.\" Man page generated from reStructuredText. . .TH "OBITAXONOMY" "1" "Jul 27, 2019" " 1.02 13" "OBITools" .SH NAME obitaxonomy \- description of obitaxonomy . .nr rst2man-indent-level 0 . .de1 rstReportMargin \\$1 \\n[an-margin] level \\n[rst2man-indent-level] level margin: \\n[rst2man-indent\\n[rst2man-indent-level]] - \\n[rst2man-indent0] \\n[rst2man-indent1] \\n[rst2man-indent2] .. .de1 INDENT .\" .rstReportMargin pre: . RS \\$1 . nr rst2man-indent\\n[rst2man-indent-level] \\n[an-margin] . nr rst2man-indent-level +1 .\" .rstReportMargin post: .. .de UNINDENT . RE .\" indent \\n[an-margin] .\" old: \\n[rst2man-indent\\n[rst2man-indent-level]] .nr rst2man-indent-level -1 .\" new: \\n[rst2man-indent\\n[rst2man-indent-level]] .in \\n[rst2man-indent\\n[rst2man-indent-level]]u .. .sp The \fI\%obitaxonomy\fP command can generate an ecoPCR database from a NCBI taxdump (see NCBI ftp site) and allows managing the taxonomic data contained in both types of database. .sp Several types of editing are possible: .sp \fBAdding a taxon to the database\fP .INDENT 0.0 .INDENT 3.5 The new taxon is described by three values: its scientific name, its taxonomic rank, and the \fItaxid\fP of its first ancestor. Done by using the \fB\-a\fP option. .UNINDENT .UNINDENT .sp \fBDeleting a taxon from the database\fP .INDENT 0.0 .INDENT 3.5 Erases a local taxon. Done by using the \fB\-D\fP option and specifying a \fItaxid\fP\&. .UNINDENT .UNINDENT .sp \fBAdding a species to the database\fP .INDENT 0.0 .INDENT 3.5 The genus of the species must already exist in the database. The species will be added under its genus. Done by using the \fB\-s\fP option and specifying a species scientific name. .UNINDENT .UNINDENT .sp \fBAdding a preferred scientific name for a taxon in the database\fP .INDENT 0.0 .INDENT 3.5 Adds a preferred name for a taxon in the taxonomy, by specifying the new favorite name and the \fItaxid\fP of the taxon whose preferred name should be changed. Done by using the \fB\-f\fP option. .UNINDENT .UNINDENT .sp \fBAdding all the taxa from a sequence file in the \(ga\(gaOBITools\(ga\(ga extended :doc:\(gafasta <../fasta>\(ga format to the database\fP .INDENT 0.0 .INDENT 3.5 All the taxon from a file in the \fBOBITools\fP extended fasta format, and eventually their ancestors, are added to the taxonomy database. .sp The header of each sequence record must contain the attribute defined by the \fB\-k\fP option (default key: \fBspecies_name\fP), whose value is the scientific name of the taxon to be added. .sp A taxonomic path for each sequence record can be specified with the \fB\-p\fP option, as the attribute key that contains the taxonomic path of the taxon to be added. .sp A restricting ancestor can be specified with the \fB\-A\fP option, either as a \fItaxid\fP (integer) or a key (string). If it is a \fItaxid\fP, this \fItaxid\fP is the default \fItaxid\fP under which the new taxon is added if none of his ancestors are specified or can be found. If it is a key, \fI\%obitaxonomy\fP looks for the ancestor \fItaxid\fP in the corresponding attribute, and the new taxon is systematically added under this ancestor. By default, the restricting ancestor is the root of the taxonomic tree for all the new taxa. .sp If neither a path nor an ancestor is specified in the header of the sequence record, \fI\%obitaxonomy\fP tries to read the taxon name as a species name and to find the genus in the taxonomic database. If the genus is found, the new taxon is added under it. If not, it is added under the restricting ancestor. .sp It is highly recommended checking what was exactly done by reading the output, since \fI\%obitaxonomy\fP uses \fIad hoc\fP parsing and decision rules. .sp Done by using the \fB\-F\fP option. .UNINDENT .UNINDENT .sp \fBNotes:\fP .INDENT 0.0 .IP \(bu 2 When a taxon is added, a new \fItaxid\fP is assigned to it. The minimum for the new \fItaxids\fP can be specified by the \fB\-m\fP option and is equal to 10000000 by default. .IP \(bu 2 For each modification, a line is printed with details on what was done. .UNINDENT .SH OBITAXONOMY SPECIFIC OPTIONS .INDENT 0.0 .TP .B \-a , \-\-add\-taxon= .INDENT 7.0 .INDENT 3.5 Adds a new taxon to the taxonomy. The new taxon is described by three values separated by colons: its scientific name, its taxonomic rank, and the taxid of its first ancestor. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obitaxonomy \-d my_ecopcr_database \e \-a \(aqGentiana alpina\(aq:\(aqspecies\(aq:49934 .ft P .fi .UNINDENT .UNINDENT .sp Adds a taxon with the scientific name \fIGentiana alpina\fP and the rank \fIspecies\fP under the taxon whose taxid is 49934. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-m <####>, \-\-min\-taxid=<####> .INDENT 7.0 .INDENT 3.5 Minimum \fItaxid\fP for the newly added \fItaxid(s)\fP\&. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obitaxonomy \-d my_ecopcr_database \-m 1000000000 \e \-a \(aqGentiana alpina\(aq:\(aqspecies\(aq:49934 .ft P .fi .UNINDENT .UNINDENT .sp Adds a taxon with the scientific name \fIGentiana alpina\fP and the rank \fIspecies\fP under the taxon whose \fItaxid\fP is 49934, with a \fItaxid\fP greater than or equal to 1000000000. