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wget and downloading BLAST results

Hi,

If I use the following url directly in the browser window, the associated file directly downloads into my computer: https://www.ncbi.nlm.nih.gov/sviewer/viewer.cgi?tool=portal&save=file&log$=seqview&db=nuccore&report=genbank&id=1741021740&from=891317&to=891649&

However, how to I fetch this URL using wget, which is designed to fetch and download. It did not work with the above URL.

What I want to do is to download hundreds of genbandID (url form like above) automatically by putting them in a file.

Thanks

wget alignment
• 1,457 views • link
updated by Ram Ram • written by supertech supertech

1 answer

Use NCBI EUtils, if you want to use wget.

$ wget -O - -q "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&rettype=gb&id=1741021740&from=891317&to=891649&"

Otherwise using NCBI Entrezdirect:

 $ efetch -db nuccore -id 1741021740 -format gb -seq_start 891317 -seq_stop 891649
• 0 views • link
written by GenoMax GenoMax

Thanks. I will look into these options.

• 0 views • link
written by supertech supertech

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