/mnts/stemcell-bioinfo/git/gencode_regions/create_regions_from_gencode.R /mnts/stemcell-bioinfo/genomes/gencode.mm10.vM14.annotation.gtf /mnts/stemcell-bioinfo/genomes/gencode_mm10.vM14
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
[1] 0
Error in unlist_obj(introns.data) :
could not find function "elementNROWS"
Execution halted

I also checked this wasn't just a GTF issue by trying the same with the equivalent GFF file:

wget ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_mouse/release_M14/gencode.vM14.annotation.gff3.gz
gunzip gencode.vM14.annotation.gff3.gz
mv gencode.vM14.annotation.gff3 /mnts/stemcell-bioinfo/genomes/.

/mnts/stemcell-bioinfo/git/gencode_regions/create_regions_from_gencode.R /mnts/stemcell-bioinfo/genomes/gencode.vM14.annotation.gff3 /mnts/stemcell-bioinfo/genomes/gencode_mm10.vM14
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
[1] 0
Error in unlist_obj(introns.data) :
could not find function "elementNROWS"
Execution halted

Hi:

I tried to use your code to get UTR and CDS from a gtf file from emsembl. For that, I download the gtfToGenePred file and do the following steps:
$ chmod +x gtfToGenePred` `conda install -c bioconda pybedtools conda install -c bioconda gffutils`

But when I typed
$ gtfToGenePred
-bash: gtfToGenePred: command not found

I am running under anaconda3 so the python version is >=3

What is the solution for the first step?

I am a little bit confused about the first intron, just using the first one in the introns.bed of each gene or we should also use the *.genepred file and consider more things about it.

Thank you so much, your code is pretty valuable.
I am looking forward to your reply.

transcripts.data <- unlist(transcripts.data) ###ERROR
exons.data <- unlist(exons.data)
threeUTRs.data <- unlist(threeUTRs.data)
fiveUTRs.data <- unlist(fiveUTRs.data)
cds.data <- unlist(cds.data)
introns.data <- unlist(introns.data)
genes.data <- unlist(genes.data) ####ERROR

There error is:

Error in getListElement(x, i, ...) : 
  GRanges objects don't support [[, as.list(), lapply(), or unlist() at
  the moment
Calls: unlist ... FUN -> [[ -> [[ -> getListElement -> getListElement
Execution halted

I did not need those lines to work for my purposes, but just an FYI on the issue.

Hi,

Are promoters also output specifically? It does not seem to be in the master data, nor does it say it is one of the outputs.
I understand that what makes a promoter is variable, but extracting xxx bp upstream/down of TSS would be good enough.

Thanks!

I tried to run GRCg6.ipynb notebook in google colab first but I ran into many errors,
Later, after searching a lot I came to realize we need gffutils version 9.0 to run them.
After installing gffutils 9.0 I reran the notebook this time ran into new errors.
Then after spending some time on Stack overflow, I realized that we need Anaconda environment.
I installed Anaconda, then tried again and later figured out that pybedtools is not available for Windows ( only available for MacOS and Linux).
Then I installed the Anaconda in Linux operating system, and then realized that pybedtools doesn't support python 3.8 or 3.9, however I was able to install the library in python 3.7.

I re-ran the notebook and it worked perfectly :).

Conclusion:
We need anaconda environment with python <=3.7 and Linux/macOs operating system.
Also, we need gffutils version 0.9 ( corresponding command conda install -c bioconda gffutils=0.9 )

If you will allow me, then I can put up a PR adding these in the form of FAQ in the readME, which can help others.

The script looks great.

However, is it possible to get some extra information on the genomic features than just the coordinates ? For example, for the exons, would it be possible to know

• which gene a particular exon belongs to
• its position in the exon set - first, second ... last
  etc.

Thanks!

I'm running the following command:
/home/zyh/software/gencode_regions/create_regions_from_gencode.R /home/zyh/ref/gencode.v30.annotation.gff3 /home/zyh/ref/gffutils/

and it gives error message:

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning messages:
1: In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
2: In .extract_transcripts_from_GRanges(tx_IDX, gr, mcols0$type, mcols0$ID,  :
  the transcript names ("tx_name" column in the TxDb object) imported
  from the "transcript_id" attribute are not unique
[1] 207646
Warning message:
In .set_group_names(ans, use.names, txdb, "tx") :
  some group names are NAs or duplicated
Warning message:
In .set_group_names(ans, use.names, txdb, "tx") :
  some group names are NAs or duplicated
Warning message:
In .set_group_names(grl, use.names, txdb, by) :
  some group names are NAs or duplicated
Warning message:
In .set_group_names(grl, use.names, txdb, by) :
  some group names are NAs or duplicated
Warning message:
In .set_group_names(ans, use.names, x, "tx") :
  some group names are NAs or duplicated
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'obj' in selecting a method for function 'unname': GRanges objects don't support [[, as.list(), lapply(), or unlist() at
  the moment
Calls: unlist ... FUN -> [[ -> [[ -> getListElement -> getListElement
Execution halted

Using gtf as input caused another error:

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning message:
In .get_cds_IDX(mcols0$type, mcols0$phase) :
  The "phase" metadata column contains non-NA values for features of type
  stop_codon. This information was ignored.
[1] 0
Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'obj' in selecting a method for function 'unname': GRanges objects don't support [[, as.list(), lapply(), or unlist() at
  the moment
Calls: unlist ... FUN -> [[ -> [[ -> getListElement -> getListElement
Execution halted

Both original gtf and gff3 files downloaded from ensembl or gencode do not work. May I ask how to debug it?