.\" Man page generated from reStructuredText. . .TH "OBICUT" "1" "Jul 27, 2019" " 1.02 13" "OBITools" .SH NAME obicut \- description of obicut . .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\%obicut\fP is a command that trims sequence objects based on two integer values: the \fB\-b\fP option gives the first position of the sequence to be kept, and the \fB\-e\fP option gives the last position to be kept. Both values can be computed using a python expression. .INDENT 0.0 .INDENT 3.5 \fIExample:\fP .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obicut \-b 50 \-e seq_length seq1.fasta > seq2.fasta .ft P .fi .UNINDENT .UNINDENT .sp Keeps only the sequence part from the fiftieth position to the end. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 0.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obicut \-b 50 \-e seq_length\-50 seq1.fasta > seq2.fasta .ft P .fi .UNINDENT .UNINDENT .sp Trims the first and last 50 nucleotides of the sequence object. .UNINDENT .UNINDENT .UNINDENT .UNINDENT .SH OBICUT SPECIFIC OPTIONS .INDENT 0.0 .TP .B \-b , \-\-begin= Integer value (possibly calculated using a python expression) indicating the first position of the sequence to be kept. .UNINDENT .INDENT 0.0 .TP .B \-e , \-\-end= Integer value (possibly calculated using a python expression) indicating the last position of the sequence to be kept. .UNINDENT .SH SEQUENCE RECORD SELECTION OPTIONS .INDENT 0.0 .TP .B \-s , \-\-sequence= .INDENT 7.0 .INDENT 3.5 Regular expression pattern to be tested against the sequence itself. The pattern is case insensitive. .UNINDENT .UNINDENT .sp \fIExamples:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obigrep \-s \(aqGAATTC\(aq seq1.fasta > seq2.fasta .ft P .fi .UNINDENT .UNINDENT .sp Selects only the sequence records that contain an \fIEcoRI\fP restriction site. .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obigrep \-s \(aqA{10,}\(aq seq1.fasta > seq2.fasta .ft P .fi .UNINDENT .UNINDENT .sp Selects only the sequence records that contain a stretch of at least 10 \fBA\fP\&. .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obigrep \-s \(aq^[ACGT]+$\(aq seq1.fasta > seq2.fasta .ft P .fi .UNINDENT .UNINDENT .sp Selects only the sequence records that do not contain ambiguous nucleotides. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-D , \-\-definition= .INDENT 7.0 .INDENT 3.5 Regular expression pattern to be tested against the definition of the sequence record. The pattern is case sensitive. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obigrep \-D \(aq[Cc]hloroplast\(aq seq1.fasta > seq2.fasta .ft P .fi .UNINDENT .UNINDENT .sp Selects only the sequence records whose definition contains \fBchloroplast\fP or \fBChloroplast\fP\&. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-I , \-\-identifier= .INDENT 7.0 .INDENT 3.5 Regular expression pattern to be tested against the identifier of the sequence record. The pattern is case sensitive. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obigrep \-I \(aq^GH\(aq seq1.fasta > seq2.fasta .ft P .fi .UNINDENT .UNINDENT .sp Selects only the sequence records whose identifier begins with \fBGH\fP\&. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-\-id\-list= .INDENT 7.0 .INDENT 3.5 \fB\fP points to a text file containing the list of sequence record identifiers to be selected. The file format consists in a single identifier per line. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obigrep \-\-id\-list=my_id_list.txt seq1.fasta > seq2.fasta .ft P .fi .UNINDENT .UNINDENT .sp Selects only the sequence records whose identifier is present in the \fBmy_id_list.txt\fP file. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-a :, .UNINDENT .INDENT 0.0 .TP .B \-\-attribute=: .INDENT 7.0 .INDENT 3.5 Regular expression pattern matched against the attributes of the sequence record\&. the value of this attribute is of the form : key:regular_pattern. The pattern is case sensitive. Several \fB\-a\fP options can be used on the same command line and in this last case, the selected sequence records will match all constraints. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obigrep \-a \(aqfamily_name:Asteraceae\(aq seq1.fasta > seq2.fasta .ft P .fi .UNINDENT .UNINDENT .sp Selects the sequence records containing an attribute whose key is \fBfamily_name\fP and value is \fBAsteraceae\fP\&. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-A , \-\-has\-attribute= .INDENT 7.0 .INDENT 3.5 Selects sequence records having an attribute whose key = . .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obigrep \-A taxid seq1.fasta > seq2.fasta .ft P .fi .UNINDENT .UNINDENT .sp Selects only the sequence records having a \fItaxid\fP attribute defined. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-p , \-\-predicat= .INDENT 7.0 .INDENT 3.5 Python boolean expression to be evaluated for each sequence record. The attribute keys defined for each sequence record can be used in the expression as variable names. An extra variable named ‘sequence’ refers to the sequence record itself. Several \-p options can be used on the same command line and in this last case, the selected sequence records will match all constraints. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obigrep \-p \(aq(forward_error<2) and (reverse_error<2)\(aq \e seq1.fasta > seq2.fasta .ft P .fi .UNINDENT .UNINDENT .sp Selects only the sequence records whose \fBforward_error\fP and \fBreverse_error\fP attributes have a value smaller than two. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-L <##>, \-\-lmax=<##> .INDENT 7.0 .INDENT 3.5 Keeps sequence records whose sequence length is equal or shorter than \fBlmax\fP\&. .UNINDENT .UNINDENT .sp \fIExample:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obigrep \-L 100 seq1.fasta > seq2.fasta .ft P .fi .UNINDENT .UNINDENT .sp Selects only the sequence records that have a sequence length equal or shorter than 100bp. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-l <##>, \-\-lmin=<##> .INDENT 7.0 .INDENT 3.5 Selects sequence records whose sequence length is equal or longer than \fBlmin\fP\&. .UNINDENT .UNINDENT .sp \fIExamples:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obigrep \-l 100 seq1.fasta > seq2.fasta .ft P .fi .UNINDENT .UNINDENT .sp Selects only the sequence records that have a sequence length equal or longer than 100bp. .UNINDENT .UNINDENT .UNINDENT .INDENT 0.0 .TP .B \-v, \-\-inverse\-match .INDENT 7.0 .INDENT 3.5 Inverts the sequence record selection. .UNINDENT .UNINDENT .sp \fIExamples:\fP .INDENT 7.0 .INDENT 3.5 .INDENT 0.0 .INDENT 3.5 .sp .nf .ft C > obigrep \-v \-l 100 seq1.fasta > seq2.fasta .ft P .fi .UNINDENT .UNINDENT .sp Selects only the sequence records that have a sequence length shorter than 100bp. .UNINDENT .UNINDENT .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 .INDENT 0.0 .TP .B \-\-require\-rank= select sequence with taxid tag containing a parent of rank .UNINDENT .INDENT 0.0 .TP .B \-r , \-\-required= required taxid .UNINDENT .INDENT 0.0 .TP .B \-i , \-\-ignore= ignored taxid .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 AUTHOR The OBITools Development Team - LECA .SH COPYRIGHT 2019 - 2015, OBITool Development Team .\" Generated by docutils manpage writer. .