similar to: R script from Python

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'm trying to schedule R tasks in Windows Server 2003. I can run the following from the DOS prompt without any difficulty: c:\Reports>c:\r\rw2001\bin\rterm.exe --no-restore --no-save <test.R> test.out where test.r has two lines: library(tools); Sweave("rlr.Rnw"). When I try to run the same from the task scheduler, I fill in the dialogue box as follows: Run:

Hello R-people, I have the following problem : In order to run R script from DOS prompt in BATCH mode and pass it some parameters I do the following : Rterm --slave --no-save --no-restore <args.R> args.out ARG1=1 ARG2=2 It works fine : the result is that the script args.R is isexecuted. Sys.getenv() sees the arguments ARG1 and ARG2, and the R creates output file args.out Now I want

I have made many different attempts to run a R program in Batch mode. I run a DOS command like: C:\Progra~1\R\rw1061\bin\rterm.exe -q --no-restore --no-save myprogram.R out.txt What happens: 1. DOS Shell starts up well 2. R starts 3. I get the messages: "ARGUMENT 'myprogram.R' __ignored__" "ARGUMENT 'out.txt' __ignored__" 4. R Shell is ready to

Dear all, I'm trying to invoke R from an application which I'm developing. I have indications that the problem is specific to R. I'm able to e.g. invoke a Python script in the same way with success, but R is giving me problems. Last year a guy with nickname vital101 posted a message on the Java forums website about invoking R from Java. The link to that thread is:

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 want to write a python script and visual interface to manage glusterfs, such as creating and deleting volumes.This can be easier to manage glusterfs? But,now ,I execute the glusterfs command using python's subprocess.popen function?such as subprocess.Popen(GLUSTER_CMD, shell=True,stdout=subprocess.PIPE, stderr=subprocess.PIPE)...... But this does not feel like a good program, Because it has

Dear all, In R<=1.6.2 I usually used the following code (in DOS prompt) to run R in batch mode C:\documents> Rcmd BATCH myfile.R and I could see the results (including warning messages) in the file myfile.Rout In R.1.7.0 I'm experiencing the followings: (1) even if I type "Rcmd BATCH myfile.R myfile.Rout", no file myfile.Rout is created, but just a "&1" file

Maybe consider extending the functionality of http://docs.ansible.com/ansible/latest/gluster_volume_module.html? Best regards, Marcin On Mon, Jan 15, 2018 at 11:53 AM, ?? <mrchenx at 126.com> wrote: > I want to write a python script and visual interface to manage glusterfs, > such as creating and deleting volumes.This can be easier to manage > glusterfs? > But,now ,I execute

the script works... root at probe28:~# cat test.dat dn: CN=userxxxx,OU=Users,OU=xxxxx,OU=Organizations,DC=xxxxx,DC=xxxxx proxyAddresses: SMTP:xxxxx.xxxxx at xxxxx.org objectGUID: 637f4e70-8c1e-4e89-a6fc-82d525e584f2 pwdLastSet: 0 objectSid: S-1-5-21-1608159440-4144762864-1017073214-27184 sAMAccountName: userxxxx mail: xxxxx.xxxxx at xxxxx.xxxxx userAccountControl: 514 virtualClearTextUTF8::

Hi, I need to be able to run an R script by double-clicking the file name in Windows. I've tried associating the .r extension with the different R .exe's in /bin but none seems to work. Some open R then close right away, and Rgui.exe gives the message ARGUMENT "/my/file.r" __ignored__ before opening a new, blank session. I've tried Google and looking in the R for

I have a crude hack to allow auto_complete to work with indexed text fields. I needed it for a timecard entry form with an arbtirary number of records which can be added/changed/delete willy-nilly by users. One of the fields is a perfect candidate for autocomplete since it references a database object with a large number of choices and long descriptions. Using a select list is extremely ugly in

On Mon, Jan 15, 2018 at 2:53 AM, ?? <mrchenx at 126.com> wrote: > I want to write a python script and visual interface to manage glusterfs, > such as creating and deleting volumes.This can be easier to manage > glusterfs? > But,now ,I execute the glusterfs command using python's > subprocess.popen function?such as subprocess.Popen(GLUSTER_CMD, >

You should try libgfapi: https://libgfapi-python.readthedocs.io/en/latest/ On Mon, Jan 15, 2018 at 9:01 PM, Marcin Dulak <marcin.dulak at gmail.com> wrote: > Maybe consider extending the functionality of > http://docs.ansible.com/ansible/latest/gluster_volume_module.html? > > Best regards, > > Marcin > > On Mon, Jan 15, 2018 at 11:53 AM, ?? <mrchenx at 126.com>

It seems that the system() and system2() functions don't close file descriptors between the fork() and exec() (on Unix platforms, of course). This means that the child processes inherit open files and socket connections. Running this (from a terminal) will result in the child process writing to a file that was opened by R: R f <- file('foo.txt', 'w') system('echo

I am trying to setup samba as a dc using bind dlz I'm not sure how much I need to setup on bind before I can use it. I did the following check. [root at dc1 ~]# named -V | sed 's/ /\n/g'| grep '\-\-' |grep -e gssapi -e dlopen '--with-dlopen=yes' '--with-gssapi=yes' I am using the default config for samba that came with Fedora Rawhide. I wanted to try out the

This only affects non-HostVG volume groups. rhbz#733578 Signed-off-by: Mike Burns <mburns at redhat.com> --- scripts/storage.py | 14 +++++++++++--- 1 files changed, 11 insertions(+), 3 deletions(-) diff --git a/scripts/storage.py b/scripts/storage.py index 5f7f0e3..047bcd1 100644 --- a/scripts/storage.py +++ b/scripts/storage.py @@ -90,13 +90,19 @@ class Storage: vg =

Hi, I'm using R 2.7.2 for Windows.I have also installed gtk-dev-2.12.9 and rattle 2.3.65. When I work in rattle, I occasionally get these messages : GLib-WARNING (recurser) **: g_main_context_prepare() called recursively from within a source's check() or prepare() member. aborting.... or GLib-WARNING (recurser) **: g_main_context_prepare() called recursively from within a source's

Version 4.0.7-GIT-d4cd828 openSUSE 12.04 with bind9 installed but not configured. Hi Attempting to provision with BIND9_DLZ or samba_upgradedns from a functioning SAMBA_INTERNAL install produces: Creating DomainDnsZones and ForestDnsZones partitions Populating DomainDnsZones and ForestDnsZones partitions Failed to setup database for BIND, AD based DNS cannot be used ERROR(<type

Hello, I use rsync with the option --out-format '%o %n? but want to have the contents of the mesages to be overwritten. This means that the actual message while synchronisation shall overwritte the previous one. Therefore i wanted to add a carriage return ?\r? at the end of the ?out-format string but this did not work. How can I do this? Regards Michael