PopGenome Not Reading In FASTA File
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4 months ago
Simone • 0

I'm trying to run my alignment of a gene (CDS) with multiple species and multiple individuals per species. When using the 'readData()' function in the PopGenome package, I can see that it's reading in my file because it shows the correct number of sites, but doesn't show anything else (# gaps, unknowns, trans/transv ratio, etc).

> get.sum.data(Croc_AVP.class)
                                       n.sites n.biallelic.sites n.gaps n.unknowns n.valid.sites n.polyallelic.sites trans.transv.ratio
ExonCap-Crocodylus_AVP_outNT_MKTtest.fasta     858                 0      0          0             0                   0                NaN
popgenome MKT selection R phylogenomics • 302 views
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Could your fasta file have Microsoft style linebreaks instead of proper *nix linebreaks?

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I thought about that when comparing my file to their example file! I'm on Unix but my collaborator could have been using Windows. How could I "convert" the file if that's the issue?

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dos2unix yourFile
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4 months ago
Simone • 0

Apparently the linebreaks weren't the issue. I converted the file but having the same problem

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