My first contribution to an open source software package

Oct 7, 2017

Yuppiiii!!! You know how you feel, when your work is getting recognized, right? ;)

Some time back, I was working on an issue with - yes, again - with PhyloProfile, where I need to sort a list of taxa based on their taxonomy distance. From Bastian - the guy who knows everything, I got to know taxize, a greate library from rOpenSci project for playing with NCBI taxonomy database. taxize has a function called class2tree() which create a tree object from a given list of species.

>library(taxize)
> spnames <- c('Homo_sapiens',
+              'Pan_troglodytes',
+              'Macaca_mulatta',
+              'Mus_musculus',
+              'Rattus_norvegicus',
+              'Bos_taurus',
+              'Canis_lupus',
+              'Ornithorhynchus_anatinus',
+              'Xenopus_tropicalis',
+              'Takifugu_rubripes')
> out <- classification(spnames, db='ncbi')
> tr <- class2tree(out)
> plot(tr)

and this is the tree tr we got

This tree has many unresolved splits, since class2tree() remove all unrank levels from the taxonomy ranks leading to a missing information for separating those splits (unrank levels are ranks that are named as “no rank” on the following table).

> out$Homo_sapiens
name         rank      id
1    cellular organisms      no rank  131567
2             Eukaryota superkingdom    2759
3          Opisthokonta      no rank   33154
4               Metazoa      kingdom   33208
5             Eumetazoa      no rank    6072
6             Bilateria      no rank   33213
7         Deuterostomia      no rank   33511
8              Chordata       phylum    7711
9              Craniata    subphylum   89593
10           Vertebrata      no rank    7742
11        Gnathostomata      no rank    7776
12           Teleostomi      no rank  117570
13         Euteleostomi      no rank  117571
14        Sarcopterygii      no rank    8287
15 Dipnotetrapodomorpha      no rank 1338369
16            Tetrapoda      no rank   32523
17              Amniota      no rank   32524
18             Mammalia        class   40674
19               Theria      no rank   32525
20             Eutheria      no rank    9347
21        Boreoeutheria      no rank 1437010
22     Euarchontoglires   superorder  314146
23             Primates        order    9443
24          Haplorrhini     suborder  376913
25          Simiiformes   infraorder  314293
26           Catarrhini    parvorder    9526
27           Hominoidea  superfamily  314295
28            Hominidae       family    9604
29            Homininae    subfamily  207598
30                 Homo        genus    9605
31         Homo sapiens      species    9606

Bastian opened an issue in taxize github repository. At that time, I could already solve the issue (mostly) with my Perl code. But while writing the manuscript for PhyloProfile, we decided to convert the Perl code into R, so that we don’t have many scripts in many different languages in one program :-D

Eventually, I’ve not only improved the sorting result while implementing the algorithm in R (by using APE tree object), but I could also rewrite the class2tree() function to include the full taxonomy information for creating the species tree. By that I can sucessfully reconstruct the NCBI taxonomy tree, yahooo!!

Bastian and I made a pull request in taxize. He helped me to run the tests they require. And finally, my code & our effort have been accepted ^_^

I have learned so many practical things with this first contribution. Thank you so much, Bastian ;-)