Wednesday, September 16, 2015

MByant 20150916

Convert PDF into WORD.
MB manually copy-pasted Table 2 into an Excel file.

Get FASTA sequences using NCBI Gene ID


echo -e "19084\n112407\n18113" | while read G; do curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=protein&id=${G}" | grep -A 1 "<Link>" | grep "<Id>" | cut -d '>' -f 2 | cut -d '<' -f 1 | while read S ; do curl -s "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=${S}&retmode=text&rettype=fasta" ; done;  done

See https://www.biostars.org/p/52652/

HQ tested with 1029 and it returned the correct sequences. 

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