20220306

Contents

1. Working directories
2. Randomly select a file from a directory
3. Zinc finger
4. CRAN
5. ITIS
1. 5.1. Integrated Taxonomic Information System - Database Download

Working directories

##############################################################
# Journal club for NFX1
# 
i=/media/ht/ht_5T/Work/Projects/PABP/Summary/PABP_Project.pptx; \
setsid wps ${i}
# NCBI-BLAST+ installation
i=https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.12.0+-x64-linux.tar.gz
axel ${i}
tar zxvpf *.gz

Randomly select a file from a directory

ls |sort -R |tail -$N |while read file; do
    # Something involving $file, or you can leave
    # off the while to just get the filenames
done

ls dirname | shuf -n 1
# probably faster and more flexible:
find dirname -type f | shuf -n 1
# etc..
# 
shuf -ezn 5 * | xargs -0 -n1 echo
# 
LENGTH=${#ARRAY[@]}
RANDOM=${a[RANDOM%$LENGTH]}

1 2	a=( * ) randf=( "${a[RANDOM%${#a[@]}]"{1..42}"}" )

Zinc finger

https://www.spandidos-publications.com/10.3892/ijo.2019.4860# https://www.uniprot.org/uniprot/Q9FFK8 https://www.ncbi.nlm.nih.gov/Structure/cdd/cd06008 https://www.ncbi.nlm.nih.gov/protein/72391068 https://en.wikipedia.org/wiki/Zinc_finger#Zn2/Cys6 https://en.wikipedia.org/wiki/Conserved_Domain_Database https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml http://genexplain.com/tfclass/huTF_classification_Families.html https://www.frontiersin.org/articles/10.3389/fpls.2020.00115/full https://academic.oup.com/nar/article/31/2/532/2375953 https://www.annualreviews.org/doi/pdf/10.1146/annurev-biochem-010909-095056 https://epigenie.com/key-epigenetic-players/chromatin-modifying-and-dna-binding-proteins/zinc-finger-proteins/ https://jbiomedsci.biomedcentral.com/articles/10.1186/s12929-016-0269-9 https://www.nature.com/articles/cddiscovery201771 https://www.ncbi.nlm.nih.gov/gene/4799

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0042578 https://www.ebi.ac.uk/interpro/entry/InterPro/IPR000967/

CDD/SPARCLE: the conserved domain database in 2020 - PubMed, Database

CRAN

# ERROR: dependencies ‘crul’, ‘ape’, ‘bold’, ‘rredlist’, ‘rotl’,' ‘ritis’, ‘worrms’, ‘natserv’, ‘wikitaxa’, ‘phangorn’ are not available for package ‘taxize’
# 
# ERROR: dependencies 'crul', 'ape', 'bold', 'rredlist', 'rotl',' 'ritis', 'worrms', 'natserv', 'wikitaxa', 'phangorn' are not available for package 'taxize'
# 
i <- c('crul', 'ape', 'bold', 'rredlist', 'rotl', 'ritis', 'worrms', 'natserv', 'wikitaxa', 'phangorn')
install.packages(i, dependencies = TRUE)
install.packages("taxizedb", dependencies = TRUE)

ITIS

Integrated Taxonomic Information System - Database Download

ITIS Downloads

The following files are available for download:

ITIS Database Downloads

Note: Database download files are currently from the 28-Feb-2022 data load.

Full ITIS Data Set (Informix 7) – itisInformix.tar.gz

Full ITIS Data Set (MS SQL Server) – itisMSSql.zip

Full ITIS Data Set (MySQL bulk load) – itisMySQLBulk.zip

Full ITIS Data Set (MySQL by table) – itisMySQLTables.tar.gz

Full ITIS Data Set (PostgreSql) – itisPostgreSql.zip

Full ITIS Data Set (SQLite) – itisSqlite.zip

Other ITIS Downloads

Taxonomic Workbench (TWB) Executable – TWB Executable

Download Validation Instructions – MD5_Instr.txt

Download Validation File – MD5SUMS

Please let us know at the ITIS Webmaster address if you have issues using these database files.