MF2ASN           OGMP SEQUENCE UTILITIES           MF2ASN

NAME
    mf2asn - Converts an OGMP masterfile into an ASN.1 record suitable for     
	submission to Genbank. It is updated from the old program mf2asn

SYNOPSIS
    mf2asn masterfile [-S subinfofile] [-M seqtype] [> & outputfile]
    masterfile.asn and masterfile.gbk are created in your masterfile directory

DESCRIPTION
    This program converts a masterfile into an ASN.1 submission
    record and a Genbank flatfile too.
    	
    The masterfile must absolutely be flawless; using the cleanmf(1)
    program is a good start, but mf2asnew is even more strict and may
    report errors that even cleanmf did not check.

    mf2asn works in five stages:
       1) The masterfile is read and a preliminary parsing of the
          annotations is done. Any error causes the program to
          report it and quit.
       2) The user is asked for all the submission information.
       3) NCBI's validator is called, which may report more
          errors (in a very cryptic manner) but will not prevent
          the creation of the ASN.1 dump.
       4) (OPTION) NCBI's asn2ff(1) program is called to create
          the Genbank flatfile from the ASN.1 dump.
OPTIONS
    	
	-S subinfo file
		Use subinfo file instead create new subinfo file
	-M seqtype
		The seqtype can be M or S. When the masterfile contains multiple
		contigs, we can create ASN.1 files as multiple indepentent segments
		if seqtype is M or one compound segment if seqtype is S. But both of
		the two ASN.1 file will be translated into exectly same GenBank
		flatfiles with the function asn2ff from NCBI toolkit. When the
		masterfile contains only one contig, it does not make any different in
		ASN.1 file for different options. By default, the seqtype is M.
	
USER INTERACTION
    You can use your existing subinfo file or create a new subinfo 
    file with the user interface.
    
    The user interface are like this:
 
    *Locus          : [ AMACMG ]
    Accession      : [ U41288 ]
     ( Chose the correspondant letter
      L  ->  TOPOLOGY_LINEAR
      C  ->  TOPOLOGY_CIRCULAR
      T  ->  TOPOLOGY_TANDEM )
   	TOPOLOGY : [L]

    The default values are in the square brackets. You can use it
    by hiting RETURN or type a new one and hiting RETURN.
    Fields that are preceded by an asterisk are mandatory and must
    be filled; other fields may be left blank. Some fields are of
    enumerated types are require a keyword (Ex: field "Topology"
    requires one of "TOPOLOGY_CIRCULAR", "TOPOLOGY_LINEAR" or
    "TOPOLOGY_TANDEM").

FILES
    masterfile.subinfo
        All information supplied by the user (such as submission
        information, references etc) are cached in this file, 

    /share/supported/apps/ogmp/lib/ogmp_qualifiers.lst
        List of qualifiers

    /share/supported/apps/ogmp/lib/genome_name.lst
        Genome information database

    /share/supported/apps/ogmp/lib/gene_names.lst
        Gene information database

    $NCBI/data/gc.prt
        NCBI genetic codes database

AUTHOR
    Liusong Yang
    Organelle Genome Megasequencing Project, Mar. 2003.