How To Download Text Files From Swissprot?
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11.9 years ago
philip34 ▴ 20

Hello,

I have a list of swissprot IDs. How can I download the complete data in text format from the swissprot based on these IDs? I need only the data of these IDs.

Your suggestions would be appreciated!!

protein • 4.6k views
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11.9 years ago
Neilfws 49k

Assuming there is one ID per line in a file named "ids.txt", do this from a bash shell:

while read id; do wget http://www.uniprot.org/uniprot/$id.txt; done < ids.txt
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11.9 years ago

For a non-programatic way of addressing the question...

If you go to the "Retrieve" tab at the top of the UniProt webpage http://www.uniprot.org/ , you can upload a file with a list of IDs in it, or just copy-and-paste into the query box. You can then get them in GFF, "Flat Text", FASTA, XML formats. This help page on the UniProt site gives more information about this http://www.uniprot.org/help/batch

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This method is much faster than using wget to download fasta files separately.

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It won't be "much faster" than wget, unless using the website magically increases the bandwidth of your network connection :)

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I was also using wget before to download thousands of sequences separately which was taking ages. Thanks to batch download, it is very fast now.

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Excellent solution; I had forgotten that UniProt offers batch retrieval.

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11.9 years ago
Naren ▴ 1000

If you want few files sequences do it manually via http://www.uniprot.org/uniprot/SWISSPROT_ID_YOU_WANT.txt
changing ID every time.
or If you are using windows "wget" is the best tool for downloads via command prompt.

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