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https://github.com/tiagofilipe12/mash_wrapper
This script runs MASH given a set of reads against specified references.
https://github.com/tiagofilipe12/mash_wrapper
mash patlas plasmid
Last synced: about 2 months ago
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This script runs MASH given a set of reads against specified references.
- Host: GitHub
- URL: https://github.com/tiagofilipe12/mash_wrapper
- Owner: tiagofilipe12
- License: gpl-3.0
- Created: 2017-01-26T16:46:52.000Z (almost 8 years ago)
- Default Branch: master
- Last Pushed: 2018-09-08T16:44:02.000Z (over 6 years ago)
- Last Synced: 2024-10-20T12:25:12.159Z (2 months ago)
- Topics: mash, patlas, plasmid
- Language: Python
- Homepage:
- Size: 54.7 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# mash_wrapper.py
## About
mash_wrapper.py is a script that is intended to allow users to use mash. It provides options to run mash dist
as well as mash screen with different purposes. While `mash dist` is
used to calculate the similarities of any sequence with all the sequences in the (msh) database, `mash screen` is used to check if any of those sequences in database (in the msh file)
might be present in the provided reads. So, basically, this script features
two different ways to check the presence of query sequences both in sequences (Fasta)
and in reads (FastQ).
## Installation
* Download [mash 2.0.0](https://github.com/marbl/Mash/releases/tag/v2.0)
### Using pipy
* `pip3 install mash-wrapper`
### Using git release
* Download [release 1.0.4 - popcorns & unicorns](https://github.com/tiagofilipe12/mash_wrapper/releases/tag/v1.0.5)
* `pip3 install -r requirements.txt`
**Note:** Please check this [Troubleshooting](#troubleshooting), since there
seems to exist an issue with mash screen and msh files generated in other
machines.
## How to run
### Assembly or fasta comparison
`mash_wrapper.py -rs -a -t -j -o
`
### Mash screen for read samples
`mash_wrapper.py -rs -r -o -t
-j -ms -w`
#### Troubleshooting
If for some reason the above command for Mash screen mode doesn't work.
Download [reference fasta file](https://github.com/tiagofilipe12/mash_wrapper/releases/download/v1.0.4/reference.fasta).
And run the following command:
`mash_wrapper.py -rf reference.fasta -r -o -t -j -ms`
### Options:
```
optional arguments:
-h, --help show this help message and exit
-i INPUTFILE [INPUTFILE ...], --input_references INPUTFILE [INPUTFILE ...]
Provide the input fasta files to parse. Not required
for multiple comparisons between assemblies.
-rs REF_SKETCH, --reference_sketch REF_SKETCH
If you have a reference sketch for references provide
it with this option.
-rf REF_FASTA, --reference_fasta REF_FASTA
If you have a reference fasta provide it with this
option.
-r READS [READS ...], --reads READS [READS ...]
Provide the input read files to parse. Usually fastq 1
or 2 files. This option is mutually with "-f".
-f SEQUENCES [SEQUENCES ...], --sequences SEQUENCES [SEQUENCES ...]
Provide the input sequence files to parse. Usually
fasta files. This option is mutually exclusive with
"-r".
-o OUTPUT_TAG, --output OUTPUT_TAG
Provide an output tag
-t THREADS, --threads THREADS
Provide the number of threads to be used. Default: 1
-no_rm, --no-remove Specify if you do not want to remove the output
concatenated fasta.
-j, --json If you desire to export a json file with all
significant entries use this options.
-m, --mashix Perform a matrix of all mash distance, taking all
files.
MASH related options:
-k KMER_SIZE, --kmers KMER_SIZE
Provide the number of k-mers to be provided to mash
sketch. Default: 21
-p PVALUE, --pvalue PVALUE
Provide the p-value to consider a distance
significant. Default: 0.05.
-md MASHDISTANCE, --mashdist MASHDISTANCE
Provide the maximum mash distance to be parsed to the
matrix. Default: 0.1.
-ms, --mashscreen Runs mash screen. This will prevent mash dist to run.
-w, --winner_takes_it_all
Uses the winner takes it all function to remove
redundancy from mash screen results. NOTE: DO NOT USE
FOR PLASMID ID!
-id MIN_IDENTITY, --min_identity MIN_IDENTITY
Provide the minimum identity for mash screen run.
Default is 0, reporting all values
```
---
#### Outputs:
* A **text** file with MASH distance outputs as well as .msh files for each input read file.
* A **html** file with a bar plot graphical visualization, with each input read file as a series of data.
* A **json** file with keys as accession numbers and values as the results from mash.