Question

GenomicFeatures package ERROR

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Entering edit mode

liangwu887 • 0

@liangwu887-9332

Last seen 8.4 years ago

Hi guys;

I get an error when I following the GenomicRanges HOWTOs protocal (http://bioconductor.org/packages/devel/bioc/vignettes/GenomicRanges/inst/doc/GenomicRangesHOWTOs.pdf) to loading my GTF file or the package's extdata using the GenomicFeatures package on linux system. And I had tried to reinstall R and the package, but error was still been report. I also try to use the package on win's R, it's work!

I had compared the sessionInfo() between the win's R and the linux's R, the R version and the packages version are the same, the difference is just install on different system!!!

It's an bug for linux's R? Thanks For Any Help!!

Bests

Liang

The code, the error and sessionInfo() of the linux's R are as following:

> library(GenomicFeatures)

> gtffile=system.file("extdata","GTF_files","test.gtf",package="GenomicFeatures") ## test.gtf is the reference I want to use to counting the gene expression.
> txdb=makeTxDbFromGFF(gtffile,format="gtf")
Import genomic features from the file as a GRanges object ... Error in parseURI("") : cannot parse URI
> gff_file=system.file("extdata","GFF3_files","a.gff3",package="GenomicFeatures")
> gff_file
[1] "/lfs1/ST_PMO2015G/STN11023/software/R-3.2.2/library/GenomicFeatures/extdata/GFF3_files/a.gff3"
> txdb=makeTxDbFromGFF(gff_file,format="gff3")
Import genomic features from the file as a GRanges object ... Error in parseURI("") : cannot parse URI

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
[3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
[5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915
[7] LC_PAPER=en_US.iso885915 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] GenomicFeatures_1.22.6 AnnotationDbi_1.32.0 Biobase_2.30.0
[4] GenomicRanges_1.22.1 GenomeInfoDb_1.6.1 IRanges_2.4.5
[7] S4Vectors_0.8.4 BiocGenerics_0.16.1 BiocInstaller_1.20.1

loaded via a namespace (and not attached):
[1] XVector_0.10.0 zlibbioc_1.16.0
[3] GenomicAlignments_1.6.1 BiocParallel_1.4.0
[5] tools_3.2.2 SummarizedExperiment_1.0.1
[7] DBI_0.3.1 lambda.r_1.1.7
[9] futile.logger_1.4.1 rtracklayer_1.30.1
[11] futile.options_1.0.0 bitops_1.0-6
[13] RCurl_1.95-4.7 biomaRt_2.26.1
[15] RSQLite_1.0.0 Biostrings_2.38.2
[17] Rsamtools_1.22.0 XML_3.98-1.3

software error genomicfeatures • 3.0k views

ADD COMMENT • link updated 6.9 years ago by Michael Lawrence ★ 11k • written 8.4 years ago by liangwu887 • 0

score 1 · Answer 1 · 2015-12-07

1

Entering edit mode

Hervé Pagès 16k

@herve-pages-1542

Last seen 1 day ago

Seattle, WA, United States

Hi,

Please provide your sessionInfo() as you're probably using an old and unsupported version of Bioconductor.

Your 1st path (system.file("extdata","GTF_files","test.gtf",package="GenomicFeatures")) is invalid: there is no test.gtf file in the GenomicFeatures package, but there is a test1.gtf file. BTW and AFAIK this code does not belong to the GenomicRanges HOWTO.

Your 2nd path (system.file("extdata","GFF3_files","a.gff3",package="GenomicFeatures")) is OK and should work (granted you use the current version of Bioconductor). It works for me.

So make sure you use the latest Bioconductor release (BioC 3.2, released in October). You'll need R-3.2.2 for that. To find out which version you have, just load the BiocInstaller package.

Cheers,

H.

PS: system.file() not failing by default when specifying an invalid path is a silly "feature" but I guess that's how it is and we have to live with it :-/

ADD COMMENT • link 8.4 years ago Hervé Pagès 16k

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Entering edit mode

Hi，Herve. Thanks for your respone.

The test.gtf is the reference which I want to use to counting the genes expression in my analysis. So , it was invalid for you.

And I had tried again to loading the a.gff3, the error was stiil been reported.

