Hello, going back to the original question I just wanted to indicate http://dirk.eddelbuettel.com/code/littler.html which works just fine for me, also with the getops package. Steffen Cei Abreu-Goodger wrote: > may I suggest the following: > > 1) First get all unique Ensembl transcript IDs > > 2) If there are too many, split into groups of ~1-5 thousand (I don't > know what the optimum would be) > > 3) For each group of ids, use getSequence() to retrieve the 3'UTR. > > 4) rbind the results, check, save > > Cheers, > > Cei > > > mauede at alice.it wrote: >> I reattached my script. I had attached it to an earlier message that >> maybe was overlooked. >> >> As you can see yourself, I scan a big data set, named hsTargets, that >> contains plenty of target gene transcript IDs with a handle to the >> relative miRNA. >> I process such a data base one miRNA at a time. That is, I gather all >> the transcript IDs for the current miRNA >> and query biomaRT asking for the 3'utr for all such transcrpts whose >> ENST are in a vector that I pass as input parameter to the query. >> Therefore I do use the vectorized capabilities of R, don't I ? >> >> My mistake is to keep the connection to biomaRt opened while >> processing as many miRNAs as I can. >> Therefore I acknowledge I have to improve my script and catch the >> exception so that I have to delete the file currently being written >> (as in general it will be incomplete) and have the script die gently. >> Then I have to get my script pause and disconnect from biomaRT >> regularly to avoid hammering the provided >> service. Eventually my process can even end itself instead of >> sleeping, after saving its current status. However, I need to set up >> the task scheduler to restart it some time later ... >> >> Regards, >> Maura >> >> >> >> >> >> >> -----Messaggio originale----- >> Da: Kasper Daniel Hansen [mailto:khansen at stat.berkeley.edu] >> Inviato: ven 20/11/2009 15.12 >> A: mauede at alice.it >> Cc: Bioconductor List >> Oggetto: Re: [BioC] Can an R script be run through a cron job ? >> >> Maura >> >> Unfortunately you never showed us your code, despite repeated >> requests to do so. That makes it hard to help (and frankly, ignoring >> requests for information from people trying to help you is extremely >> counterproductive). >> >> Your comments in your last email in the last thread indicates that >> you have code that essentially do this >> >> for(i in 1:100) >> getBM(...) >> >> If this is true (which we would know if we can see the code), this is >> why your script fail. There are two problems with this (1) you are >> not using the vectorized capabilities of R, but more important is (2) >> you are sending many requests to Biomart and typically such behaviour >> might mean your IP address will be banned temporarily. They don't >> like people hammering their services with repeated requests. >> >> Instead you should create a query that essentially asks for all your >> return objects in one request. That should be easy to write, and >> will be much faster. You might think that processing the output is >> slightly harder, but that is the thing to do (and with more R >> experience, processing a big output is actually easier). >> >> Regarding your actual question in this email, you seem to be very >> confused regarding the meaning of a batch job. This word has many >> different interpretations (not related to R), so it is hard to google >> for. What you are specifically asking for has everything to do with >> what operating system you are using (Windows, Linux, OS X) and >> nothing to do with R. >> >> Kasper >> >> >> On Nov 19, 2009, at 18:24 , <mauede at="" alice.it=""> <mauede at="" alice.it=""> wrote: >> >>> I am running a script that extracts many long strings from remote >>> data bases. >>> Every now and then the remote data base gets out of sync and closes >>> the connection. >>> I have been adviced to implement an R script that queries the data >>> base in batch modality. >>> I never ran an R script in batch modality. I think I have to use R >>> CMD BATCH or something similar >>> Given the amount of data I am extracting, I am concerned about >>> having to parse a huge data file looking for the >>> informattion I need. >>> The less painful modification would consist in running the R script >>> as is but through a cron job. So that the script >>> should be set to sleep on an established frequency and when >>> awakened it should resume from where it was interrupted. >>> Is such a scheme doable in R ? If it is then what are the most >>> important commands to make a script sleep and wake up >>> on a regular basis ? >>> >>> Thank you in advance, >>> Maura >>> >>> >>> >>> >>> tutti i telefonini TIM! >>> >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> >> >> >> >> e tutti i telefonini TIM! >> Vai su >> >> ------------------------------------------------------------------- ----- >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor