Avian Plasmid Read-Mapping Plot

NOTE: This script has been modified from a pre-existing script available at https://github.com/cerebis/antarctic_ha

It contains scripts supporting an investigation titled - "Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene"

Paper available here

The python script 'chooklord.py' was used to produce the described heatmap:

BWA Index

The reference used was pCERC4 (Accession No. KU578032.1).

bwa index pCERC4_KU578032.fasta

Array definition

An array was defined as below to facilitate the subsequent step

array=($(ls read_directory/*.fastq.gz))

BWA mem

A for loop was used to feed read pairs into an executable 'bwa.qsub'.

for ((i=0; i<${#array[@]}; i+=2));
do qsub -v REF=pCERC4_KU578032.fasta,R1=${array[i]},R2=${array[i+1]},OUT=${array[i]%R1_001.fastq.gz} bwa.qsub;
done

'bwa.qsub' contained, along with the appropriate job submission syntax, the following

bwa mem -t16 -MY $REF $R1 $R2 | samtools view -ubS -F 0x904 - | samtools sort -@8 -T $REF - -o ${R1}.bam

SAMtools depth

for fn in `ls ./*.bam`;
do samtools depth ${fn} > ${fn%.bam}_coverage.txt;
done

Heatmap generation

Here the binsize and ticksize were 250 and 100, respectively.

python chooklord.py -b <binsize> -t <ticksize> pCERC4_KU578032.fasta Heatmap_plot.pdf

Python and Package versions

Python 2.7
bwa - 0.7.17
matplotlib - 2.1.0
numpy - 1.13.3
pandas - 0.20.3
samtools - 0.1.18
scipy - 0.19.1

Acknowledgements

Many thanks to Matt DeMaere for his efforts in putting together the original script and helping to adapt and repurpose it for our investigation.

License

See LICENSE for more information

maxlcummins/chooklord