.\" Man page generated from reStructuredText. . .TH "OBISTAT" "1" "Jul 27, 2019" " 1.02 13" "OBITools" .SH NAME obistat \- description of obistat . .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 \fBobistats\fP computes basic statistics for attribute values of sequence records. The sequence records can be categorized or not using one or several \fB\-c\fP options. By default, only the number of sequence records and the total count are computed for each category. Additional statistics can be computed for attribute values in each category, like: .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .IP \(bu 2 minimum value (\fB\-m\fP option) .IP \(bu 2 maximum value (\fB\-M\fP option) .IP \(bu 2 mean value (\fB\-a\fP option) .IP \(bu 2 variance (\fB\-v\fP option) .IP \(bu 2 standard deviation (\fB\-s\fP option) .UNINDENT .UNINDENT .UNINDENT .sp The result is a contingency table with the different categories in rows, and the computed statistics in columns. .SH OBISTAT SPECIFIC OPTIONS .INDENT 0.0 .TP .B \-c , \-\-category\-attribute= .INDENT 7.0 .INDENT 3.5 Attribute used to categorize the sequence records. Several \fB\-c\fP options can be combined. .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 > obistat \-c sample \-c seq_length seq.fasta .ft P .fi .UNINDENT .UNINDENT .sp This command prints the number of sequence records and total count for each combination of sample and sequence length. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-m , \-\-min= .INDENT 7.0 .INDENT 3.5 Computes the minimum value of attribute for each category. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obistat \-c sample \-m seq_length seq.fastq .ft P .fi .UNINDENT .UNINDENT .sp This command computes the minimum sequence length observed for each sample. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-M , \-\-max= .INDENT 7.0 .INDENT 3.5 Computes the maximum value of attribute for each category. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obistat \-c sample \-M seq_length seq.fastq .ft P .fi .UNINDENT .UNINDENT .sp This command computes the maximum sequence length observed for each sample. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-a , \-\-mean= .INDENT 7.0 .INDENT 3.5 Computes the mean value of attribute for each category. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obistat \-c sample \-a seq_length seq.fastq .ft P .fi .UNINDENT .UNINDENT .sp This command computes the mean sequence length observed for each sample. .UNINDENT .UNINDENT .INDENT 7.0 .TP .B \-v , \-\-variance= Computes the variance of attribute for each category. .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obistat \-c genus_name \-v reverse_error seq.fastq .ft P .fi .UNINDENT .UNINDENT .sp This command computes the variance of the number of errors observed in the reverse primer for each genus. .UNINDENT .UNINDENT .INDENT 7.0 .TP .B \-s , \-std\-dev= Computes the standard deviation of attribute for each category. .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obistat \-c genus_name \-s reverse_error seq.fastq .ft P .fi .UNINDENT .UNINDENT .sp This command computes the standard deviation of the number of errors observed in the reverse primer for each genus. .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 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 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 OBISTAT 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. .