-
```
When parsing DIP db (human only, PSI-MI 2.5,
ftp://dip.doe-mbi.ucla.edu/2014/mif25/Hsapi20140117.mif25.gz)
I am getting hundreds of warnings from
psidev.psi.mi.xml.dao.inMemory.InMemoryDAO clas…
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I'm having issues with the performance of stevedore, as of right now, most of the startup time
is dominated by stevedore loading modules.
For instance if I try to open a non-existent document as in …
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Hi,
Your program `medic` looks extremely useful.
I am trying to create a medline sql database using files downloaded from ` ftp://ftp.ncbi.nlm.nih.gov/pubmed/baseline`.
After the download, I…
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**Describe the bug**
Every time a PR is done, GitHub conducts two checks: `test` and `docs`. Both checks fail.
**To Reproduce**
Go to [link](https://github.com/titipata/pubmed_parser/actions/runs…
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Similar to the work on variant index (#3350), we would like to serve a `gwas_study_index` dataset through OS + API.
This dataset is created by different upstream ETL processes ([gentropy](https://g…
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Suggestions provided by @haruosuz
- bactopia can accept GFF3 files (.gff) instead of FASTA files (.fna) as input, like PIRATE and Roary, to skip Prokka?
- bactopia can do alignment trimming (e.g. …
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I would like to create MassBank records from *.msp spectral libraries as this format is exported by raw-data-processing software like MS-DIAL.
For this, I would add the option 'msp' to parameter 're…
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I just updated to version 112 to make use of the --individual_zyg function, but i'm getting errors triggered when I run it.
My command is:
`./vep --cache --dir_cache /opt/.vep/ --no_stats --che…
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Said variant is a (disruptive) `inframe_insertion` in the stop codon with `stop_retained` effect. This corresponds to SPDI `GRCh37:10:5139789:A:AGTG`.
Based on the current `main` branch, the follow…
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## Problem description
Hey there! I'm trying to convert ChIP peaks (in a bed file format) to gff3. Below is the command and the resulting error:
```
$ time gt bed_to_gff3 -force yes -o 0hr-CTCF_C…