ete3: allow taxids in species tree input #163
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now one can submit a list of taxids as input (or even mixed)
| @@ -29,7 +29,7 @@ Nomascus leucogenys Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Noma | |||
| Pongo abelii Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Pongo Pongo abelii | |||
| Gorilla gorilla gorilla Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Gorilla Gorilla gorilla | |||
| Pan troglodytes Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Pan Pan troglodytes | |||
| Homo sapiens Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Homo Homo sapiens | |||
| 9606 Eukaryota Chordata Mammalia Euarchontoglires Hominoidea Homo Homo sapiens | |||
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I'm not sure it's good that this and the following output files are changed, probably need to modify ete_lineage_generator.py to print the species name instead of the input taxid in the first column?
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I also noted this. The change is because the first column is just a copy of the input. I liked this because it gives a mapping between the original inputs and the ete outputs.
Should be easy to change it if you like. But we can also document it better.
In most use cases people will input either taxids of species names.
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@anilthanki Any opinion on this?
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Hi @nsoranzo can we interpret no answer as positive feedback?
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@anilthanki is back from holidays, ping?
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Hi @anilthanki: any chance the get feedback? If not, can we just have a decision on how to continue here?
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Hi @bernt-matthias I did have a look before and tried to remember what It supposed to do but TBH its been long I worked on it so I couldnt really make a comment..
I will try to review it again this weekend and make a comment by monday
Apologies for this
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
…hub.com/bernt-matthias/earlham-galaxytools into topic/ete-species_tree_generator-taxids
now one can submit a list of taxids as input (or even mixed)