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Tutorials on phylogenetic and phylogenomic inference
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convert_vcf_to_nexus does not write tab b/w species and sequence #2

Closed ClaudiaPaetzold closed 5 years ago

ClaudiaPaetzold commented 5 years ago

Dear Michael, thank you for the great tutorial for using SNP data in SVD quartets. I have used the ruby script "convert_vcf_to_nexus.rb" you so kindly provided on my data set, which consists of SNPs generated from RADseq data using the IpyRAD assembly pipeline. When I tried to open the data with Paup, I got an error message telling me the file was corrupted. When I inspected the nexus, I saw that there were no spaces between the sample identifier and the sequence. So it looked like this: (MeoahTTCNN...). Could you look into that? If necessary, I can provide my .vcf file. Thank You.

Claudia

mmatschiner commented 5 years ago

Hi Claudia, thanks for testing and the feedback! That part of the script was a bit sloppy, because it expected all IDs to be shorter than 10 charactes. I assume you didn't actually get "MeoahTTCNN..." but that instead of "Meoah" you had an ID with at least ten characters? I changed the script now that it should handle longer IDs. Could you check if it works now?

ClaudiaPaetzold commented 5 years ago

Hi Michael, you were right, my sample IDs were longer than 10 digits. I just tested the new script, which works fine. Thank you for the quick response and the fix. And also: thank you for the tutorial for SVD quartets with SNP data. It helps me a great deal. I will close this issue now. Cheers Claudia