search for: ncbi

Hello! I am crossposting this to R-help and BioC, since it is relevant to both groups. I wrote a wrapper for Entrez search utility (link for this is provided bellow), which can add some new search functionality to existing code in Bioconductor's package 'annotate'*. http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html Entrez search utuility returns a XML document but I have a problem to use URI to retrieve that file, since URI can also contain characters, which should not be there according to http://www.faqs.org/rfcs/rfc2396.html I encountered problems with...

I'm trying to read some web tables directly into R. These are both genome sequencing projects (eukaryotes and metagenomes) from NCBI and look very similar; however, only the first one works. http://www.ncbi.nlm.nih.gov/genomes/leuks.cgi http://www.ncbi.nlm.nih.gov/genomes/lenvs.cgi I added ?dump=selected to the end of the url string to get a tab- delimited file (which is what happens if you click the Save button on eith...

Dear All, The following code extracts from NCBI very nice output for ONE allele of a SNP (often the allele with the second largest frequency - usually termed the minor allele). It gives an average minor allele frequency from all NCBI sources (which is what I want, except I'd like the addition of data for all the other alleles of one SNP) plu...

Hi, Trying to access files on the ftp server at ftp.ncbi.nih.gov will either give a time out or sometimes even a segfault on Linux. The 2 following methods give the same results: f <- url("ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS10.soft.gz", open="r") download.file("ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/...

Dear R folks: I am trying to use SSOAP (version 0.2-2) package in R (version 2.1.0,linux) to access SOAP service on NCBI (http://www.ncbi.nlm.nih.gov) its WSDL file is at http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl but some errors occured: > ncbi <- processWSDL("http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl") > ff <- genSOAPClientInterface(ncbi at operations[[1]],...

Hi, > url <- "ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.13.assembly.txt" > download.file(url, tempfile()) trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.13.assembly.txt' Error in download.file(url, tempfile()) : cannot open URL 'ftp://ftp.ncbi...

...a problem where the data must be supplied via POST - but I don't know the keyword for the argument. The data to be sent is an XML fragment. I can do this via the command line using curl: I save the XML string to a file called query.xml and then do curl -d @query.xml "http://pubchem.ncbi.nlm.nih.gov/pug/pug.cgi" I get the expected response. More importantly, the verbose option shows: > Accept: */* > Content-Length: 1227 > Content-Type: application/x-www-form-urlencoded However, when I try to do this via RCurl, the data doesn't seem to get sent: q <- &q...

...GSE3524, which cannot be open on my computer. I hope some of you would be kind to give me some advice. Thanks! The code is as follow: ################## library(GEOquery) gsename="GSE3524" gse=getGEO(gsename) ################## The error information follows as ÊÔ¿ªURL'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/by_series/GSE3524/GSE3524_family.soft.gz' ftp data connection made, file length 3586385 bytes ´ò¿ªÁËURL downloaded 3502Kb File stored at: C:\DOCUME~1\ADMINI~1\LOCALS~1\Temp\Rtmpturmrb/GSE3524.soft.gz Parsing.... ^PLATFORM = GPL96 ^SAMPLE = GSM80461 ´íÎóÔÚsubstr(x, sta...

Hi, I wanted to download a file and did the following: --------------------------------------------------------- > fileLink <- 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE1000/GSE1000_RAW.tar' > download.file(fileLink,'/geoDat') trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE1000/GSE1000_RAW.tar' ftp data connection made, file length 35307520 bytes opened URL downloaded 3448...

...ems, if it doesn''t fix them outright: http://www.swig.org/Doc1.3/SWIGPlus.html#SWIGPlus_default_args Just a thought. Kevin -------- Original Message -------- Subject: Re: [Swig] typemap + default argument bug? Date: Tue, 27 Sep 2005 15:57:52 -0400 (EDT) From: Josh Cherry <jcherry@ncbi.nlm.nih.gov> To: Charles@Schwieters.org CC: swig@cs.uchicago.edu On Tue, 27 Sep 2005 Charles@Schwieters.org wrote: > _wrap_new_ClassB calls SWIG_ConvertPtr to convert the instanceName > argument to a p_String, thereby ignoring the typemap. > > Previous versions of swig do not seem...

