 exp-file2.txt SCA_1.271105 SCA_1.512793 SCA_1.546604...

Kevin, I am not clear here, how do i use your suggestion to work with 2 arrays. Could you please show some more.. Thanks

Hi! I am trying to compare 2 arrays and when there is match in the second array, wants to print the element, the one before and the one after the match. when using only one matching element, it works, see below. my @num = (1..20); foreach $num(@num){ $count++; if ($num == 2) { print...

My bad, there was an additional space in the actual file. Your script rocks. Thanks.

rharsh, thanks for the solution. It does work as long as the end of the file has 'DWN'. That will do for me.

Hi! I have 4 columns of tab-delimited data. column 1 has two patterns, 'UA' and 'DWN'. I want to select all the rows where coulmn 4 has a value above zero. From these, print rows where column 1 is 'DWN' and print all the 'UA' rows when there are 3 or more UA's between 'DWN'. I am stuck...

does this help. it reads old.txt file line by line and prints them to new.txt file. #!/usr/bin/perl -w open(FILER1, "old.txt") || die "couldn't open the file\n"; open(FILEW1, ">new.txt") || die "couldn't create the file\n"; while(!eof(FILER1)){ my $line=<FILER1>...

open ( my $file, ">@{[++$x]}-times-fileA.txt") or die "$!"; adding the ">" sign made it work now. thanks kevinADC for the solution. it has been a frustating afternoon. sorry for the late response. i updated my perl version from 5.8.8 to 5.10 just to rule out that possibility, and that took...

thanks KevinADC. i will go with the first solution you posted. only fileA in the file name is what i want. however, when i run your code, it give me the error massage, "no such file or directory at line 8."

Ok, i work in genetics area. i am generating 100 combination files with two sequences, fileA and fileB (in percentages from 1 to 100 of fileA (sequence A) and will be randomizing them. then i want to extract a set number of sequences from each file (out of 100 entries) and want to generate an...