lattice-automation/seqparse

Parse sequence files (GenBank, FASTA, SnapGene, SBOL) and accession IDs (NCBI, iGEM) to a common format

seqparse's Issues

InvertBio Buggy Annotations

Buggy annotations
We mostly use SeqViz with genbank files and have noticed that annotation parsing is off without us being able to really figure out why/how to fix it in the files. I can try to find an example for you we can share (hard because it's mainly customer IP we're working with). But the same file in SeqViz and in Snapgene render differently and it results in both more, but wrong, annotation shown in SeqViz and fewer/hidden annotations that doesn't appear in SeqViz.

Visualisation of unassembled strains
Some of the genbank files we have contain multiple strains (typically unassembled reads), which SeqViz by default concatenates the sequences as it was one – which is wrong and hard to catch. Snapgene let's you select which of the sequences to view, which is what we've now built ourselves too, so that we add a select-step before rendering just one of the sequences in the file with SeqViz.

from Holger Thorup at https://invertbio.com/
whatever the fixes are they're go into https://github.com/Lattice-Automation/seqparse

Add sequence file generation

Make it possible to generate sequence files from the SeqParse simple, common format. File formats:

• GenBank
• FASTA
• GTF
• GFF

Error when querying by NP

I get an error when I call the seqparse function using a NP ID (e.g., NP_000229.1).

I looked at the queries and found that it uses the nuccore database:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=NP_000229.1&rettype=gbwithparts&retmode=text

I think that it should use the protein database, which would lead to the following URL:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=NP_000229.1&rettype=gbwithparts&retmode=text

This query does return a successful result. My code is the following:

// ...
useEffect(() => {
    seqparse("NP_000229.1")
      .then(console.log)
      .catch(console.error);
  }, []);
// ...

Am I doing something wrong or is there an error in the code?