cparsania / phylor Goto Github PK
View Code? Open in Web Editor NEWAn R package to prepare data for phylogenetic analysis
Home Page: https://cparsania.github.io/phyloR/
License: Other
An R package to prepare data for phylogenetic analysis
Home Page: https://cparsania.github.io/phyloR/
License: Other
Hi there,
I am add NCBI taxonomy classifications to my DIAMOND output file. I ran PhyloR as follows:
library (phyloR)
library (readr)
library (taxize)
setwd("/home/ymgwatyu/lustre/000_GenomeData/01_MinION/phylor")
data <- read_tsv("/home/ymgwatyu/lustre/000_GenomeData/01_MinION/phylor/diamond_data.txt", show_col_types = FALSE)
add_taxonomy_columns(data, ncbi_accession_colname = "ncbi_accession", ncbi_acc_key = "98845081e276ecedd2e2b92d339fb7354108", taxonomy_level = "family", map_superkindom = FALSE, batch_size = 20)
The output file looks like this :
?^?^? Done. Time taken 6.39
?^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^$
?^?? Rank search begins...
?^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^?^??^$
?^?^? Done. Time taken 0.95
Gene ncbi_accession taxid family
1 g2420.t1 XP_019440838.1 3871 Fabaceae
2 g20534.t1 XP_057737287.1 217475 Fabaceae
3 g37802.t1 XP_031279371.1 55513 Anacardiaceae
4 g13363.t1 QHN77035.1 3818 Fabaceae
5 g30858.t1 KAE9615640.1 3870 Fabaceae
6 g24702.t1 OIW14831.1 3871 Fabaceae
7 g17954.t1 KAE9590247.1 3870 Fabaceae
8 g20072.t1 XP_019420191.1 3871 Fabaceae
9 g12935.t1 WAX01758.1 649199 Fabaceae
10 g914.t1 XP_019444688.1 3871 Fabaceae
So it only annotated the first 10 accessions. How do I get it to process more than 10? or to print out more than 10 lines in the output file?
A declarative, efficient, and flexible JavaScript library for building user interfaces.
π Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. πππ
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google β€οΈ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.