bigbio / bigbio/pgatk

Header of the proteins for search engines

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enhancement
Dominant language
Python
Stars
17
Forks
14
PR merge metrics
No merged PRs in 30d

Description

@husensofteng the header of the proteins should be modified to be understood by SEARCH engines. SearchGUI don't understand the ENSEMBL ids. We probably need to move to the following header (
https://github.com/compomics/searchgui/wiki/DatabaseHelp#non-standard-fasta):

```
>generic[your tag]|[protein accession]|[protein description]

or

>generic[your tag]|[protein accession]
```

Note that `[your tag]` can be empty.

Examples:

```
>generic_contig-535081|AC:123132|Hypothetical protein
>generic|AC:123132|Hypothetical protein
>generic|AC:123132
```

Contributor guide

No contributing guide indexed for this repository

Research direction

No file or test is named. Locate the code that generates protein FASTA headers, then compare its output with the SearchGUI non-standard FASTA examples linked in the issue; done means generated headers follow the requested generic|accession|description or generic|accession format.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
bioinformatics
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
38/100

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