/*
From gilbertd@bio.indiana.edu Wed Mar 18 01:22:09 EST 1998
Article: 982 of bionet.molbio.genbank
Path: news.indiana.edu!not-for-mail
From: gilbertd@bio.indiana.edu (Don Gilbert)
Newsgroups: bionet.molbio.genbank
Subject: Re: Cross-referencing protein/nucleotide sequences
Date: 18 Mar 1998 06:00:27 GMT
Organization: Biology, Indiana University - Bloomington
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The Perl scripts that Bill Pearson gave are a good example
of how biologists can use programs to automate data analysis.
I think learning a programming language is a useful
skill for most students in biology, certainly those dealing with
biosequence analysis.  My suggestion is to start with Java
as a first language. Java provides a very rich set of standard methods
(graphic interfaces, standard network functions, database connectivity),
is easy to learn, and can be used for projects small and large,
and there are a very large number of Java resources (people,
software libraries) out there.

See below for a rough Java equivalent of the Perl script to fetch
sequences from Entrez.  It requires nothing beyond a standard, free
java compiler and standard java libraries (version 1.1).

B.F. Francis Ouellette noted:
| It makes good use of the bandwith between your site and that of NCBI in
| setting up a session where the whole request of multiple records is
| transfered as one file, as opposed to a transfer for each accession/gi
| back and forth that a "foreach" loop would create.

Francis,

I tried programming an http post request to your batch server,
but couldn't get past a Proxy error response (it worked on an echo server).  
Are there any instructions around for programmatic access to this?
  http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/nph-batch/

Anyway, the attached java example does batch the requests by
default, using your Entrez/query server. (&uid=a,b,c,...)

-- Don

--------------------- cut -----------------*/
// FetchFromEntrez.java
// a simple example of a biocomputing network tool written in java
// d.gilbert, mar'98
// to compile:  javac FetchFromEntrez.java
// test run  :  java FetchFromEntrez  - dna gb_U30153 gb_M81833 gb_L13173
// test run  :  java FetchFromEntrez  - prot gi_304809 gi_2286196 
   

import java.io.*;
import java.net.*;
import java.util.*;

public class FetchFromEntrez
{
  static boolean batch= true;   
  public static String entrezUrl=
    "http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=6";
  public static String usage=
    "This java program extracts dna or protein sequences using gid numbers.\n"+
    "from a perl script by Bill Pearson, converted to java by d. gilbert\n\n"+
    "Usage:  java FetchFromEntrez [options] gid gid gid ...\n"+
    "options:\n"+
    " dna|protein     - choose dna or protein output\n"+
    " fasta|genbank   - sequence format\n"+
    " html|text       - html or plain text\n"+
    " -               - write to standard output\n"+
    " output=somefile - output filename\n"+
    " single|batch    - do single or batch request\n";
    
  public static void main(String[] args) 
  {
    if (args.length==0) System.out.println(usage);
    else {
      boolean html= false;
      String db= "n", form= "f",  outname= "entrez_fetch";
      for (int i=0 ; i<args.length; i++) {
        if (args[i].startsWith("-")) { outname= "-"; args[i]= null; }
        else if (args[i].startsWith("output=")) { outname= args[i].substring(7); args[i]= null; }
        else if (args[i].startsWith("dna")) { db= "n"; args[i]= null; }
        else if (args[i].startsWith("prot")) { db= "p"; args[i]= null; }
        else if (args[i].startsWith("fasta")) { form= "f"; args[i]= null; }
        else if (args[i].startsWith("genbank")) { form= "g"; args[i]= null; }
        else if (args[i].startsWith("html")) { html= true; args[i]= null; }
        else if (args[i].startsWith("text")) { html= false; args[i]= null; }
        else if (args[i].startsWith("batch")) { batch= true; args[i]= null; }
        else if (args[i].startsWith("single")) { batch= false; args[i]= null; }
        }
      if (html) outname += ".html";
      singleEntrez(args, outname, html, db, form);
      }
  }

  static PrintStream openout(String outname) 
  {
    if (outname.startsWith("-")) return System.out;
    else {
      try { return new PrintStream( new FileOutputStream( outname, true)); }  
      catch (IOException e) { 
        System.err.println("Can't write to "+outname+", err=" + e.getMessage()); 
        System.exit(1); return null;
        }
      }
  }
  
  static void singleEntrez(String[] args, String outname, boolean html, String db, String form)
  {
    String url= entrezUrl + (html ? "" : "&html=no") + "&db=" + db + "&Dopt=" + form + "&uid=";
    String startKey= null;
    if (!html) { startKey= (form.equals("f") ? ">" : "LOCUS"); }
    if (batch) {
      String gids= "";
      for (int i=0; i<args.length; i++) {
        if (args[i]==null) continue;
        gids += args[i].replace('_','|') + ",";
        }
      callEntrez( url, gids, openout(outname), startKey);    
      }
    else for (int i=0; i<args.length; i++) {
      if (args[i]==null) continue;
      String gid= args[i].replace('_','|');    
      outname= args[i].toLowerCase();
      callEntrez( url, gid, openout(outname), startKey);    
      }
  }
    
  static void callEntrez(String url, String gid, PrintStream pr, String startKey)
  {
    boolean haveStart= (startKey == null);
    try {
      DataInputStream din= new DataInputStream(new URL(url + gid).openStream());
      while (true) { 
        String s= din.readLine();
        if (s==null) break;
        else if (s.startsWith("ERROR") || s.startsWith("*** No Documents Found")) {
          System.err.println("ERROR - "+gid+" not found: " + s); 
          break; 
          }
        else if (startKey!=null && s.startsWith(startKey)) haveStart= true;
        if (haveStart) pr.println(s);
        } 
      pr.close();
      }
    catch (Exception e) { System.err.println("Error reading from "+url + gid); }
  }

}