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download from protein database #7

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@olgabot

olgabot commented Dec 10, 2014

Hello,
I am attempting to add the protein database, in addition to SRA and Assembly to download fasta files (or a big fasta file). I was going off of assemblyURL, and I tried putting in the URL I got from searching for a protein fasta, which looked like this: http://www.ncbi.nlm.nih.gov/protein/XP_009457936.1?report=fasta&log$=seqview&format=text (this isn't a pure fasta file, it still has html formatting, so not sure what to do about that)

I'd like to download all protein sequence files for the gene "POLR2L", which I'm doing with:

bionode-ncbi download protein polr2l

This is the error I'm currently getting with this code:

TypeError: Cannot read property 'Run' of undefined
    at Object.proteinURL [as protein] (/usr/local/lib/node_modules/bionode-ncbi/lib/bionode-ncbi.js:431:26)
    at DestroyableTransform.transform [as _transform] (/usr/local/lib/node_modules/bionode-ncbi/lib/bionode-ncbi.js:410:17)
    at DestroyableTransform.Transform._read (/usr/local/lib/node_modules/bionode-ncbi/node_modules/through2/node_modules/readable-stream/lib/_stream_transform.js:184:10)
    at DestroyableTransform.Transform._write (/usr/local/lib/node_modules/bionode-ncbi/node_modules/through2/node_modules/readable-stream/lib/_stream_transform.js:172:12)
    at doWrite (/usr/local/lib/node_modules/bionode-ncbi/node_modules/through2/node_modules/readable-stream/lib/_stream_writable.js:237:10)
    at writeOrBuffer (/usr/local/lib/node_modules/bionode-ncbi/node_modules/through2/node_modules/readable-stream/lib/_stream_writable.js:227:5)
    at DestroyableTransform.Writable.write (/usr/local/lib/node_modules/bionode-ncbi/node_modules/through2/node_modules/readable-stream/lib/_stream_writable.js:194:11)
    at write (/usr/local/lib/node_modules/bionode-ncbi/node_modules/pumpify/node_modules/duplexify/node_modules/readable-stream/lib/_stream_readable.js:623:24)
    at flow (/usr/local/lib/node_modules/bionode-ncbi/node_modules/pumpify/node_modules/duplexify/node_modules/readable-stream/lib/_stream_readable.js:632:7)
    at pipeOnReadable (/usr/local/lib/node_modules/bionode-ncbi/node_modules/pumpify/node_modules/duplexify/node_modules/readable-stream/lib/_stream_readable.js:664:5)

I think this bug originates from my misunderstanding of what runURL does in the <database>URL functions. Can you clarify?

Thanks!
Olga

@coveralls

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coveralls commented Dec 11, 2014

Coverage Status

Coverage decreased (-2.82%) when pulling 0c4de64 on olgabot:protein into bc4c56a on bionode:master.

@coveralls

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coveralls commented Dec 11, 2014

Coverage Status

Coverage decreased (-2.82%) when pulling 5853377 on olgabot:protein into bc4c56a on bionode:master.

@bmpvieira

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bmpvieira commented Apr 4, 2015

Moving discussion to #10

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