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dariober / ASCIIGenome

Text Only Genome Viewer!
http://asciigenome.readthedocs.io/en/latest/description.html
MIT License
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gffNameAttr on gtf file does not set attribute name #74

Closed marbeno closed 7 years ago

marbeno commented 7 years ago

Neither gffNameAttr gene_name hg19_genes.gtf .*gtf nor gffNameAttr gene_name hg19_genes.gtf .*gff works. Changing attribute (e.g. transcript_id) doesn't work either.

dariober commented 7 years ago

Hi- Thanks for reporting this. Setting name for GTF files is not supported (yet) and it's been on my TODO list for a while. I haven't used this feature much so I left it behind. Indeed the documentation should mention this.

GFF features should work though. For example:

ASCIIGenome ftp://ftp.ensembl.org/pub/release-89/gff3/homo_sapiens/Homo_sapiens.GRCh38.89.chromosome.Y.gff3.gz
...
[h] for help: gffNameAttr Alias .*gff

Could you post a few lines of or a link to your GFF file? (What version of ASCIIGenome are you running? Check with ASCIIGenome -v).

marbeno commented 7 years ago

Hi, thank you for your answer. I am using ASCIIGenome 1.7.0. I tried gffNameAttr gene_name hg19_genes.gtf .*gff on a .gtf file since gtf and gff2 are basically the same format, as it also described here: issue #46

I'll try with a gff3.

marbeno commented 7 years ago

Hi again, I created a gff3 file from the gtf, which looks like chr1 unknown exon 11874 12227 . + . gene_id=DDX11L1;transcript_id=NR_046018_1;gene_name=DDX11L1;tss_id=TSS14523 chr1 unknown exon 12613 12721 . + . gene_id=DDX11L1;transcript_id=NR_046018_1;gene_name=DDX11L1;tss_id=TSS14523 chr1 unknown exon 13221 14408 . + . gene_id=DDX11L1;transcript_id=NR_046018_1;gene_name=DDX11L1;tss_id=TSS14523 chr1 unknown exon 14362 14829 . - . gene_id=WASH7P;transcript_id=NR_024540;gene_name=WASH7P;tss_id=TSS7359 chr1 unknown exon 14970 15038 . - . gene_id=WASH7P;transcript_id=NR_024540;gene_name=WASH7P;tss_id=TSS7359 chr1 unknown exon 15796 15947 . - . gene_id=WASH7P;transcript_id=NR_024540;gene_name=WASH7P;tss_id=TSS7359 chr1 unknown exon 16607 16765 . - . gene_id=WASH7P;transcript_id=NR_024540;gene_name=WASH7P;tss_id=TSS7359 chr1 unknown exon 16858 17055 . - . gene_id=WASH7P;transcript_id=NR_024540;gene_name=WASH7P;tss_id=TSS7359 chr1 unknown exon 17233 17368 . - . gene_id=WASH7P;transcript_id=NR_024540;gene_name=WASH7P;tss_id=TSS7359 chr1 unknown exon 17606 17742 . - . gene_id=WASH7P;transcript_id=NR_024540;gene_name=WASH7P;tss_id=TSS7359

However, when I try to find a gene, I get:

java.lang.NullPointerException at tracks.TrackIntervalFeature.flatListOfPrintableFeatures(TrackIntervalFeature.java:1008) at tracks.TrackIntervalFeature.stackFeatures(TrackIntervalFeature.java:634) at tracks.TrackIntervalFeature.printToScreen(TrackIntervalFeature.java:509) at tracks.Track.concatTitleAndTrack(Track.java:723) at samTextViewer.TrackProcessor.iterateTracks(TrackProcessor.java:76) at samTextViewer.InteractiveInput.processInput(InteractiveInput.java:405) at samTextViewer.Main.main(Main.java:198) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:58)

dariober commented 7 years ago

Hi- Thanks for sharing this. I fixed this on my local code and I hope to upload soon a version with this bug fixed together with support for naming gtf features.

For the record, the reason you get the ugly error is that your GFF has only feature type "exon" in the 3rd column but no "transcript" or other feature type that can be used to group exons into transcripts.

dariober commented 7 years ago

Hi- version 1.8.0 I uploaded just now should have these issues fixed. You should be able to set feature names for gtf files also. Feel free to re-open this or another issue if you have more questions.