childers
childers
Using FireFox 36.0.1, OS X 10.10.2. When selecting a file for the blastdb, the "Select" button if not visible in firefox. It is present in Chrome.
Would it be possible to have the HSPs colored dynamically so it follows the same coloring scale currently in the BLAST output? The idea came to me from an update...
Currently the exported gff3 includes only e-value. Could you also export the bitscore and percent identity for each hsp?
To prevent name collisions, can you add an option to add a prepend string to the defline? Changing this tag would require rerunning all of the processing steps.
Could there be more informative error reporting? Currently, it simply flashes an error and then disappears without describing what caused the problem. The issue ended up being filesystem permissions, but...
command: seqconv convert --ref Myoluc2.0 --out uc ref_Myoluc2.0_top_level.gff3.gz ```text GL430047 Gnomon exon 1591810 1591932 . + . ID=id351777;Parent=rna30996;Dbxref=GeneID:102441866,Genbank:XM_014465163.1;gbkey=mRNA;gene=MYO9B;product=myosin IXB%2C transcript variant X4;transcript_id=XM_014465163.1 GL430047 Gnomon exon 1592894 1593043 . + ....
```text $ time seqconv convert --ref felCat4 --out rs cat_felCat4_UCSC_2008.gtf >test_cat_4.rs.gtf Converting from None to rsStarting Conversion Cannot convert id: chrM No corresponding id for chrX from None FORMAT detected:...
When running a conversion, the first line of the output is a link to the assembly_report file. ```shell $ time seqconv convert --ref ICSASG_v2 --out gb ref_ICSASG_v2_top_level.gff3.gz> test_salmon.gff3 ``` ```text...
```shell $ time seqconv convert --ref felCat4 --out rs cat_felCat4_UCSC_2008 ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/003/115/GCA_000003115.1_catChrV17e/GCA_000003115.1_catChrV17e_assembly_report.txt Converting from None to rsStarting Conversion Cannot convert id: exon Traceback (most recent call last): File "/usr/local/bin/seqconv", line 11,...
We found that some scaffolds in Ensembl gtf do not follow the _accession.version_ format, and only have the accession. In this case the assembly report entry will **not** match the...