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  • Users: 3inen
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  1. 3inen

    Extracting DNA sequences from GenBank files

    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...
  2. 3inen

    help with subroutine

    Learning one thing at a time. Now it works. Thanks a lot prex1.
  3. 3inen

    help with subroutine

    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)...
  4. 3inen

    Issue with program efficiency

    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.
  5. 3inen

    Issue with program efficiency

    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; }...
  6. 3inen

    help with subroutine

    charming rharsh. done!
  7. 3inen

    help with subroutine

    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...
  8. 3inen

    about array matching

    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.
  9. 3inen

    about array matching

    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.
  10. 3inen

    about array matching

    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
  11. 3inen

    about array matching

    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...
  12. 3inen

    about array matching

    Kevin, I am not clear here, how do i use your suggestion to work with 2 arrays. Could you please show some more.. Thanks
  13. 3inen

    about array matching

    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...
  14. 3inen

    sorting array elements

    My bad, there was an additional space in the actual file. Your script rocks. Thanks.
  15. 3inen

    sorting array elements

    rharsh, thanks for the solution. It does work as long as the end of the file has 'DWN'. That will do for me.
  16. 3inen

    sorting array elements

    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...
  17. 3inen

    Renaming Files with Perl

    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>...
  18. 3inen

    looping through array

    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...
  19. 3inen

    looping through array

    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."
  20. 3inen

    looping through array

    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...

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