Haruo Suzuki
Last Update: 2016-10-25
Project started 2015-11-16.
DNA and protein sequences of bacterial virulence factors were retrieved from the Virulence Factors Database (VFDB). Analyses of the DNA and protein sequences were performed using the R SeqinR package. Homologous sequences were identified by the BLAST (Basic Local Alignment Search Tool) program.
vfdb/
README.md: project documentation
data/: contains sequence data in FASTA or BLAST database format
scripts/: contains Perl, R and Shell scripts
analysis/: contains results of data analyses
DNA (VFDB_setA_nt.fas) and Protein (VFDB_setA_pro.fas) sequences of core dataset were downloaded on 2015-11-16 from http://www.mgc.ac.cn/VFs/download.htm into data/.
The perl script blast_parser.pl was downloaded on 2015-11-16 from http://kirill-kryukov.com/study/tools/blast-parser/ into scripts/.
The shell script scripts/run.sh automatically carries out the entire steps: creating directories, downloading data and scripts,
running the R scripts for FASTA amino acid and nucleotide of coding regions (scripts/my_faa.R and scripts/my_ffn.R), and
running the shell script scripts/run_blast.sh for BLAST analysis.
Let's run the driver script in the project's main directory vfdb/ with:
bash scripts/run.sh > log.txt 2>&1 &
Inspecting and Manipulating Text Data with Unix Tools
cd data/
# `ls -lh` reports human-readable file sizes
ls -lh *.fas
# Inspecting Data with Head and Tail
head -n 2 *.fas
tail -n 2 *.fas
# use `grep` to extract lines of a file that match a pattern
grep '^>' *.fas
# count how many lines match a pattern
grep -c '^>' *.fas
# the matching part of a pattern is colored, using:
grep --color 'shock' *.fas
# To search text and highlights matches, open a file in `less`, and
# then press / and enter text (e.g. 'O157'). To quit `less`, press q.
less VFDB_setA_pro.fas