MF2SQN           OGMP SEQUENCE UTILITIES           MF2SQN

NAME
    mf2sqn - Converts an OGMP masterfile into an SQN record that can be converted
    by NCBI's SEQUIN tool to the ASN.1 format, which in turn is suitable for 
    submission to Genbank. 

SYNOPSIS
    mf2sqn [-d] [-t] [-g] -a author -m masterfile

    The files masterfile.sqn masterfile.gbf are created in the working directory
    Further, unless present, a masterfile.subInfo file will be created as well
    that contains general information about the submitter and the sequence. 
    This file can be edited as pleases and the mf2sqn run a second time.
        

DESCRIPTION
    This program converts a masterfile into an SQN file.
    	
    The masterfile must absolutely be flawless; using the cleanmf(1)
    program is a good start, but mf2sqn is even more strict and may
    report errors that even cleanmf did not check.

    mf2sqn 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) NCBI's validator is called, which may report more
          errors (in a very cryptic manner) but will not prevent
          the creation of the SQN dump.

SWITCHES and OPTIONS    	
-a author      :  All submitter file need to be in "/share/supported/apps/mf2sqn/"
                  and have following format name "SubmitterName.sbt" (need to respect case).
                  A template can be found in "SubmitterGeneric.sbt" (never remove it, it
                  is used by mfannot online).
                  Each file contain a text ASN.1 Submit-block object.
                  The Submit-block contains contact information (to whom questions
                  on the submission can be addressed) and a submission citation (which lists
                  the authors who get scientific credit for the sequencing).

-m masterfile : Is the masterfile for submission.

-d            : Create GenBank file in output.
-t            : Create Table file in output.
-g            : 'personal' gene_names_file; otherwise, the default gene_names.lst is used


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
    Pierre Rioux, Natacha Beck
    2009-2011.