cyklee

# Quick conversion from latitude/longitude formats ("degrees decimal minutes" or "degrees minutes seconds") to decimal coordinates.
# This conversion needs to be verified since I know little of geodesy

# Load the list data
LL <- read.delim("~/Dropbox/POLAR GRADIENTS/latitude_longitude.tsv", quote="")
library(sp)

as.numeric(char2dms(as.character(LL$Latitude), chd="d", chm = "'", chs = "\""))
as.numeric(char2dms(as.character(LL$Longitude), chd="d", chm = "'", chs = "\""))

cyklee

# This is an exercise in 16S rRNA gene sequence processing in R

library(phyloseq)
library(dada2)
library(Biostrings)

# Load OTU table generated by USEARCH with phyloseq
# Load the "classic" OTU table converted from .uc to .txt via uc2otutab.py
otuFile <- read.delim("example_readmap.txt", header=TRUE, row.names=1)
otu <- otu_table(otuFile,taxa_are_rows = TRUE)

cyklee

mv ./*/**/*(.D) ./

cyklee

# In order to using the plotting script in `compare_alpha_diversity.py` we need to convert the output from `alpha_diversity.py`
# to resemble that coming out of `collate_alpha.py`, which involves transposing the column of sample name and ouput to rows.
# In theory, we will have only two rows, one for site names and one for the alpha diversity.

# Here's the transposition workflow for my own reproducibility purposes:

awk '
{ 
    for (i=1; i<=NF; i++)  {
            a[NR,i] = $i

cyklee

tmux cheat sheet

(C-x means ctrl+x, M-x means alt+x)

Prefix key

The default prefix is C-b. If you (or your muscle memory) prefer C-a, you need to add this to ~/.tmux.conf:

remap prefix to Control + a

cyklee

#!/bin/zsh
# Load OTU table generated by fastq2biom into phyloseq
# I'm converting from HDF5 to JSON format because otherwise phyloseq would drop low abundance OTU for me 
biom convert -i ${project}_tax.biom -o ${project}_tax.json --to-json

# I have problem where the "id" and "type" field values are malformed:
# My conversion output: "b'No Table ID'" & "b'OTU table'"
# Should be: "No Table ID" & "OTU table"
# Fixing this with sed:
sed -i "s/b'//g; s/'//g" ${project}_tax.json

cyklee

su
systemctl enable vboxservice
systemctl start vboxservice
groupadd vboxsf
gpasswd -a $USER vboxsf
exit

sudo usermod -aG vboxsf $(whoami) 
# Log off & log back in

cyklee

# https://www.biostars.org/p/49820/
# https://github.com/mdshw5/pyfaidx can be used as a drop-in replacement
xargs samtools faidx test.fa < names.txt

cyklee

import_biom2 <- function(x, 
                         treefilename=NULL, refseqfilename=NULL, refseqFunction=readDNAStringSet, refseqArgs=NULL,
                         parseFunction=parse_taxonomy_default, parallel=FALSE, version=1.0, ...){
  
  # initialize the argument-list for phyloseq. Start empty.
  argumentlist <- list()
  
  x = read_biom(x)
  b_data = biom_data(x)
  b_data_mat = as(b_data, "matrix")

cyklee

#!/bin/bash

infile=$1

if [ "$infile" == "" ] ; then
    echo "Usage: prokkagff2gtf.sh <PROKKA gff file>"
    exit 0
fi

grep -v "#" $infile | grep "ID=" | cut -f1 -d ';' | sed 's/ID=//g' | cut -f1,4,5,7,9 |  awk -v OFS='\t' '{print $1,"PROKKA","CDS",$2,$3,".",$4,".","gene_id " $5}'