Re: Importing into Mathematica from URL (PubMed)
- To: mathgroup at smc.vnet.net
- Subject: [mg117696] Re: Importing into Mathematica from URL (PubMed)
- From: Zach Bjornson <zachb at wolfram.com>
- Date: Wed, 30 Mar 2011 04:08:55 -0500 (EST)
- References: <imfadj$iu7$1@smc.vnet.net>
The URL you're trying to access returns a java-requiring page designed for human interface. Instead: asn1=Import["http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&id=CAA76847.1";, "Text"] Notice the different url (eutils). This returns an ASN.1 file, which is much like XML. Your protein sequence is in there, as is the mRNA sequence (which is in the packed ncbi2na format). To yank out just the AA sequence: StringJoin@ StringReplace[ StringDrop[ StringDrop[StringCases[asn1, Shortest["ncbieaa \"" ~~ __ ~~ "\""]], 9], -2], "\n" -> ""] Best, Zach W|A Computational Biology On 3/24/2011 4:37 AM, Thomas Dowling wrote: > Hello, > > Does anyone know how to import a protein sequence from the PubMed database > into Mathematica, or > can anyone advise me as to where I am going wrong in the following approach? > > > 1. As an example, I'd like to import the data for BSA (bovine serum albumin) > from the following site: > > > http://www.ncbi.nlm.nih.gov/protein/CAA76847.1 > > > I wish to import all meaningful data from this page, but the bit I am > particularly interested in is the amino acid sequence > > (in one-leter code) which is right at the end (between ORIGIN and //): > > ORIGIN > 1 mkwvtfisll llfssaysrg vfrrdthkse iahrfkdlge ehfkglvlia fsqylqqcpf > 61 dehvklvnel tefaktcvad eshagceksl htlfgdelck vaslretygd madccekqep > 121 ernecflshk ddspdlpklk pdpntlcdef kadekkfwgk ylyeiarrhp yfyapellyy > 181 ankyngvfqe ccqaedkgac llpkietmre kvltssarqr lrcasiqkfg eralkawsva > 241 rlsqkfpkae fvevtklvtd ltkvhkecch gdllecaddr adlakyicdn qdtissklke > 301 ccdkplleks hciaevekda ipenlpplta dfaedkdvck nyqeakdafl gsflyeysrr > 361 hpeyavsvll rlakeyeatl eeccakddph acystvfdkl khlvdepqnl ikqncdqfek > 421 lgeygfqnal ivrytrkvpq vstptlvevs rslgkvgtrc ctkpesermp ctedylslil > 481 nrlcvlhekt pvsekvtkcc teslvnrrpc fsaltpdety vpkafdeklf tfhadictlp > 541 dtekqikkqt alvellkhkp kateeqlktv menfvafvdk ccaaddkeac favegpklvv > 601 stqtala > // > > 2. Import["http://www.ncbi.nlm.nih.gov/protein/CAA76847.1","Elements";] > > gives the following > > {Data,FullData,Hyperlinks,Images,ImageURLs,Plaintext,Source,Title,XMLObject} > > However, > > Import["http://www.ncbi.nlm.nih.gov/protein/CAA76847.1","Data";]; > > only gives what looks like a load of rubbish, and there is NO SEQUENCE > > 3. Trying in FASTA format (which is supported by Mathematica) > > Import["http://www.ncbi.nlm.nih.gov/protein/3336842?report=fasta > ","Elements"] > > gives > > {Data,FullData,Hyperlinks,Images,ImageURLs,Plaintext,Source,Title,XMLObject} > > but > > Import["http://www.ncbi.nlm.nih.gov/protein/3336842?report=fasta","Data";] > > also gives only rubbish. > > (Changing the Element to FullData or Plaintext has no effect) > > > 4. NO SUCH PROBLEMS OCCUR with Uniprot (Swiss-Prot). > > Import["http://www.uniprot.org/uniprot/P02769","Elements";] > > Import["http://www.uniprot.org/uniprot/P02769","Data";] > > (Note that the sequence is now imported) > > Or, BEST, using the FASTA format and importing from this site > > Flatten@Characters@StringReplace[Import[" > http://www.uniprot.org/uniprot/P02769.fasta";, "Plaintext"] , Whitespace-> > ""]//Short > > giving > > {M,K,W,V,T,F,I,S,<<592>>,S,T,Q,T,A,L,A} > > which is where I'd like to get to. > > > So my question is the following: What is so unusual about the PubMed site, > and what am I doing wrong in the approach I am taking? It would > be a great advantage to me to be able to import from PubMed in the manner > shown above for Uniport. > > > Thanks for your help > > Tom Dowling