bioextr is a simple command line tool to extract information from text or json files.
# windows
wget https://github.com/openanno/bioextr/releases/download/v0.1.0/bioextr_0.1.0_Windows_64-bit.tar.gz
# osx
wget https://github.com/openanno/bioextr/releases/download/v0.1.0/bioextr_0.1.0_Darwin_64-bit.tar.gz
# linux
wget https://github.com/openanno/bioextr/releases/download/v0.1.0/bioextr_0.1.0_Linux_64-bit.tar.gz
# get latest version
go get -u github.com/openanno/bioextr- support calculate correlations between any keywords at the sentence level (PubMed)
- support extract URLs from PubMed and SRA abstract
# extract from pubmed abstract
bget api ncbi -q "Galectins control MTOR and AMPK in response to lysosomal damage to induce autophagy OR MTOR-independent autophagy induced by interrupted endoplasmic reticulum-mitochondrial Ca2+ communication: a dead end in cancer cells. OR The PARK10 gene USP24 is a negative regulator of autophagy and ULK1 protein stability OR Coordinate regulation of autophagy and the ubiquitin proteasome system by MTOR." | bioctl cvrt --xml2json pubmed - | bioextr --mode pubmed -w 'MTOR,AMPK,autophagy' --call-cor - > final.json
bget api ncbi -q "Galectins control MTOR and AMPK in response to lysosomal damage to induce autophagy OR MTOR-independent autophagy induced by interrupted endoplasmic reticulum-mitochondrial Ca2+ communication: a dead end in cancer cells. OR The PARK10 gene USP24 is a negative regulator of autophagy and ULK1 protein stability OR Coordinate regulation of autophagy and the ubiquitin proteasome system by MTOR." | bioctl cvrt --xml2json pubmed - > test0.json
for i in {1..100}
do
cp test0.json test${i}.json
done
bioextr test*json --mode pubmed -w 'MTOR,AMPK,autophagy' --call-cor -t 30 > final2.json
rm final.json final2.json test*json
# extract from sra json
bget api ncbi -d 'sra' -q PRJNA527714 | bioctl cvrt --xml2json sra - | bioextr --mode sra --call-cor -w "Chromatin,mouse" -Academic Free License version 3.0