MiFishデータの検索

http://sra.dbcls.jp/result.html?target_db=sra&term=mifish&rows=100&sort=Updated&order=desc

でヒットしたプロジェクトについて、https://www.ncbi.nlm.nih.gov/sraで、「SRP286684 or DRP006505 or DRP006495 or DRP006192 or SRP267202 or SRP259710 or DRP004174 or DRP003415 or DRP005037 or SRP187190 or DRP004525 or DRP004492 or DRP004089 or SRP113732 or DRP003662 or SRP072060 」などとやって検索。結果をSend to: →Accession ListでSRR, DRRなどの番号を保存。

上記の番号を作るには、dbclsのページで開発者ツールのコンソールを開いて下記を入力。

let arr=[]; document.querySelectorAll(".tabulator-cell[tabulator-field='_id']").forEach(x=>arr.push(x.textContent)); console.log(arr.join(' or '));

id=DRR125636; curl https://www.ncbi.nlm.nih.gov/biosample/`curl "https://www.ncbi.nlm.nih.gov/sra/?term=$id"|grep SAM|sed 's/SAM/\nSAM/g;'|sed 's/".*//; s/<.*//; s/ .*//'|grep "^SAM"|head -n 1`|grep -i lat|grep -i long

とやると、経度緯度を抜き出せそう。

#@/home/yoshitake.kazutoshi/work2/eDNA-db/
for id in `cat SraAccList.txt`; do a=$(curl https://www.ncbi.nlm.nih.gov/biosample/`curl "https://www.ncbi.nlm.nih.gov/sra/?term=$id"|grep SAM|sed 's/SAM/\nSAM/g;'|sed 's/".*//; s/<.*//; s/ .*//'|grep "^SAM"|head -n 1`); echo "$id"$'\t'`echo "$a"|grep -i lat|grep -i long|sed 's/<[^>]*>/\t/g'|sed 's/\t\+/\n/g'|grep -A 1 long|tail -n 1`$'\t'`echo "$a"|grep -i "collection date"|sed 's/<[^>]*>/\t/g'|sed 's/\t\+/\n/g'|grep -A 1 -i "collection date"|tail -n 1`; done > lat-long-date.txt

more lat-long-date.txt |cut -f 2|awk '{if($2=="N"){b=""}else{b="-"}; if($4=="W"){a="-"}else{a=""}; print b$1","a$3}'

で出てきた値をhttps://1-dot-tree-maps-152415.appspot.com/prot/に貼り付けてみる。

#@/suikou/files/m512/backup/r311/eDNA/
for i in `cat SraAccList.txt`; do /data/eDNA/bin/prefetch $i --output-file $i.sra; (/data/eDNA/bin/fastq-dump --gzip --split-files $i.sra; rm $i.sra) & done