|
0
|
1 # ECTyper (an easy typer)
|
|
|
2 **ECTyper** wraps a standalone serotyping module.
|
|
|
3 Supports _fasta_ and _fastq_ file formats
|
|
|
4
|
|
|
5 # Dependencies:
|
|
|
6 - python 3.6.3.*
|
|
|
7 - pandas 0.21.0.*
|
|
|
8 - samtools 1.5.*
|
|
|
9 - bowtie2 2.3.0.*
|
|
|
10 - mash 1.1.*
|
|
|
11 - bcftools 1.6.*
|
|
|
12 - biopython 1.69.*
|
|
|
13 - blast 2.2.31 .*
|
|
|
14 - seqtk 1.2.*
|
|
|
15
|
|
|
16 # Installation
|
|
|
17 1. Get `miniconda` if you do not already have `miniconda` or `anaconda`:
|
|
|
18 1. `wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh`
|
|
|
19 1. `bash miniconda.sh -b -p $HOME/miniconda`
|
|
|
20 1. `export PATH="$HOME/miniconda/bin:$PATH"`
|
|
|
21 2. Install ectyper
|
|
|
22 * Directly via `conda`
|
|
|
23 1. `conda install -c anaconda -c bioconda -c ubcsamsung ectyper`
|
|
|
24 * Through `github`
|
|
|
25 1. Install dependencies
|
|
|
26 `conda install pandas samtools bowtie2 mash bcftools biopython nose blast seqtk tqdm python=3.6`
|
|
|
27 1. Download git repository then unzip
|
|
|
28 `wget https://github.com/phac-nml/ecoli_serotyping/archive/master.zip`
|
|
|
29 1. Install ectyper inside unzipped directory
|
|
|
30 `python setup.py install`
|
|
|
31
|
|
|
32 # Basic Usage
|
|
|
33 1. Put all of your fasta/fastq files in one folder (concatenate paired files if you want the result to be considered a single entity)
|
|
|
34 1. `ectyper -i [file path]`
|
|
|
35 1. View the results on the console or in `output/[datatime]/output.csv`
|
|
|
36
|
|
|
37 # Example Usage
|
|
|
38 * `ectyper -i ecoliA.fasta` for a single file
|
|
|
39 * `ectyper -i ecoliA.fasta,ecoliB.fastq,ecoliC.fna` for multiple files
|
|
|
40 * `ectyper -i ecoli_folder` for a folder
|
|
|
41
|
|
|
42 # Advanced Usage
|
|
|
43 ```
|
|
|
44 usage: ectyper [-h] -i INPUT [-d PERCENTIDENTITY] [-l PERCENTLENGTH]
|
|
|
45 [--verify] [-s] [-v] [-o OUTPUT]
|
|
|
46
|
|
|
47 optional arguments:
|
|
|
48 -h, --help show this help message and exit
|
|
|
49 -i INPUT, --input INPUT
|
|
|
50 Location of new file(s). Can be a single file or a
|
|
|
51 directory
|
|
|
52 -d PERCENTIDENTITY, --percentIdentity PERCENTIDENTITY
|
|
|
53 Percentage of identity wanted to use against the
|
|
|
54 database. From 0 to 100, default is 90%.
|
|
|
55 -l PERCENTLENGTH, --percentLength PERCENTLENGTH
|
|
|
56 Percentage of length wanted to use against the
|
|
|
57 database. From 0 to 100, default is 50%.
|
|
|
58 --verify Enable E. Coli. verification
|
|
|
59 -s, --species Enable species identification when non-ecoli genome is
|
|
|
60 found Note: refseq downloading is required when
|
|
|
61 running this option for the first time.
|
|
|
62 -v, --verbose Enable detailed output
|
|
|
63 -o OUTPUT, --output OUTPUT
|
|
|
64 Directory location of output files.
|
|
|
65 ```
|
|
|
66 * The first time species identification is enabled you will need to wait for **ectyper** to download the reference sequence.
|