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-D , \-\-delete\-local\-taxon= .INDENT 7.0 .INDENT 3.5 Deletes the local taxon with the \fItaxid\fP from the taxonomic database. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obitaxonomy \-d my_ecopcr_database \-D 10000832 .ft P .fi .UNINDENT .UNINDENT .sp Deletes the local taxon with the taxid 10000832 from the taxonomic database. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-s , \-\-add\-species= .INDENT 7.0 .INDENT 3.5 Adds a new species to the taxonomy. The new species is described by its scientific name. The genus of the species must already exist in the database. The species will be added under its genus. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obitaxonomy \-d my_ecopcr_database \-s \(aqGentiana alpina\(aq .ft P .fi .UNINDENT .UNINDENT .sp Adds the species with the scientific name \fIGentiana alpina\fP under the genus \fIGentiana\fP\&. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-f :, \-\-add\-favorite\-name=: .INDENT 7.0 .INDENT 3.5 Adds a new favorite scientific name to the taxonomy. The new name is described by two values separated by a colon: the new favorite name and the \fItaxid\fP of the taxon. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obitaxonomy \-d my_ecopcr_database \e \-f \(aqGentiana algida\(aq:50748 .ft P .fi .UNINDENT .UNINDENT .sp Adds the favorite scientific name \fIGentiana algida\fP for the \fItaxid\fP 50748 in the taxonomic database. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-F , \-\-file\-name= .INDENT 7.0 .INDENT 3.5 Adds all the taxa from a sequence file in \fBOBITools\fP extended doc:\fIfasta <../fasta>\fP format, and eventually their ancestors to the database (see documentation). Each sequence record must contain the attribute specified by the \fB\-k\fP option. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obitaxonomy \-d my_ecopcr_database \e \-k my_taxon_name_key \-F my_sequences.fasta .ft P .fi .UNINDENT .UNINDENT .sp Adds the taxon of each sequence record from the file \fBmy_sequences.fasta\fP in the taxonomic database, based on the scientific name contained in the \fBmy_taxon_name_key\fP attribute. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-k , \-\-key\-name= Works with the \fB\-F\fP option. Defines the key of the attribute that contains the scientific name of the taxon to be added. See example above. .UNINDENT .INDENT 0.0 .TP .B \-A , \-\-restricting_ancestor= .INDENT 7.0 .INDENT 3.5 Works with the \fB\-F\fP option. Can be a \fItaxid\fP (integer) or a key (string). If it is a \fItaxid\fP, this \fItaxid\fP is the default \fItaxid\fP under which the new taxon is added if none of his ancestors are specified or can be found. If it is a key, \fI\%obitaxonomy\fP looks for the ancestor \fItaxid\fP in the corresponding attribute, and the new taxon is \fIsystematically\fP added under this ancestor. By default, the restricting ancestor is the root of the taxonomic tree for all the new taxa. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obitaxonomy \-d my_ecopcr_database \-a 33090 \e \-k my_taxon_name_key \-F my_sequences.fasta .ft P .fi .UNINDENT .UNINDENT .sp Adds the taxon of each sequence record from the file \fBmy_sequences.fasta\fP in the taxonomic database, based on the scientific name contained in the \fBmy_taxon_name_key\fP attribute. If the genus of the new taxon cannot be found, the new taxon is added under the taxon whose \fItaxid\fP is 33090. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-p , \-\-path= .INDENT 7.0 .INDENT 3.5 Works with the \fB\-F\fP option. Key of the attribute containing the taxonomic paths of the taxa if they are in the headers of the sequence records. The value contained in this attribute must be of the form ‘Fungi, Agaricomycetes, Thelephorales, Thelephoraceae’ with the highest ancestors first and commas between ancestors. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obitaxonomy \-d my_ecopcr_database \-p my_taxonomic_path_key \e \-k my_taxon_name_key \-F my_sequences.fasta .ft P .fi .UNINDENT .UNINDENT .sp Adds the taxon of each sequence record from the file \fBmy_sequences.fasta\fP in the taxonomic database, based on the scientific name contained in the \fBmy_taxon_name_key\fP attribute. Each ancestor contained in the \fBmy_taxonomic_path_key\fP attribute is added if it does not already exist, and the new taxon is added under the latest ancestor of the path. .UNINDENT .UNINDENT .UNINDENT .SH TAXONOMY RELATED OPTIONS .INDENT 0.0 .TP .B \-d , \-\-database= ecoPCR taxonomy Database name .UNINDENT .INDENT 0.0 .TP .B \-t , \-\-taxonomy\-dump= NCBI Taxonomy dump repository name .UNINDENT .SH COMMON OPTIONS .INDENT 0.0 .TP .B \-h, \-\-help Shows this help message and exits. .UNINDENT .INDENT 0.0 .TP .B \-\-DEBUG Sets logging in debug mode. .UNINDENT .SH AUTHOR The OBITools Development Team - LECA .SH COPYRIGHT 2019 - 2015, OBITool Development Team .\" Generated by docutils manpage writer. .