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chado-utils

tools to add/extract data from Chado

This package contains several tools that can be used to extract data from Chado database or prepare data before upload. It is a subset above the Chado database schema and libraries.

Chado is a relational database schema that underlies many GMOD installations. It is capable of representing many of the general classes of data frequently encountered in modern biology such as sequence, sequence comparisons, phenotypes, genotypes, ontologies, publications, and phylogeny.

Homepage:
Package version:1.22-4
Architecture:all
Distribution:Debian
Filename:chado-utils_1.22-4_all.deb

/usr/share/man/man1/man1/gmod_add_organism.pl.1p.gz

GMOD_ADD_ORGANISMUser Contributed Perl DocumentGMOD_ADD_ORGANISM(1p)



NAME
       $0 - Adds an entry to the organism table

SYNOPSIS
         % gmod_add_organism.pl [options]

COMMAND-LINE OPTIONS
        --name_only      Check just for a name, and return a 1 if present
        --common_name
        --genus
        --species
        --abbreviation
        --comment
        --dbprofile      Speci
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/usr/share/man/man1/man1/gmod_bulk_load_gff3.pl.1p.gz

GMOD_BULK_LOAD_GFUserpContributed Perl DocumeGMOD_BULK_LOAD_GFF3(1p)



NAME
       $0 - Bulk loads gff3 files into a chado database.

SYNOPSIS
         % $0 [options]
         % cat <gff-file> | $0 [options]

OPTIONS
        --gfffile         The file containing GFF3 (optional, can read
                            from stdin)
        --fastafile       Fasta file to load sequence from
        --or
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/usr/share/man/man1/man1/gmod_bulk_load_pubmed.pl.1p.gz

GMOD_BULK_LOAD_PUUser(Contributed Perl DocuGMOD_BULK_LOAD_PUBMED(1p)



NAME
       gmod_bulk_load_pubmed.pl - stores pubmed entries in the
       database

DESCRIPTION
        Usage: perl gmod_bulk_load_pubmed.pl -H [dbhost] -D [dbname]  [-vt] -i file

       parameters

       -H    hostname for database

       -D    database name

       -i    input file [required]

       -v    verbose output
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/usr/share/man/man1/man1/gmod_chado_properties.pl.1p.gz

GMOD_CHADO_PROPERUser(Contributed Perl DocuGMOD_CHADO_PROPERTIES(1p)



NAME
       $0 - reads or mo
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/usr/share/man/man1/man1/gmod_extract_dbxref_from_gff.pl.1p.gz

GMOD_EXTRACT_DBXRUserRContributed PeGMOD_EXTRACT_DBXREF_FROM_GFF(1p)



NAME
       gmod_extract_dbx
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/usr/share/man/man1/man1/gmod_fasta2gff3.pl.1p.gz

GMOD_FASTA2GFF3(1User Contributed Perl DocumentatGMOD_FASTA2GFF3(1p)



NAME
       $O - Convert FAS
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/usr/share/man/man1/man1/gmod_gff3_preprocessor.pl.1p.gz

GMOD_GFF3_PREPROCUserRContributed Perl DocGMOD_GFF3_PREPROCESSOR(1p)



NAME
       $0 - Prepares a 
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/usr/share/man/man1/man1/gmod_load_cvterms.pl.1p.gz

GMOD_LOAD_CVTERMSUser Contributed Perl DocumentGMOD_LOAD_CVTERMS(1p)



NAME
       load_cvterms.pl 
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