similar to: Read from HTML file, print if see a specific string

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

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.

I have seen two main styles in examples for using rsync with exclude-from. The first is simply a list of filename, one per line. The second is a list of filenames, one per line, prefixed with either a - or a + to indicate exclude/include. Which is correct? Also, none show the correct style with a filname containing spaces, though I assumed quoting is OK Exclude1.txt: - filename1 - ?file name

Hi I am trying to read genbank est flat files. Is there any function in R to do that. I was looking for something similar to SeqIO.parse(input_handle, "genbank") in bioPython that convert the genebank sequence into fasta sequence. (One option is to call biopython from R but I am not familiar with python functions so I want to avoid that and I am keeping it as last resort) Thanks and

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

Full_Name: Jens Oehlschl?gel Version: 2.5.1 OS: Windows Submission from: (NULL) (62.159.183.42) Even when specifying the full path, the output of fc is not sent to R (neither shown nor returned). For example > system('c:\\WINDOWS\\system32\\fc.exe /?',intern=TRUE) character(0) When I do the same from python 2.3, I get >>> import os >>>

Hello: I have problems generating big JPG plots in functions. the following code runs fine in the script: #### runs fine in script, generate 40k "test1.jpg" in the given directory plotPlatesAlong <- c(1:5) plotDirPath <- paste(dataPath, "OutputPlots\\", sep="") filename <- paste(plotDirPath,"test1.jpg", sep="") jpeg(file=filename)

Hi all, I'm using an Ubuntu 7.10 and the latest (?) version of Wine ( 0.9.58 ). I'm running a windows application that seems to work properly, but i cannot manage to redirect the output to a file: $ wine cmd.exe Usage : cmd.exe [filename1] [filename2] ... $ wine cmd.exe > /dev/null Usage : cmd.exe [filename1] [filename2] ... $ wine cmd.exe 2> /dev/null Usage : cmd.exe [filename1]

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:

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

hi, actually i have done single file attachment in ruby on rails, now i want to do multiple attachment, but the problem is when i am trying to display the second file name from the params for the testing purpose, i got the error, please can anyone correct the error. in view: <tr> <td bgcolor="#F6F6F6"><%= file_field("picture", "file")

I read the following about memdisk : .... For any other size, the image is assumed to be a hard disk image, and should typically have an MBR and a partition table. The disk C/H/S geometry is determined by examining the partition table, so the entire image should be partitioned for proper operation. .... I'd like to create a bootable cd, wich boots a linux and some other tools. While

I have the following code: list1 <- list() for (i in list.files(pattern="filename1")){ x <- read.table(i) list1[[i]] <- x } list2 <- list() for (i in list.files(pattern="filename2*")){ x <- read.table(i) list2[[i]] <- x } anslist <- vector('list', length(list1)) for(i in 1:length(list1)) if (list1[[i]] & list2[[i]] >1)

Dear All, Along with the files that suddenly disappear, we have a bit of a problem with these that do not. Namely, in my test runs I can see a small but stable set of files, that rsync is repeatedly trying to transfer, and then repeatedly fails to updates their times ; and then the story repeats itself. The situation is illustrated by the log snippet below, where I have changed file names to

Hi, all I am new to actionmailer. I am writing a script that sends emails contains lots of file names. So the email will look like: hi, filename1 filename2 filename3 . . . filenameN So I want to pass an array containing all the filenames into the email body. My code is below: class Notifier < ActionMailer::Base def log_report(recipient, files) from

Hi List I've experienced some problems with rsync. I'm backuping a complete machine's rootdirectory. After completion I see in the log of the output, that rsync links some files which are surely *not* the same on the source System. Or well, it says, that it makes links, using the filename1 => filename2 notation. On the source System this files are not the same and some files are

Hi, Is there an easy way to convert numbers into a form such that they all have the same number of digits? e.g.: "1", "10", and "100" ...become... "0001", "0010", "0100" etc. I ask because I am producing a large number of files that need to sort consistently by filename. Currently I get this kind of sorting: filename1 filename10

I have several models that will be using file_column by way of the "Picture" class (HABTM). Right now, all pictures are stored in: public/picture/image/1/filename1.jpg public/picture/image/2/filename2.jpg Is there a way I can dynamically define the "store_dir" based on the model? For example, if I have "user", "product" and "place" models all

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