PopGenome Not Reading In FASTA File

Question

[Simone]

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

[5heikki]

Could your fasta file have Microsoft style linebreaks instead of proper *nix linebreaks?

[Simone]

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?

[5heikki]

dos2unix yourFile

Answer 1

[Simone]

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