Consolidate BED, FASTA file input validation - Githubissues

formbio / laava

LAAVA: Long-read AAV Analysis

MIT License

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Consolidate BED, FASTA file input validation #20

Open etal opened 4 months ago

etal commented 4 months ago

Check FASTA sequences:

Ensure terminal EOL (so concatenation works) – dos2unix, or append "\n"
Ensure sequence uses nucleotide alphabet? – seqkit or biopython; see minimap2 input requirements

Check BED versus FASTA sequences (currently handled but roundabout):

"vector" contig name from annotation BED matches contig name in the vector FASTA
"repcap" contig name from annotation BED matches one contig name in either the vector FASTA or packaging FASTA
"vector" contig name is not used in packaging or host FASTA files
Contig names are not reused between packaging and host FASTA files