I am having an issue with the PanSN naming for pggb fastas and would love thoughts!
I am running:
fastix -p "NP117#hap#" 117_Assembly.fasta > 117_shasta_fastix_output.fasta
But run into naming issues with:
pggb -i combined_aligned_contigs.fasta.gz -o pangenome
[pggb] warning: there are sequence names (like 'NP117#hap#178') that do not match the Pangenome Sequence Naming (PanSN). [pggb] ERROR: -n/--n-haplotypes must be greater than or equal to 1 when the Pangenome Sequence Naming (PanSN) is not respected.
Unsure what the issue is as the fastix example is:
fastix -p "gen#1#" genome.fa > genome_prefixed.fa
Any thoughts?
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Whirlingdaf •
2 answers
looks like the naming scheme pggb wants has an integer in between those two #, so 1 is allowed but hap is not
the regex it checks appears to be ^([^#]+#)[0-9]+#[^#]+$ (from https://github.com/pangenome/pggb/blob/cc332526727a9cc99f4194ef47212e7c06175106/pggb#L312C20-L312C42)
gemini explains the regex as follows
This regex aims to match strings that:
- Start with any sequence of characters followed by a single "#".
- Continue with one or more digits.
- Followed by another single "#".
- End with any sequence of characters.
this confirms what https://github.com/pangenome/PanSN-spec says: the haplotype id is the middle part which is a number
Exactly what cmdcolin said.
You can check your fasta headers using
samtools faidx 117_Assembly.fasta
cat 117_Assembly.fasta.fai
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