bp_query_entrez_taxa(1p) [debian man page]

BP_QUERY_ENTREZ_TAXA(1p)				User Contributed Perl Documentation				  BP_QUERY_ENTREZ_TAXA(1p)

NAME

       query_entrez_taxa - query Entrez taxonomy database and print out information

USAGE

       query_entrez_taxa "Homo sapiens" "Saccharomyces cerevisiae" Rhizopus Metazoa query_entrez_taxa -gi 28800981 -gi 54301680 -db nucleotide
       query_entrez_taxa -gi 71836523 -db protein

	Provide the genus and species name in quotes, you can also query for
	a non-species node like Family or Order

       Command-line options:
	  -v or --verbose  : print verbose debugging info
	  -gi		   : one or many GI numbers to lookup taxon id for
	  -db		   : the sequence db (nucleotide or protein) the GI is for

	  other arguments are assumed to be species names to lookup in taxonomy db

AUTHOR

       Jason Stajich jason-at-bioperl-dot-org

perl v5.14.2							    2012-03-02						  BP_QUERY_ENTREZ_TAXA(1p)

BP_CLASSIFY_HITS_KINGDOM(1p)				User Contributed Perl Documentation			      BP_CLASSIFY_HITS_KINGDOM(1p)

NAME

       classify_hits_kingdom - classify BLAST hits by taxonomic kingdom

   USAGE
       classify_hits_kingdom [-i tab_file] [-i second_BLAST_file] [-e evalue_cutoff]
			     [-t dir_where_TAXONOMY_files_are] [-g gi2taxid]
			     [-z PATH_TO_zcat] [-v]

   DESCRIPTION
       Will print out the taxonomic distribution (at the kingdom level) for a set of hits against the NR database.  This script assumes you've
       done a search against the protein database, you'll have to make minor changes in the gi_taxid part to point to the gi_taxid_nuc.dump file.

       This expects BLAST files in tabbed -m9 or -m8 format.  Output with -m 8 or use blast2table.pl to convert (or fastam9_to_table.PLS if using
       FASTA).

	 Input values:
	  -t/--taxonomy  directory where the taxonomy .dmp files are (from NCBI)
	  -g/--gi	 Location of gi_taxid_prot.dmp (or gi_taxid_nucl.dmp if
			 the search was against a NT db)
	  -i/--in	 The name of the tab delimited -m8/-m9 output files to
			 process.

	   -e/--evalue	 Provide an E-value cutoff for hits to be considered
	   -z/--zcat	 Path to the 'zcat' executable, can also be 'gunzip -c'
			 if no zcat on your system.
	  Flags
	   -v/--verbose  To turn on verbose messages
	   -h/--help	 Display this helpful information

       This is intended to be useful starting script, but users may want to customize the output and parameters.  Note that I am summarizing the
       kingdoms here and Eukaryota not falling into Metazoa, Viridiplantae, or Fungi gets grouped into the general superkingdom Eukaryota. for
       simplicity.  There are comments in the code directing you to where changes can be made if you wanted to display hits by phylum for example.
       Note that you must wipe out the cache file 'gi2class' that is craeed in your directory after making these changes.

   AUTHOR
       Jason Stajich jason_at_bioperl_dot_org

perl v5.14.2							    2012-03-02					      BP_CLASSIFY_HITS_KINGDOM(1p)