.\" Man page generated from reStructuredText. . .TH "OBICOUNT" "1" "Jan 28, 2019" " 1.02 12" "OBITools" .SH NAME obicount \- description of obicount . .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\%obicount\fP counts the number of sequence records and/or the sum of the \fBcount\fP attributes. .sp \fIExample:\fP .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obicount seq.fasta .ft P .fi .UNINDENT .UNINDENT .sp Prints the number of sequence records contained in the \fBseq.fasta\fP file and the sum of their \fBcount\fP attributes. .UNINDENT .UNINDENT .SH OBICOUNT SPECIFIC OPTIONS .INDENT 0.0 .TP .B \-a, \-\-all .INDENT 7.0 .INDENT 3.5 Prints only the sum of \fBcount\fP attributes. If a sequence has no \fIcount\fP attribute, its default count is 1. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obicount \-a seq.fasta .ft P .fi .UNINDENT .UNINDENT .UNINDENT .UNINDENT .sp For all sequence records contained in the \fBseq.fasta\fP file, prints only the sum of \fBcount\fP attributes. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-s, \-\-sequence .INDENT 7.0 .INDENT 3.5 Prints only the number of sequence records. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obicount \-s seq.fasta .ft P .fi .UNINDENT .UNINDENT .sp Prints only the number of sequence records contained in the \fBseq.fasta\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 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 OBICOUNT ADDED 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. .