NCBI C Toolkit Cross Reference

C/doc/README.asn2xml

  1 Last updated: Fri, March 16, 2001
  2 File Locator: ftp://ftp.ncbi.nih.gov/toolbox/xml/asn2xml/README.asn2xml
  3 
  4 asn2xml
  5 
  6 Program Description: asn2xml is a utility program designed to read 
  7 sequence data in ASN.1 and output the sequence data as "full XML". For
  8 further description on "full XML", refer to the NCBI Data in XML Doc.
  9 
 10 Binary: ftp://ftp.ncbi.nih.gov/toolbox/xml/asn2xml/
 11 Source: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/ncbi.tar.Z   
 12 NCBI XML DTDs: ftp://ftp.ncbi.nih.gov/toolbox/xml/xmlspecs/
 13 NCBI Data in XML Doc: ftp://ftp.ncbi.nih.gov/toolbox/xml/ncbixml.txt
 14 
 15 BASIC INSTRUCTIONS:
 16 1. Obtain GenBank ASN.1 data file at
 17 ftp://ftp.ncbi.nih.gov/ncbi-asn1/
 18 
 19 /ncbi-asn1/daily/ directory: ASN.1 Cumulative Update: gbcu.aso.gz
 20 /ncbi-asn1/daily-nc/ directory: contains individual files for each day's
 21 new or updated entries since close-of-data for the last GenBank Release,
 22 in ASN.1 format.
 23 
 24 Additional documentation:
 25 /ncbi-asn1/README.asn1
 26 /ncbi-asn1/README.asn1.daily-nc
 27 /ncbi-asn1/README.asn1.daily
 28 
 29 2. Download the appropriate asn2xml binary for your platform
 30 ftp://ftp.ncbi.nih.gov/toolbox/xml/asn2xml/
 31      asn2xml.alphaOSF1.tar.Z      OSF1 V5.1
 32      asn2xml.linux.tar.Z          Intel x86/Linux
 33      asn2xml.sgi.tar.Z            IRIX 6.4/IRIX 6.5 
 34      asn2xml.sgi5.tar.Z           IRIX 5.3
 35      asn2xml.solaris.tar.Z        Sparc/Solaris 2.6/2.7/8
 36      asn2xml.solarisintel.tar.Z   Intel x86/Solaris 2.7/8
 37      asn2xml.win32.exe            Intel x86/Microsoft NT or Windows 95 (32bit)
 38 
 39 3. Running the program. As usual with any NCBI application, providing a
 40 hyphen with no arguments provide a basic help.
 41 
 42 prompt> asn2xml -
 43 
 44 asn2xml 1.0   arguments:
 45 
 46   -i  Filename for asn.1 input [File In]
 47     default = stdin
 48   -e  Input is a Seq-entry [T/F]  Optional
 49     default = F
 50   -b  Input asnfile in binary mode [T/F]  Optional
 51     default = T
 52   -o  Filename for XML output [File Out]  Optional
 53     default = stdout
 54   -l  Log errors to file named: [File Out]  Optional
 55 
 56 Example:
 57 (Efficient method)
 58 
 59 ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily-nc/nc0305.aso.gz
 60 gunzip -c nc0305.aso.gz | asn2xml -l error.log > nc0305.xml
 61 
 62 or
 63 ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily-nc/nc0305.aso.gz
 64 gunzip nc0305.aso.gz
 65 asn2xml -i nc0305.aso -o nc0305.xml2 -l error3.log
 66 
 67 
 68 
 69 ----------------
 70 
 71 Notes:
 72 
 73 1. The uncompressed XML file is about 10 times the size of the compressed
 74 binary ASN.1 file. The uncompressed XML can be extremely big. Note, the
 75 ASN.1 contains more than the GenBank files; it includes other databases
 76 like PDB and RefSeq, gaps of HTG records, and shows the quality scores of
 77 HTG records. For further information, read 
 78 ftp://ftp.ncbi.nih.gov/ncbi-asn1/README.asn1
 79 
 80 
 81 Email any questions not answered in this documentation to:
 82 info@ncbi.nih.gov
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