.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.15.
.TH NCBI-ACC-DOWNLOAD "1" "June 2020" "ncbi-acc-download 0.2.6" "User Commands"
.SH NAME
ncbi-acc-download \- download genome files from NCBI by accession
.SH SYNOPSIS
.B ncbi\-acc\-download
[\-h] [\-m {nucleotide,protein}] [\-e {none,loads,all}]
.SH DESCRIPTION
Script to download sequences from GenBank/RefSeq
by accession through the NCBI ENTREZ API.
.SH OPTIONS
[\-F {fasta,genbank,featuretable,gff3}] [\-o OUT]
[\-p PREFIX] [\-r] [\-\-url] [\-v]
NCBI\-accession [NCBI\-accession ...]
.SS "positional arguments:"
.IP
NCBI\-accession
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-m\fR {nucleotide,protein}, \fB\-\-molecule\fR {nucleotide,protein}
Molecule type to download. Default: nucleotide
.TP
\fB\-e\fR {none,loads,all}, \fB\-\-extended\-validation\fR {none,loads,all}
Perform extended validation. Possible options are
\&'none' to skip validation, 'loads' to check if the
sequence file loads in Biopython, or 'all' to run all
checks. Default: none
.TP
\fB\-F\fR {fasta,genbank,featuretable,gff3}, \fB\-\-format\fR {fasta,genbank,featuretable,gff3}
File format to download nucleotide sequences in.
Default: genbank
.TP
\fB\-o\fR OUT, \fB\-\-out\fR OUT
Single filename to use for the combined output.
.TP
\fB\-p\fR PREFIX, \fB\-\-prefix\fR PREFIX
Filename prefix to use for output files instead of
using the NCBI ID.
.TP
\fB\-r\fR, \fB\-\-recursive\fR
Recursively get all entries of a WGS entry.
.TP
\fB\-\-url\fR
Instead of downloading the sequences, just print the
URLs to stdout.
.TP
\fB\-v\fR, \fB\-\-verbose\fR
Print a progress indicator.
.SH AUTHOR
 This manpage was written by Andreas Tille for the Debian distribution and
 can be used for any other usage of the program.