|
0
|
1 pMLST
|
|
|
2 ===================
|
|
|
3
|
|
|
4 Plasmid Multi-Locus Sequence Typing
|
|
|
5
|
|
|
6
|
|
|
7 Documentation
|
|
|
8 =============
|
|
|
9
|
|
|
10 The pMLST service contains one python script *pmlst.py* which is the script of the latest
|
|
|
11 version of the pMLST service. The method enables investigators to determine the ST based on WGS data.
|
|
|
12
|
|
|
13 ## Content of the repository
|
|
|
14 1. pmlst.py - the program
|
|
|
15 2. README.md
|
|
|
16 3. Dockerfile - dockerfile for building the pmlst docker container
|
|
|
17 4. test.fsa - test fasta file
|
|
|
18
|
|
|
19
|
|
|
20 ## Installation
|
|
|
21
|
|
|
22 Setting up pMLST program
|
|
|
23 ```bash
|
|
|
24 # Go to wanted location for pmlst
|
|
|
25 cd /path/to/some/dir
|
|
|
26 # Clone and enter the pmlst directory
|
|
|
27 git clone https://bitbucket.org/genomicepidemiology/pmlst.git
|
|
|
28 cd pmlst
|
|
|
29 ```
|
|
|
30
|
|
|
31 Build Docker container
|
|
|
32 ```bash
|
|
|
33 # Build container
|
|
|
34 docker build -t pmlst .
|
|
|
35 ```
|
|
|
36
|
|
|
37 #Download and install pMLST database
|
|
|
38 ```bash
|
|
|
39 # Go to the directory where you want to store the pmlst database
|
|
|
40 cd /path/to/some/dir
|
|
|
41 # Clone database from git repository (develop branch)
|
|
|
42 git clone https://bitbucket.org/genomicepidemiology/pmlst_db.git
|
|
|
43 cd pmlst_db
|
|
|
44 pMLST_DB=$(pwd)
|
|
|
45 # Install pMLST database with executable kma_index program
|
|
|
46 python3 INSTALL.py kma_index
|
|
|
47 ```
|
|
|
48
|
|
|
49 If kma_index has not bin install please install kma_index from the kma repository:
|
|
|
50 https://bitbucket.org/genomicepidemiology/kma
|
|
|
51
|
|
|
52 ## Dependencies
|
|
|
53 In order to run the program without using docker, Python 3.5 (or newer) should be installed along with the following versions of the modules (or newer).
|
|
|
54
|
|
|
55 #### Modules
|
|
|
56 - cgecore 1.5.5
|
|
|
57 - tabulate 0.7.7
|
|
|
58
|
|
|
59 Modules can be installed using the following command. Here, the installation of the module cgecore is used as an example:
|
|
|
60 ```bash
|
|
|
61 pip3 install cgecore
|
|
|
62 ```
|
|
|
63 #### KMA and BLAST
|
|
|
64 Additionally KMA and BLAST version 2.8.1 or newer should be installed.
|
|
|
65 The newest versions of KMA and BLAST can be installed from here:
|
|
|
66 ```url
|
|
|
67 https://bitbucket.org/genomicepidemiology/kma
|
|
|
68 ```
|
|
|
69
|
|
|
70 ```url
|
|
|
71 ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
|
|
|
72 ```
|
|
|
73
|
|
|
74 ## Usage
|
|
|
75
|
|
|
76 The program can be invoked with the -h option to get help and more information of the service.
|
|
|
77 Run Docker container
|
|
|
78
|
|
|
79
|
|
|
80 ```bash
|
|
|
81 # Run pmlst container
|
|
|
82 docker run --rm -it \
|
|
|
83 -v $pMLST_DB:/database \
|
|
|
84 -v $(pwd):/workdir \
|
|
|
85 pmlst -i [INPUTFILE] -o . -s [SCHEME] [-x] [-mp] [-p] [-t]
|
|
|
86 ```
|
|
|
87
|
|
|
88 When running the docker file you have to mount 2 directory:
|
|
|
89 1. pmlst_db (pMLST database) downloaded from bitbucket
|
|
|
90 2. An output/input folder from where the input file can be reached and an output files can be saved.
|
|
|
91 Here we mount the current working directory (using $pwd) and use this as the output directory,
|
|
|
92 the input file should be reachable from this directory as well.
|
|
|
93
|
|
|
94 ` -i INPUTFILE input file (fasta or fastq) relative to pwd `
|
|
|
95
|
|
|
96 ` -s SCHEME pMLST scheme to be used, details are in config file `
|
|
|
97
|
|
|
98 ` -o OUTDIR outpur directory relative to pwd `
|
|
|
99
|
|
|
100 ` -x extended output. Will create an extented output `
|
|
|
101
|
|
|
102 ` -mp METHOD_PATH Path to executable of the method to be used (kma or blast)`
|
|
|
103
|
|
|
104 ` -p DATABASE Path to database directory `
|
|
|
105
|
|
|
106 ` -t TMP_DIR Temporary directory for storage of results from external software. `
|
|
|
107
|
|
|
108
|
|
|
109 ## Web-server
|
|
|
110
|
|
|
111 A webserver implementing the methods is available at the [CGE website](http://www.genomicepidemiology.org/) and can be found here:
|
|
|
112 https://cge.cbs.dtu.dk/services/pMLST/
|
|
|
113
|
|
|
114 Citation
|
|
|
115 =======
|
|
|
116
|
|
|
117 When using the method please cite:
|
|
|
118
|
|
|
119 PlasmidFinder and pMLST: in silico detection and typing of plasmids.
|
|
|
120 Carattoli A, Zankari E, Garcia-Fernandez A, Volby Larsen M, Lund O, Villa L, Aarestrup FM, Hasman H.
|
|
|
121 Antimicrob. Agents Chemother. 2014. April 28th.
|
|
|
122 [Epub ahead of print]
|
|
|
123
|
|
|
124 References
|
|
|
125 =======
|
|
|
126
|
|
|
127 1. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL. BLAST+: architecture and applications. BMC Bioinformatics 2009; 10:421.
|
|
|
128 2. Clausen PTLC, Aarestrup FM, Lund O. Rapid and precise alignment of raw reads against redundant databases with KMA. BMC Bioinformatics 2018; 19:307.
|
|
|
129
|
|
|
130 License
|
|
|
131 =======
|
|
|
132
|
|
|
133 Copyright (c) 2014, Ole Lund, Technical University of Denmark
|
|
|
134 All rights reserved.
|
|
|
135
|
|
|
136 Licensed under the Apache License, Version 2.0 (the "License");
|
|
|
137 you may not use this file except in compliance with the License.
|
|
|
138 You may obtain a copy of the License at
|
|
|
139
|
|
|
140 http://www.apache.org/licenses/LICENSE-2.0
|
|
|
141
|
|
|
142 Unless required by applicable law or agreed to in writing, software
|
|
|
143 distributed under the License is distributed on an "AS IS" BASIS,
|
|
|
144 WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
|
|
|
145 See the License for the specific language governing permissions and
|
|
|
146 limitations under the License.
|
