.\" Man page generated from reStructuredText. . .TH "OBIUNIQ" "1" "Jul 27, 2019" " 1.02 13" "OBITools" .SH NAME obiuniq \- description of obiuniq . .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\%obiuniq\fP command is in some way analog to the standard Unix \fBuniq \-c\fP command. .sp Instead of working text line by text line as the standard Unix tool, the processing is done on sequence records. .sp A sequence record is a complex object composed of an identifier, a set of attributes (\fBkey=value\fP), a definition, and the sequence itself. .sp The \fI\%obiuniq\fP command groups together sequence records. Then, for each group, a sequence record is printed. .sp A group is defined by the sequence and optionally by the values of a set of attributes specified with the \fB\-c\fP option. .sp As the identifier, the set of attributes (\fBkey=value\fP) and the definition of the sequence records that are grouped together may be different, two options (\fB\-m\fP and \fB\-i\fP) allow refining how these parts of the records are reported. .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .IP \(bu 2 By default, only attributes with identical values within a group of sequence records are kept. .IP \(bu 2 A \fBcount\fP attribute is set to the total number of sequence records for each group. .IP \(bu 2 For each attribute specified by the \fB\-m\fP option, a new attribute whose key is prefixed by \fBmerged_\fP is created. These new attributes contain the number of times each value occurs within the group of sequence records. .UNINDENT .UNINDENT .UNINDENT .SH OBIUNIQ AND TAXONOMIC INFORMATION .sp When a taxonomy is loaded (\fB\-d\fP or \fB\-t\fP options), the \fBmerged_taxid\fP attribute is created and records the number of times each \fItaxid\fP has been found in the group (it may be empty if no sequence record has a \fItaxid\fP attribute in the group). In addition, a set of taxonomy\-related attributes are generated for each group having at least one sequence record with a \fItaxid\fP attribute. The \fItaxid\fP attribute of the sequence group is set to the last common ancestor of the \fItaxids\fP of the group. All other taxonomy\-related attributes created (\fBspecies\fP, \fBgenus\fP, \fBfamily\fP, \fBspecies_name\fP, \fBgenus_name\fP, \fBfamily_name\fP, \fBrank\fP, \fBscientific_name\fP) give information on the last common ancestor. .SH OBIUNIQ SPECIFIC OPTIONS .INDENT 0.0 .TP .B \-m , \-\-merge= Attribute to merge. .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obiuniq \-m sample seq1.fasta > seq2.fasta .ft P .fi .UNINDENT .UNINDENT .sp Dereplicates sequences and keeps the value distribution of the \fBsample\fP attribute in the new attribute \fBmerged_sample\fP\&. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-i, \-\-merge\-ids Adds a \fBmerged\fP attribute containing the list of sequence record ids merged within this group. .UNINDENT .INDENT 0.0 .TP .B \-c , \-\-category\-attribute= Adds one attribute to the list of attributes used to define sequence groups (this option can be used several times). .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obiuniq \-c sample seq1.fasta > seq2.fasta .ft P .fi .UNINDENT .UNINDENT .sp Dereplicates sequences within each sample. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-p, \-\-prefix Dereplication is done based on prefix matching: .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .IP 1. 3 The shortest sequence of each group is a prefix of any sequence of its group .IP 2. 3 The shortest sequence of a group is the prefix of only the sequences belonging to its group .UNINDENT .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 OPTIONS TO SPECIFY INPUT FORMAT .SS Restrict the analysis to a sub\-part of the input file .INDENT 0.0 .TP .B \-\-skip The N first sequence records of the file are discarded from the analysis and not reported to the output file .UNINDENT .INDENT 0.0 .TP .B \-\-only Only the N next sequence records of the file are analyzed. The following sequences in the file are neither analyzed, neither reported to the output file. This option can be used conjointly with the \fI–skip\fP option. .UNINDENT .SS Sequence annotated format .INDENT 0.0 .TP .B \-\-genbank Input file is in genbank format. .UNINDENT .INDENT 0.0 .TP .B \-\-embl Input file is in embl format. .UNINDENT .SS fasta related format .INDENT 0.0 .TP .B \-\-fasta Input file is in fasta format (including OBITools fasta extensions). .UNINDENT .SS fastq related format .INDENT 0.0 .TP .B \-\-sanger Input file is in Sanger fastq format (standard fastq used by HiSeq/MiSeq sequencers). .UNINDENT .INDENT 0.0 .TP .B \-\-solexa Input file is in fastq format produced by Solexa (Ga IIx) sequencers. .UNINDENT .SS ecoPCR related format .INDENT 0.0 .TP .B \-\-ecopcr Input file is in ecoPCR format. .UNINDENT .INDENT 0.0 .TP .B \-\-ecopcrdb Input is an ecoPCR database. .UNINDENT .SS Specifying the sequence type .INDENT 0.0 .TP .B \-\-nuc Input file contains nucleic sequences. .UNINDENT .INDENT 0.0 .TP .B \-\-prot Input file contains protein sequences. .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 OBIUNIQ ADDED SEQUENCE ATTRIBUTES .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .INDENT 2.0 .IP \(bu 2 count .IP \(bu 2 merged_* .IP \(bu 2 merged .IP \(bu 2 scientific_name .IP \(bu 2 rank .UNINDENT .INDENT 2.0 .IP \(bu 2 family .IP \(bu 2 family_name .IP \(bu 2 genus .IP \(bu 2 genus_name .UNINDENT .INDENT 2.0 .IP \(bu 2 order .IP \(bu 2 order_name .IP \(bu 2 species .IP \(bu 2 species_name .UNINDENT .UNINDENT .UNINDENT .UNINDENT .SH OBIUNIQ USED SEQUENCE ATTRIBUTE .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .IP \(bu 2 taxid .UNINDENT .UNINDENT .UNINDENT .SH AUTHOR The OBITools Development Team - LECA .SH COPYRIGHT 2019 - 2015, OBITool Development Team .\" Generated by docutils manpage writer. .