.\" Man page generated from reStructuredText. . .TH "OBIEXTRACT" "1" "Jan 28, 2019" " 1.02 12" "OBITools" .SH NAME obiextract \- description of obiextract . .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\%obiextract\fP command extract a subset of samples from a complete dataset. .sp Extracted sample names can be specified or by indicating their names using option on the command line or by indicating a file name containing a sample name per line .sp The count attribute of the sequence and the slot describing distribution of the sample occurrences among samples are modified according to the selected samples. .sp A sequence not present in at least one of the selected samples is not conserved in the output of \fI\%obiextract\fP\&. .SH OBIEXTRACT SPECIFIC OPTIONS .INDENT 0.0 .TP .B \-s , \-\-sample= Attribute containing sample descriptions. By default the attribute name used for describing samples is set to \fBmerged_sample\fP\&. .UNINDENT .INDENT 0.0 .TP .B \-e , \-\-extract= .INDENT 7.0 .INDENT 3.5 Attribute indicating which have to be extracted. Several \fB\-p\fP options can be added for specifying several samples. If you want to extract a large number of samples, please refer to the \fB\-E\fP option described below .sp \fBTIP:\fP .INDENT 0.0 .INDENT 3.5 The \fB\fP can be simply the key of an attribute, or a \fIPython\fP expression similarly to the \fB\-p\fP option of \fBobigrep\fP\&. .UNINDENT .UNINDENT .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obiextract \-e sampleA \-e sampleB allseqs.fasta > samplesAB.fasta .ft P .fi .UNINDENT .UNINDENT .sp This command extracts from the \fBallseqs.fasta\fP file data related to samples \fBA\fP and \fBB\fP\&. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-E , \-\-extract\-list= .INDENT 7.0 .INDENT 3.5 Allows for indicating a file name where a list of sample is stored. The file must be a simple text file with a sample name per line. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obiextract \-E subset.txt allseqs.fasta > subset_samples.fasta .ft P .fi .UNINDENT .UNINDENT .sp This command extracts from the \fBallseqs.fasta\fP file data related to samples listed in the \fBsubset.txt\fP file. .UNINDENT .UNINDENT .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 OBIEXTRACT MODIFIED SEQUENCE ATTRIBUTES .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .IP \(bu 2 count .UNINDENT .UNINDENT .UNINDENT .SH OBIEXTRACT USED SEQUENCE ATTRIBUTE .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .IP \(bu 2 count .UNINDENT .UNINDENT .UNINDENT .SH AUTHOR The OBITools Development Team - LECA .SH COPYRIGHT 2019 - 2015, OBITool Development Team .\" Generated by docutils manpage writer. .