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When use pyGTF, i Encountered KeyError: 'ID'
my code
import sys
from pyGTF import Transcript
from pyGTF import GTFReader
with GTFReader('A.gtf',flag_stream=True) as fi:
for i in fi:
…
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c_to_p fails for variant "NM_198180.2:c.408_410delGTG".
This is in-frame deletion that involves the termination codon, so I believe it is similar to issues #476, #449 and #525
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The crash in the proteome comparison tool at the tutorial this week was a result of feature fig|1945512.3.peg.14 not having a translation. That feature derived from the genbank file https://www.ncbi.n…
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I need to annotate some indels for chromosome 22, and then scale this step to the full human genome. I'm running vep locally using snakemake in a HPC environment with 75Gb of RAM. The input file has ~…
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Hi. I got the following errors in the quantification step.
> IRFinder-1.2.5/bin/IRFinder: line 562: 49201 Broken pipe gzip -cd "$1"
49202 Aborted (core dumped) | "…
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Indicate default value of propose.by.prior for initializeParameterObject in parameterObject.R (and c++ code) and how the values are generated if set to FALSE.
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# **OrthoFinder version 2.5.4 installed by conda:**
```
$ orthofinder -f rep_type_out_more_genomes_faa -M msa -S mmseqs -a 10 -o rep_type_out_more_genomes_faa_orthofinder_test
OrthoFinder versi…
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MAFFT V7 https://mafft.cbrc.jp/alignment/software/tips.html
Download from NCBI with Batch https://astrobiomike.github.io/bash/ncbi_eutils
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This benchmark is from https://lemire.me/blog/2012/06/20/do-not-waste-time-with-stl-vectors/
Python:
```python
from ltypes import i32, i64
def test_list(n: i32) -> i64:
a: list[i32] = [0]…