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.TH TRNA2SAP 1 2006-01-11 NCBI "NCBI Tools User's Manual"
.SH NAME
trna2sap \- convert tRNAscan-SE output to an ASN.1 Seq-annot object
.SH SYNOPSIS
.B trna2sap
[\|\fB\-\fP\|]
[\|\fB\-a\fP\|]
[\|\fB\-c\fP\ \fIstr\fP\|]
[\|\fB\-f\fP\ \fIstr\fP\|]
[\|\fB\-i\fP\ \fIfilename\fP\|]
[\|\fB\-j\fP\|]
[\|\fB\-m\fP\ \fIstr\fP\|]
[\|\fB\-n\fP\ \fIstr\fP\|]
[\|\fB\-o\fP\ \fIfilename\fP\|]
[\|\fB\-p\fP\ \fIdir\fP\|]
[\|\fB\-r\fP\ \fIdir\fP\|]
[\|\fB\-s\fP\|]
[\|\fB\-t\fP\ \fIstr\fP\|]
[\|\fB\-u\fP\|]
[\|\fB\-x\fP\ \fIstr\fP\|]
.SH DESCRIPTION
\fBtrna2sap\fP reads a text file produced by tRNAscan-SE and produces
a corresponding ASN.1 Seq-annot in the format understood by other NCBI
tools.
.SH OPTIONS
A summary of options is included below.
.TP
\fB\-\fP
Print usage message
.TP
\fB\-a\fP
Add tRNAscan-SE citation
.TP
\fB\-c\fP\ \fIstr\fP
Comment
.TP
\fB\-f\fP\ \fIstr\fP
Substring Filter
.TP
\fB\-i\fP\ \fIfilename\fP
Single Input file (standard input by default)
.TP
\fB\-j\fP
Just produce a five-column feature table, \(`a la \fBtrna2tbl\fP(1).
.TP
\fB\-m\fP\ \fIstr\fP
ReMark
.TP
\fB\-n\fP\ \fIstr\fP
Annotation Name (normally \(lqtRNA\(rq).
.TP
\fB\-o\fP\ \fIfilename\fP
Single Output file (standard output by default)
.TP
\fB\-p\fP\ \fIdir\fP
Path to files
.TP
\fB\-r\fP\ \fIdir\fP
Path for Results
.TP
\fB\-s\fP
Ignore Pseudo tRNAs
.TP
\fB\-t\fP\ \fIstr\fP
Annotation Title (normally \(lqtRNAscan-SE\(rq).
.TP
\fB\-u\fP
Ignore Undetermined tRNAs
.TP
\fB\-x\fP\ \fIstr\fP
File selection suffix with \fB\-p\fP (\fB.trna\fP by default).
.SH AUTHOR
The National Center for Biotechnology Information.
.SH SEE ALSO
.BR sequin (1),
.BR tbl2asn (1),
.BR trna2tbl (1).
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