.\" Man page generated from reStructuredText. . .TH "OBICLEAN" "1" "Jul 27, 2019" " 1.02 13" "OBITools" .SH NAME obiclean \- description of obiclean . .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 \fI\%obiclean\fP is a command that classifies sequence records either as \fBhead\fP, \fBinternal\fP or \fBsingleton\fP\&. .INDENT 0.0 .TP .B For that purpose, two pieces of information are used: .INDENT 7.0 .IP \(bu 2 sequence record counts .IP \(bu 2 sequence similarities .UNINDENT .TP .B \fIS1\fP a sequence record is considered as a variant of \fIS2\fP another sequence record if and only if: .INDENT 7.0 .IP \(bu 2 \fBcount\fP of \fIS1\fP divided by \fBcount\fP of \fIS2\fP is lesser than the ratio \fIR\fP\&. \fIR\fP default value is set to 1, and can be adjusted between 0 and 1 with the \fB\-r\fP option. .IP \(bu 2 both sequences are \fIrelated\fP to one another (they can align with some differences, the maximum number of differences can be specified by the \fB\-d\fP option). .UNINDENT .TP .B Considering \fIS\fP a sequence record, the following properties hold for \fIS\fP tagged as: .INDENT 7.0 .IP \(bu 2 .INDENT 2.0 .TP .B \fBhead\fP: .INDENT 7.0 .IP \(bu 2 there exists \fBat least one\fP sequence record in the dataset that is a variant of \fIS\fP .IP \(bu 2 there exists \fBno\fP sequence record in the dataset such that \fIS\fP is a variant of this sequence record .UNINDENT .UNINDENT .IP \(bu 2 .INDENT 2.0 .TP .B \fBinternal\fP: .INDENT 7.0 .IP \(bu 2 there exists \fBat least one\fP sequence record in the dataset such that \fIS\fP is a variant of this sequence record .UNINDENT .UNINDENT .IP \(bu 2 .INDENT 2.0 .TP .B \fBsingleton\fP: .INDENT 7.0 .IP \(bu 2 there exists \fBno\fP sequence record in the dataset that is a variant of \fIS\fP .IP \(bu 2 there exists \fBno\fP sequence record in the dataset such that \fIS\fP is a variant of this sequence record .UNINDENT .UNINDENT .UNINDENT .UNINDENT .sp By default, tagging is done once for the whole dataset, but it can also be done sample by sample by specifying the \fB\-s\fP option. In such a case, the counts are extracted from the sample information. .sp Finally, each sequence record is annotated with three new attributes \fBhead\fP, \fBinternal\fP and \fBsingleton\fP\&. The attribute values are the numbers of samples in which the sequence record has been classified in this manner. .SH OBICLEAN SPECIFIC OPTIONS .INDENT 0.0 .TP .B \-d , \-\-distance= Maximum numbers of differences between two variant sequences (default: 1). .UNINDENT .INDENT 0.0 .TP .B \-s , \-\-sample= Attribute containing sample descriptions. .UNINDENT .INDENT 0.0 .TP .B \-r , \-\-ratio= Threshold ratio between counts (rare/abundant counts) of two sequence records so that the less abundant one is a variant of the more abundant (default: 1, i.e. all less abundant sequences are variants). .UNINDENT .INDENT 0.0 .TP .B \-C, \-\-cluster Switch \fI\%obiclean\fP into its clustering mode. This adds information to each sequence about the true. .UNINDENT .INDENT 0.0 .TP .B \-H, \-\-head Select only sequences with the head status in a least one sample. .UNINDENT .INDENT 0.0 .TP .B \-g, \-\-graph Creates a file containing the set of DAG used by the obiclean clustering algorithm. The graph file follows the \fIdot\fP format .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 OPTIONS TO SPECIFY OUTPUT FORMAT .SS Standard output format .INDENT 0.0 .TP .B \-\-fasta\-output Output sequences in \fBOBITools\fP fasta format .UNINDENT .INDENT 0.0 .TP .B \-\-fastq\-output Output sequences in Sanger fastq format .UNINDENT .SS Generating an ecoPCR database .INDENT 0.0 .TP .B \-\-ecopcrdb\-output= Creates an ecoPCR database from sequence records results .UNINDENT .SS Miscellaneous option .INDENT 0.0 .TP .B \-\-uppercase Print sequences in upper case (default is lower case) .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 OBICLEAN USED SEQUENCE ATTRIBUTES .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .INDENT 2.0 .IP \(bu 2 count .UNINDENT .INDENT 2.0 .UNINDENT .INDENT 2.0 .UNINDENT .UNINDENT .UNINDENT .UNINDENT .SH OBICLEAN ADDED SEQUENCE ATTRIBUTES .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .INDENT 2.0 .IP \(bu 2 obiclean_cluster .IP \(bu 2 obiclean_count .IP \(bu 2 obiclean_head .UNINDENT .INDENT 2.0 .IP \(bu 2 obiclean_headcount .IP \(bu 2 obiclean_internalcount .IP \(bu 2 obiclean_samplecount .UNINDENT .INDENT 2.0 .IP \(bu 2 obiclean_singletoncount .IP \(bu 2 obiclean_status .UNINDENT .UNINDENT .UNINDENT .UNINDENT .SH AUTHOR The OBITools Development Team - LECA .SH COPYRIGHT 2019 - 2015, OBITool Development Team .\" Generated by docutils manpage writer. .