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jorruior / gencode-riboseqORFs

Python script to get an unified list of Ribo-Seq ORFs from a list of compiled ORF datasets.
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No outputs generated #1

Open sherkinglee opened 1 year ago

sherkinglee commented 1 year ago

Hi,

I have tried re-generating the phaseI Ribo ORFs followed as the README indications, but no outputs were generated. Please tell me what's going on? Here are my command and its indications in the screen:

$ python3 ORF_mapper_to_GENCODE_v1.1.py -d Ens101 -f phaseI/sORFs_genomic_hg38.prot.20210329.fa -b phaseI/sORFs_genomic_hg38.prot.20210329.bed -a no
Intersecting ORFs with transcriptome
Intersecting ORFs with transcriptome
Checking for ORF overlaps in transcriptome
Collapsing shorter variants
Writing output

The files in the Ens101 are generated with script:

$ bash scripts/retrieve_ensembl_data.sh 101 GRCh38
ENST_support.txt
Homo_sapiens.GRCh38.ncrna.fa
Homo_sapiens.GRCh38.sorted.gtf_psites.bed
Homo_sapiens.GRCh38.101.gtf
Homo_sapiens.GRCh38.pep.all.fa
Homo_sapiens.GRCh38.trans.fa
Homo_sapiens.GRCh38.cdna.all.fa
Homo_sapiens.GRCh38.sorted.gtf

The outputs are list here:

-rw-r-----+ 1 lifajin dawolf 1352162 Sep  4 16:33 sORFs_genomic_hg38.prot.20210329.bed
-rw-r-----+ 1 lifajin dawolf  619407 Sep  7 14:27 sORFs_genomic_hg38.prot.20210329.bed.logs
-rw-r-----+ 1 lifajin dawolf       0 Sep  7 14:27 sORFs_genomic_hg38.prot.20210329.bed.orfs.allframes.bed
-rw-r-----+ 1 lifajin dawolf       0 Sep  7 14:27 sORFs_genomic_hg38.prot.20210329.bed.orfs.bed
-rw-r-----+ 1 lifajin dawolf       0 Sep  7 14:27 sORFs_genomic_hg38.prot.20210329.bed.orfs.fa
-rw-r-----+ 1 lifajin dawolf       0 Sep  7 14:27 sORFs_genomic_hg38.prot.20210329.bed.orfs.frames.bed
-rw-r-----+ 1 lifajin dawolf       0 Sep  7 14:27 sORFs_genomic_hg38.prot.20210329.bed.orfs.gtf
-rw-r-----+ 1 lifajin dawolf     332 Sep  7 14:27 sORFs_genomic_hg38.prot.20210329.bed.orfs.out
-rw-r-----+ 1 lifajin dawolf 2190722 Sep  7 12:17 sORFs_genomic_hg38.prot.20210329.fa

No errors generated but the output files are empty. I have no idea what's going on, could you please tell where I am wong and what should I do to generate the annotations of Ribo ORFs?

best wishes, Sherking

jorruior commented 1 year ago

Hi Sherking,

I just realized there was an error in one of the added lines in the last updated version v1.1 (although in principle the script should have printed the error instead of running). The error is now fixed and the code should work now, so feel free to re-download the package and use the updated script.

sherkinglee commented 1 year ago

Thanks very much for your kind and quick response! And now, it works in my env.

best wishes, Sherking