#!/bin/csh -f
#(ie run the cshell on this but don't read the .cshrc)

echo version = 1.09 of wgetac 2011 Jun 02
# 2011 Jun 02, 1.09: update link to source of wget
# 2007 Nov 05, 1.08: use rettype=gbwithparts
# 1.07, 2003 July 17: upgrade successful!  cleanup
# 1.06, 2003 July 17: upgrade to new pubmed tools
# 1.05, 2003 July 16: upgrade to new pubmed tools (broken)
# 1.02, 2001: &tool=yourname
# origin 1999May03.16:03:54

if ($#argv != 1) then
   echo 'usage: wgetac [accession number]'
   echo 'This program uses wget to grab a GenBank sequence file.'
   echo 'Wget grabs web pages or files.  It is available from:'
   echo "http://www.gnu.org/software/wget/"

cat << EOF

This program depends on web tools at the National Libarary
of Medicine which give entries from GenBank.  From time to time
they change and break this script.

2003 July 17 Reference for the method:
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html

Notification that the extraction method changed:

http://www.nlm.nih.gov/pubs/techbull/ma03/ma03_technote.html#eutil
PubMedŽ to Complete Transition to E-Utilities
    and Manually Constructed URLs

    April 03, 2003 [posted] 

        In July 2002, NCBI announced the availability of new
        programming for the Entrez Utilities (E-Utilities) and informed
        utility users that they should convert URLs to the new format by
        the end of 2002. 

        NCBI will phase out the old utilities completely in June 2003. This
        may affect customers of some products such as EndNoteŽ,
        ProCiteŽ, and Reference ManagerŽ. Please contact user support
        for your respective product if you have questions. Questions
        concerning the use of E-Utilities can be sent to:
        eutilities@ncbi.nlm.nih.gov. 

        If you have manually created links to PubMed that contain the
        string: /htbin-post/, these should be changed to follow the
        specifications provided on the page, Linking to PubMed and other
        Entrez Databases. These changes must be in place prior to June
        2003. 

Entrez Utilities (E-Utilities) 
http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html

Linking to PubMed and other Entrez Databases.
http://www.ncbi.nlm.nih.gov/entrez/query/static/linking.html

Retrieve 
Use Retrieve to search using unique identifiers (UIDs). UIDs include the PubMed
identifier (PMID), MEDLINE identifier (UI), and the molecular biology database
identifier (GI).  Accession numbers are not UIDs and cannot be retrieved via
cmd=Retrieve. Use cmd=Search to search by accession number. 

----
Change on 2007 Nov 05:
By using rettype=gbwithparts, the sequence is always given.
Reference:
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetchseq_help.html#rettypeparam

EOF

   exit # end of documentation

endif

echo using wget to obtain GenBank entry $1

set uid = $1
set query1 = $uid
# set request = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=$uid&rettype=gb"
set request = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=$uid&rettype=gbwithparts"

wget -O $query1 "$request"

# for testing:
#head $query1
#tail $query1