.\" Man page generated from reStructuredText. . .TH "OBISUBSET" "1" "Jul 27, 2019" " 1.02 13" "OBITools" .SH NAME obisubset \- description of obisubset . .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\%obisubset\fP command extracts a subset of samples from a sequence file after its dereplication using \fBobiuniq\fP program. .SH OBISUBSET SPECIFIC OPTIONS .INDENT 0.0 .TP .B \-s , \-\-sample=, The option \fB\-s\fP allows to specify the tag containing sample descriptions, the default value is set to \fImerged_sample\fP\&. .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 > obisubset \-s merged_sample \-n sample1 seq2.fasta > seq3.fasta .ft P .fi .UNINDENT .UNINDENT .sp After the dereplication of the sequences using the in the new attribute \fBmerged_sample\fP\&. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-o , \-\-other\-tag=, Another tag to clean according to the sample subset .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obisubset \-s merged_sample \-o \-n sample1 seq2.fasta > seq3.fasta .ft P .fi .UNINDENT .UNINDENT .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-l , \-\-sample\-list=, File containing the samples names (one sample id per line). .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obisubset \-s merged_sample \-o \-l ids.txt seq2.fasta > seq3.fasta .ft P .fi .UNINDENT .UNINDENT .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-p , \-\-sample\-pattern=, A regular expression pattern matching the sample ids to extract. .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obisubset \-s merged_sample \-o \-p "negative_.*" seq2.fasta > seq3.fasta .ft P .fi .UNINDENT .UNINDENT .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-n , \-\-sample\-name=, A sample id to extract .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obisubset \-s merged_sample \-o \-n sample1 seq2.fasta > seq3.fasta .ft P .fi .UNINDENT .UNINDENT .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 OBISUBSET MODIFIES SEQUENCE ATTRIBUTES .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .INDENT 2.0 .IP \(bu 2 count .UNINDENT .INDENT 2.0 .IP \(bu 2 merged_* .UNINDENT .INDENT 2.0 .UNINDENT .UNINDENT .UNINDENT .UNINDENT .SH OBISUBSET USED SEQUENCE ATTRIBUTE .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .IP \(bu 2 count .IP \(bu 2 merged_* .UNINDENT .UNINDENT .UNINDENT .SH AUTHOR The OBITools Development Team - LECA .SH COPYRIGHT 2019 - 2015, OBITool Development Team .\" Generated by docutils manpage writer. .