1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
|
.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
.TH GENBANK_GET_GENOMES_BY_TAXON.PY "1" "July 2021" "genbank_get_genomes_by_taxon.py 0.2.11" "User Commands"
.SH NAME
genbank_get_genomes_by_taxon.py \- genbank get genomes by taxon
.SH DESCRIPTION
usage: genbank_get_genomes_by_taxon.py [\-h] \fB\-o\fR OUTDIRNAME [\-t TAXON] [\-v] [\-f]
.TP
[\-\-noclobber] [\-l LOGFILE]
[\-\-format FORMAT] \fB\-\-email\fR EMAIL
[\-\-retries RETRIES]
[\-\-batchsize BATCHSIZE]
[\-\-timeout TIMEOUT]
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-o\fR OUTDIRNAME, \fB\-\-outdir\fR OUTDIRNAME
Output directory (required)
.TP
\fB\-t\fR TAXON, \fB\-\-taxon\fR TAXON
NCBI taxonomy ID
.TP
\fB\-v\fR, \fB\-\-verbose\fR
Give verbose output
.TP
\fB\-f\fR, \fB\-\-force\fR
Force file overwriting
.TP
\fB\-\-noclobber\fR
Don't nuke existing files
.TP
\fB\-l\fR LOGFILE, \fB\-\-logfile\fR LOGFILE
Logfile location
.TP
\fB\-\-format\fR FORMAT
Output file format [gbk|fasta]
.TP
\fB\-\-email\fR EMAIL
Email associated with NCBI queries (required)
.TP
\fB\-\-retries\fR RETRIES
Number of Entrez retry attempts per request.
.TP
\fB\-\-batchsize\fR BATCHSIZE
Entrez record return batch size
.TP
\fB\-\-timeout\fR TIMEOUT
Timeout for URL connection (s)
.SH AUTHOR
This manpage was written by Nilesh Patra for the Debian distribution and
can be used for any other usage of the program.
|