Dear all, I've noticed by trying to download gz files from here : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM907811 At the bottom one can download GSM907811.CEL.gz . If I download this manually and try oligo::read.celfiles("GSM907811.CEL.gz") everything works fine. (oligo is a bioConductor package) However, if I download using download.file(" https:...

...A B Total 5874641 6295980 a 13 30 b 36 39 c 0 5 d 40 61 e 16 20 f 13 11 g 3 3 h 9 5 i 12 35 j 157 221 k 17 39 l 6 17 m 666 1387 n 2 5 The significance of digital gene expression profiles. Audic S <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22A udic%20S%22%5BAuthor%5D&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_Result sPanel.Pubmed_RVAbstractPlusDrugs1> , Claverie JM <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22C laverie%20JM%22%5BAut...

Hi all, I am trying to download, decompress and read a csv file. My code: myurl <- "ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE24729/GSE24729_MitoNuclear_suppl_male_stats.csv.gz" # myfile <- "GSE24729_MitoNuclear_suppl_male_stats.csv.gz" # download.file(myurl, destfile=myfile, mode="w") # mycon <- gzcon(gzfile(myfile, open="r")) # mydat...

...nals articles about a particular disease are being published. Creating a pubmed search is trivial. The search provides data but obviously not as an R dataframe. I can get the search to export the data as an xml feed and the xml package seems to be able to read it. xmlTreeParse(" http://eutils.ncbi.nlm.nih.gov/entrez/eutils/erss.cgi?rss_guid=0_JYbpsax0ZAAPnOd7nFAX-29fXDpTk5t8M4hx9ytT- ",isURL=TRUE) But getting from there to a dataframe in which one column would be the name of the journal and another column would be the year (to keep things simple) seems to be beyond my capabilities. Ha...

...oject.org> > Sent: Saturday, August 8, 2015 3:57:34 PM > Subject: Re: [Rd] download.file() on ftp URL fails in windows with default download method > > > > On 08.08.2015 01:11, Dan Tenenbaum wrote: > > Hi, > > > >> url <- > >> "ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.13.assembly.txt" > >> download.file(url, tempfile()) > > trying URL > > 'ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.13.assembly.txt' > > Error in download.file(url, tempfile())...

Hi dear Rers, I am using SSOAP package to access SOAP service at NCBI. I followed the example code in SSOAP but failed. > z <- .SOAP("http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/soap_adapter.cgi", method="run_eInfo", db="pubmed", action = I("einfo")) Error: protect(): protection stack overflow what's wrong? Than...

Hi all, I'm new to Centos, just moved here from Gentoo Linux. I have to install a server for bioinformatics purposes and I see that default yum repositories do not include any bioinformatics software (i.e. ncbi-toolkit, blat, and others). I'm googling a bit but I can't find a valuable solution: which is (or which are) the best repository I should add to have a satisfying list of bioinfo rpm? Thanks d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139...

...4 PM > > Subject: Re: [Rd] download.file() on ftp URL fails in windows with > > default download method > > > > > > > > On 08.08.2015 01:11, Dan Tenenbaum wrote: > > > Hi, > > > > > >> url <- > > >> "ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.13.assembly.txt" > > >> download.file(url, tempfile()) > > > trying URL > > > 'ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.13.assembly.txt' > > > Error in download.fi...

...from a column of a table. The pattern of official name is something starting with gene_name. For detail problems, please see the according lines. Any suggestions are appreciated example of matching source (extract the Nnat, sometime it would be the character "N/A"): "AB004048|MM8;NCBI Build 36|transcript|chr2|157251580|157253958|ExemplarFor 'AB004048'; gene_id '18111'; transcript_id 'AB004048'; gene_name 'Nnat'; alt '5730414I02Rik|AW107673|Peg5'; neuronatin|http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=ful...

...eal obvious pattern in how these bytes are added, but the file downloaded using download.file() is actually larger (in this case by about 8 kb). The file xxx_inR.CEL.gz is read in using: setwd("E:/Temp/genexpr/Compare") id <- "GSM907854" flink <- paste0(" https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSM907854&format=file&file=GSM907854%2ECEL%2Egz ") fname <- paste0(id,"_inR.CEL.gz") download.file(flink, destfile = fname) The file xxx_direct.CEL.gz is downloaded from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM9078...