The R verssion is 3.2.2, and I installed the GenomicFeatures by using biocLite("GenomicFeatures").

and the information of sessionInfo() as following:

>sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
[3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
[5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915
[7] LC_PAPER=en_US.iso885915 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C

attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] GenomicFeatures_1.22.6 AnnotationDbi_1.32.0 Biobase_2.30.0
[4] GenomicRanges_1.22.1 GenomeInfoDb_1.6.1 IRanges_2.4.4
[7] S4Vectors_0.8.3 BiocGenerics_0.16.1

loaded via a namespace (and not attached):
[1] XVector_0.10.0 zlibbioc_1.16.0
[3] GenomicAlignments_1.6.1 BiocParallel_1.4.0
[5] tools_3.2.2 SummarizedExperiment_1.0.1
[7] DBI_0.3.1 lambda.r_1.1.7
[9] futile.logger_1.4.1 rtracklayer_1.30.1
[11] futile.options_1.0.0 bitops_1.0-6
[13] RCurl_1.95-4.7 biomaRt_2.26.1
[15] RSQLite_1.0.0 Biostrings_2.38.2
[17] Rsamtools_1.22.0 XML_3.98-1.3

Bests

Liang

ADD REPLY • link 8.4 years ago liangwu887 • 0

0

Entering edit mode

Hi,

system.file() is for getting the path to a file that is included in a package. Using system.file("extdata","GTF_files","test.gtf",package="GenomicFeatures") to get the path to your own test.gtf file doesn't work because the file doesn't belong to the GenomicFeatures package. All you need to do is something like:

gtffile <- "path/to/your/test.gtf"  # make sure to replace by the *real*
                                    # path to your test.gtf file
txdb <- makeTxDbFromGFF(gtffile, format="gtf")

Cheers,

H.

ADD REPLY • link 8.4 years ago Hervé Pagès 16k

0

Entering edit mode

Hi，

Maybe I didn't express my means clearly. Sorry~

My question is that I can,t use the GenomicFeatures to read the gtf file on the off-line linux system, although I tried the file which provide by the software. But I can use the Function of GenomicFeatures on my windows computer, it work without any error, by using the same command and reading the file on the off-line linux system.

The test.gtf file I had stored at the GTF_file folder of the GenomicFeatures, and I open the file by the path which provide by the system.files(). So the error didn't make by system.files(), makeTxDbFromGFF() make it!

And I think it maybe as an bug of the GenomicFeatures or R software, because it work on the windows system, but not on the linux, using the same command and reading the same files.

Cheers,

Liang

ADD REPLY • link 8.4 years ago liangwu887 • 0

0

Entering edit mode

Storing your test.gtf file in the GTF_file folder of the GenomicFeatures package is a very bad idea. Please never do that.
As I said, you should specify the path to your test.gtf file with something like gtffile <- "path/to/your/test.gtf". Do NOT use system.file() for that.
If things still don't work when doing 2., please show us the complete transcript of the following sequence:

library(GenomicFeatures)
gtffile <- "path/to/your/test.gtf"
file.exists(gtffile)  # make sure this is TRUE
makeTxDbFromGFF(gtffile)

Thanks,

H.

ADD REPLY • link 8.4 years ago Hervé Pagès 16k

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Entering edit mode

Hi, Herve.

It's work by following your suggestion, any error hadn't been reported again. And I try the commands which read the a.gff3 file as same as the first time I used, it also work as normal. It make me puzzling!! But, any way, thanks for your helps.

Bests

Liang

ADD REPLY • link 8.4 years ago liangwu887 • 0

score 0 · Answer 2 · 2017-05-26

Is there a way to export the gtf file from GenomicRanges

I have calculated intron coordinates from gtf file using exon coordinates and now I need to export it from the range , I tried following code but getting an error:

export.gtf(introns,"introns.gtf",format ="gtf") Error in export.gtf(introns, "introns.gtf", format = "gtf") : could not find function "export.gtf"

score 0 · Answer 3 · 2017-05-26

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Entering edit mode

Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 2.4 years ago

United States

There is no export.gtf(). Just call export() with the right file extension, or use the format argument if the file has some non-standard name. Also make sure rtracklayer is loaded.

export(introns, "introns.gtf")

ADD COMMENT • link 6.9 years ago Michael Lawrence ★ 11k