130 lines
4.3 KiB
R
130 lines
4.3 KiB
R
# tocID <- "RPR-UniProt_GET.R"
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#
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# ---------------------------------------------------------------------------- #
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# PATIENCE ... #
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# Do not yet work wih this code. Updates in progress. Thank you. #
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# boris.steipe@utoronto.ca #
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# ---------------------------------------------------------------------------- #
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#
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# Purpose: A Bioinformatics Course:
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# R code accompanying the RPR-Scripting_data_downloads unit.
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#
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# Version: 1.1
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#
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# Date: 2017 10 - 2019 01
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# Author: Boris Steipe (boris.steipe@utoronto.ca)
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#
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# Versions:
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# 1.1 Change from require() to requireNamespace(),
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# use <package>::<function>() idiom throughout
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# 1.0 First ABC units version
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# 0.1 First code copied from 2016 material.
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#
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#
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# TODO:
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#
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#
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# == DO NOT SIMPLY source() THIS FILE! =======================================
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#
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# If there are portions you don't understand, use R's help system, Google for an
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# answer, or ask your instructor. Don't continue if you don't understand what's
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# going on. That's not how it works ...
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#
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# ==============================================================================
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#TOC> ==========================================================================
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#TOC>
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#TOC> Section Title Line
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#TOC> ----------------------------------------------------------
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#TOC> 1 UniProt files via GET 41
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#TOC> 1.1 Task - fetchUniProtSeq() function 103
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#TOC> 2 Task solutions 110
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#TOC>
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#TOC> ==========================================================================
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# = 1 UniProt files via GET ===============================================
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# Perhaps the simplest example of scripted download is to retrieve a protein
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# FASTA sequence from UniProt. All we need is to construct an URL with the
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# correct UniProt ID.
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# An interface between R scripts and We=b servers is provided by the httr
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# package. This sends and receives information via the http protocol, just like
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# a Web browser. Since this is a short and simple request, the GET verb is the
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# right tool:
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if (! requireNamespace("httr", quietly = TRUE)) {
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install.packages("httr")
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}
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# Package information:
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# library(help = httr) # basic information
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# browseVignettes("httr") # available vignettes
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# data(package = "httr") # available datasets
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# The UniProt ID for Mbp1 is ...
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UniProtID <- "P39678"
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# and the base URL to retrieve data is ...
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# http://www.uniprot.org/uniprot/ . We can construct a simple URL to
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# retrieve a FASTA sequence:
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(URL <- sprintf("http://www.uniprot.org/uniprot/%s.fasta", UniProtID))
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# the GET() function from httr will get the data.
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response <- httr::GET(URL)
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str(response) # the response object is a bit complex ...
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as.character(response) # ... but it is easy to pull out the data.
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# to process ...
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x <- as.character(response)
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x <- strsplit(x, "\n")
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dbSanitizeSequence(x)
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# Simple.
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# But what happens if there is an error, e.g. the uniprot ID does not exist?
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response <- httr::GET("http://www.uniprot.org/uniprot/X000000.fasta")
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as.character(response)
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# this is a large HTML page that tells us the URL was not found. So we need to
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# check for errors. The Right Way to do this is to evaluate the staus code that
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# every Web server returns for every transaction.
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#
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httr::status_code(response) # 404 == Page Not Found
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# There are many possible codes, but the only code we will be happy with
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# is 200 - oK.
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# (cf. https://en.wikipedia.org/wiki/List_of_HTTP_status_codes )
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URL <- sprintf("http://www.uniprot.org/uniprot/%s.fasta", UniProtID)
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response <- httr::GET(URL)
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httr::status_code(response)
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# == 1.1 Task - fetchUniProtSeq() function =================================
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# Task: write a function that takes as input a UniProt ID, fetches the
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# FASTA sequence, returns only the sequence if the operation is successful, or
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# a vector of length 0 if there is an error.
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# = 2 Task solutions ======================================================
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# I have placed such a function into the dbUtilities script: look it up by
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# clicking on dbFetchUniProtSeq() in the Environment pane.
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# Test:
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dbFetchUniProtSeq("P39678")
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# [END]
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