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Recent content by smokinace
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Sorting list problems
kevin that is a great suggestion. So it would match NM_0010989 if I really wanted NM_0012546 because it would queu off of the NM_001? Is there a literal I can use for the hash like I can for strings? -
Sorting list problems
why is strict so good. I started using it but stopped because it wouldn't run a program because i didn't have a specific quote that wasn't even needed. Is it just to help proofread? Couldn't I just turn it on during debugging? -
Sorting list problems
that worked great thanks. Is it because hashes can't contain two of the same key so it just doesn't include repeats when printed? -
Sorting list problems
i have another problem now involving making a list of specific names taken from the sorted through list already. I now need to add the first element in each row into an array, but that entry is only put in once and won't be repeated. Here is what I am thinking open (NEW, "$outfile")... -
Sorting list problems
i realized what I did. I used STDIN instead of ARGV like I wanted to use. It kept wanting parameters but I didn't give it any. Sorry to waste your time with my error. Thanks for the help anyways! -
Sorting list problems
I am having problems sorting a fairly simple list. Here is the list: >NM_001100917.1 >NM_001100917.1 1019 100 1019 1 1 >NM_020388.3 >NM_001100917.1 0 0 0 . . >NM_001001395.1 >NM_001100917.1 18 95 20 647 2404 >NM_001048210.1 >NM_001100917.1 0 0 0 . . >NM_033157.2 >NM_001100917.1 18 95 20... -
running external command in DOS
How many sequences are you comparing? I used the same program. bl2seq is fine for maybe a couple of sequences. If you have a ton of sequences it's probably a better idea to use blastall. instead of taking 60 days to do a billion comparisons, blastall did it in 5 hours. -
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Perl performance issues
forgive me for my ignorance but do i just put at the beginning in the message and then at the end to put it into the code format? -
Perl performance issues
Query= NM_032090.1 (2553 letters) >NM_032603.2 Length = 3121 Score = 23.8 bits (12), Expect = 0.56 Identities = 12/12 (100%) Strand = Plus / Minus Query: 2320 ttcccccagccc 2331 |||||||||||| Sbjct: 464 ttcccccagccc 453 Score =... -
Perl performance issues
i determined that the problem was the blast program. somewhere in the comparison there is a major holdup. without doing that comparison the program uses the entire processor. somehow i have to find a way to speed up the blast program. Also, we experimented with loading the prgoram and all... -
Perl performance issues
I am trying to run a program that takes two fasta sequencing files and compares them. the program has to compare 38,000 file together to make 1 billion comparisons. when i run the program it does about 12,000 comparisons a minute. this would take 60 days to complete! i am noticing that the... -
variable question
what is the hierarchy of variable creation? if i create a variable inside an if statement using "my" is that variable only good in the if statement? example if (condition) { my ($var1, $var2); } -
problems redirecting from system command
it turns out putting the variable in double quotes inside the backticks treats them as an actual variable. who would have guessed. thanks for the help :) -
problems redirecting from system command
i am trying to put variables directly into the command line for example: `/home/program -i $gap > compared.txt`; -i is the parameter with $gap being the number amount. the file is being created but nothing is being put in because of the variable. if a number is used then the program works...
