Search results for query: *

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?

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?

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?

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")...

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!

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...

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.

nevermind i figured it out!

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?

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 =...

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...

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...

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); }

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 :)

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...

i am trying to call a system command but can't redirect to a file. #system ("/home/program", ">", "results/compared.txt"); it thinks the > is a parameter and won't run the program. another possibility is using backticks `/home/program > compared.txt`; but i dont know how to to use variables...

it makes the directory. makes a file by the right name, but only copies the first line of text. it then makes another directory with the second line of text containing a file with the second line of text and so forth until it dies a few files later

i am having problems with breaking a file into several files. here is my code. my $source = $ARGV [0]; my $i = 0; open STDIN, $source or die "Can't read source file $source: $! \n"; while ($line = <STDIN>) { $x = substr( $line, 3, 1); if ($x =~ /^|/){ $y = substr( $line, 18, 13)...