similar to: Is there any function to read genbank flat files.

Hi, I am trying to work with the ape package, and there is one thing I am struggling with. When calling the *read.GenBank()* function, I can get it to work with an object created like this: *>x <- c("AY395554","AY611035", ...)* *>read.GenBank(x)* However, I am trying to use the function to fetch several hundred sequences at once. So I have been testing with small

Hi I have a tab delimited file with fillowing content: "swissProtID" "entrezID" "bitVec" "Q62924" "---" "00000000100010000000000000000000" "P18897" "---" "00000000000001000100000000000000" "Q62736" "---"

Hi Is there any function to do bitwise or/and/xor on long bit vectors? "aaaaa" "0000000000000000000000000000000000000000000000000000000000000000......................" "bbbbb" "0000000000000000000000000000001000000000000100000000100000001100......................" "ccccc"

So basically I have made a HTML file with a table in it. Column 3 contains a GenBank number and is always proceeded by "=GenBank">". I want to read the file and return the number which comes directly after this (the contents of column 3). Ideally I would like to save this number as a string for use later in the script, but any help is good help. Been at this for HOURS and

I just ran this again and got this error: leelab/NCBI_Data_old/GenBank/htg write failed on leelab/NCBI_Data_old/GenBank/htg : Error 0 rsync error: error in file IO (code 11) at receiver.c(243) Received signal 16. (no core) rsync error: received SIGUSR1 or SIGINT (code 20) at rsync.c(229) The command I am running is: /usr/local/bin/rsync -auv --delete --rsh=/usr/bin/ssh lpgfs104:/share/group/*

Hi all, I am learning R by "doing". And this is my first post. I want to use R: 1- to fetch a DNA sequence from a databank (see bellow) and 2- store it as FASTA file. The problem: neither an error is prompted nor the fasta file is created. Testing the code (see bellow), I notice that everything works until the *"write.dna" *command - which is not creating the fasta file.

Hello! I don't know if there is some R-package able to associate ontology to a long list of GeneBank Name (a txt-tab file or an XML file), i.e. I would as output a formatted file with 4 columns (1:GeneBank Name 2,3,4:ontology). I know that I have to perform a mapping of genes, I got a look on AnnBuilder pkg, but I 've not idea from where to start. Some suggestion? Thanks in advance!

I suspect you meant WD <- "~/Documents/Scripting/R_Studio/Sequences/" but I am entirely unfamiliar with the packages you are using, and know nothing about what is on your hard drive. For future reference: A) Read the Posting Guide. This is a plain text email list, and your html formatting gets removed leaving a mess that is not always readable. B) Most frequent users of R

Hi, I'm trying to execute R-script from Python. I'm using R 2.7.2, Python 2.5 and WinXP. I don't won't to use Python/R interface because of nature of project. Python code : import subprocess command = 'c:\\Program Files\\R\\R-2.7.2\\bin\\Rterm.exe --vanilla -q <d:\\test\\run\\geneBank.r> d:\\output.out' subprocess.Popen(command).wait() After that, I get error

I'm trying to rsync a filesystem from a Solaris 7 server to a Solaris 8 server. I keep getting the following message when rsync attempts to update a particular file: write failed on leelab/NCBI_Data/GenBank/htg : Error 0 rsync error: error in file IO (code 11) at receiver.c(243) Received signal 16. (no core) rsync: connection unexpectedly closed (22672537 bytes read so far) rsync error:

Hi, I am trying to call a C function, that I wrote to parse a flat file, into R. The argument that will go into this function is an input file that I need to parse and write the desired output in an output file. I used some hit and trial approach but i keep on getting the "file not found" or "segmentation fault" error. I know that the error is in passing the argument but I

Anyone have any experience with MpiBlast and Lustre. We have MpiBlast-1.4.0-pio and lustre-1.6.3 and we are seeing some pretty poor performance with most of the mpiblast threads spending 20% to 50% of their time in disk wait. We have the genbank nt database split into 24 fragments (one for each of our OSTs, 3 per OSS). The individual fragments are not striped due to the

now i am using cucumber.........and i get two topic webrat and capybara........wat is the diff between them???????which one is good?????which one i use????? Regards Fahim Babar Patel -- You received this message because you are subscribed to the Google Groups "Ruby on Rails: Talk" group. To post to this group, send email to

Hi all, Can any one tell me how to use Ajax with Rails. Send me quick start up link and videos. Thanks Regards Fahim Babar PAtel -- You received this message because you are subscribed to the Google Groups "Ruby on Rails: Talk" group. To post to this group, send email to rubyonrails-talk-/JYPxA39Uh5TLH3MbocFF+G/Ez6ZCGd0@public.gmane.org To unsubscribe from this

I have a file with a data in columnar format like below: probeID rc_AI104113_at rc_AI178259_f_at rc_AI179134_i_at rc_AI179134_f_at rc_AI104113_at rc_AA819429_f_at How can I rewrite it in the format below: 'rc_AI104113_at', 'rc_AI178259_f_at', 'rc_AI179134_i_at', 'rc_AI179134_f_at', 'rc_AI104113_at', 'rc_AA819429_f_at' Is there any function to do

Hi How to access the values in the output that is an object of S4 type. I tried to access using subset ( [ ] ) but it is not allowed. Any clue?? Thanks -- Fahim #My code is as follows: require(IRanges); query <- IRanges(c(1, 4, 9), c(5, 7, 10)) subject <- IRanges(c(2, 2, 10), c(2, 3, 12)) findOverlaps(query, subject) Output of find overlap function is: ------------------ 1>

Hi I observed an interesting behavior of R. Can you find where is the bug, or it is not a bug but made deliberately. - Hide quoted text - > arr = c(); #defined the empty array > a= c("x1", "x2"); > b = c("y1", "y2"); > arr = rbind(arr,a); #row bind the first character array -a > arr =

Hi all, I follow All the steps for recaptcha , but i am confused how to test on my local host. Because when we register in google recaptcha it ask for domain URL, i stuck here. Q What should i enter in domain url ? Hope that you all understand the problem. Thanks Regards Fahim Babar Patel -- You received this message because you are subscribed to the Google Groups "Ruby on Rails:

Is there any function/way to merge/unite the following data GENEID col1 col2 col3 col4 G234064 1 0 0 0 G234064 1 0 0 0 G234064 1 0 0 0 G234064 0 1

Dear R-helpers: thank your for your attention. i am a newer to R and i am doing some protein category classification based on the amino acid sequence.while i have some questions urgently. 1. any packages for analysis amino acid sequence 2. given two sequences "AAA" and "BBB",how can i combine them into "AAABBB" 3. based on "AAABBB",how can i get some