.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.6.
.TH NCBI_SEARCH "1" "August 2018" "ncbi_search 20170919" "User Commands"
.SH NAME
ncbi_search \- visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences
.SH DESCRIPTION
.SS "USAGE:"
.IP
ncbi_search \fB\-q\fR STRING \fB\-o\fR FILE \fB\-d\fR STRING \fB\-r\fR STRING [Options]
.SS "DESCRIPTION:"
.IP
Uses NCBI's eSearch to download collections of sequences.
.SS "REQUIRED ARGUMENTS:"
.HP
\fB\-q\fR, \fB\-\-query\fR [STRING]
.IP
Raw query text.
.HP
\fB\-o\fR, \fB\-\-output\fR [FILE]
.IP
Output file to create. If the split option is given, this should be a
directory, where the returned records will be written. If the directory
does not exist it will be created.
.HP
\fB\-d\fR, \fB\-\-database\fR [STRING]
.IP
Name of the NCBI database to search, such as 'nucleotide', 'protein',
or 'gene'.
.HP
\fB\-r\fR, \fB\-\-return_type\fR [STRING]
.IP
The type of information requested. For sequences 'fasta' is often used.
The accepted formats vary depending on the database being queried.
.HP
\fB\-s\fR, \fB\-\-split\fR
.IP
Return each record as a separate file where the file name will will be
the accesssion id of the record. This option only works if the
return_type is 'gb' or 'gbwithparts'.
.HP
\fB\-m\fR, \fB\-\-max_records\fR [INTEGER]
.IP
The maximum number of records to return (default is to return all matches
satisfying the query).
.HP
\fB\-v\fR, \fB\-\-verbose\fR
.IP
Provide progress messages.
.HP
\fB\-h\fR, \fB\-\-help\fR
.IP
Show this message.
.SS "EXAMPLE:"
.IP
ncbi_search \fB\-q\fR 'dysphagia AND homo sapiens[ORGN]' \e
.HP
\fB\-o\fR results.txt \fB\-d\fR pubmed \fB\-r\fR uilist \fB\-m\fR 100
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.