bp_classify_hits_kingdom(1p) [debian man page]
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)
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SEQFRAGGLE(1e) EMBOSS Manual for Debian SEQFRAGGLE(1e) NAME
seqfraggle - Removes fragment sequences from DHF files. SYNOPSIS
seqfraggle -dhfinpath dirlist -thresh integer -dhfoutdir outdir seqfraggle -help DESCRIPTION
seqfraggle is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). It is part of the "Protein:3D Structure" command group(s). OPTIONS
Input section -dhfinpath dirlist This option specifies the location of DHF files (domain hits files) or other sequence files (input). A 'domain hits file' contains database hits (sequences) with domain classification information, in FASTA or EMBL formats. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. Alternatively, SEQFRAGGLE will accept sequence or sequence sets in any of the common formats. Default value: ./ Required section -thresh integer This option specifies the percentage of median length for definition of fragments. SEQFRAGGLE first determines the median length of all the sequences in the input file, then discards any hit sequences which are not within a threshold percentage of the median length. The remaining sequences are written to the output file. Default value: 50 Output section -dhfoutdir outdir This option specifies the location of DHF files (domain hits files) (output). A 'domain hits file' contains database hits (sequences) with domain classification information, in FASTA or EMBL formats. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH. Alternatively, SEQFRAGGLE will write output files in any of the common formats. Default value: ./ BUGS
Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031). SEE ALSO
seqfraggle is fully documented via the tfm(1) system. AUTHOR
Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> Wrote the script used to autogenerate this manual page. COPYRIGHT
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself. DOMSEARCH 0.1.0++20100721 08/11/2010 SEQFRAGGLE(1e)