PlasmidCoverage_Sdb.py

For now, this developing branch of this repo provide two versions of the same script:

• PlasmidCoverage_Sdb.py allows users to compile multiple fastas into one or having one multi-fasta file to calculate plasmid coverage.

• ./deprecated/PlasmidCoverage.py maps against only one plasmid sequence. This option is deprecated however you can still use it. Just make sure you install prettytable - pip install prettytable

In both versions, .gb files are also supported. These files will be converted into fasta files in a subdirectory named "fasta" within the directory the user specifies for plasmid.

How to install

• First install bowtie2 (v2.2.9 or higher) and samtools (v.1.3.1 or higher).
• Second, download the latest release of this script (don't forget to download indexes folder)
• Then, pip3 install -r requirements.txt

Example run

PlasmidUNCover.py -idx <path/to/indexes_folder> -r <path/to/reads_folder> -t 1 -o test -c 0.6

Note that each read or pair of reads should be inside its own folder within the path/to/reads_folder/. This allows the user to run multiple samples at once, since PlasmidUNCoverage.py will crawl this directory to search for directories with samples.

For advanced users, you may use PlasmidUNCoverage.py -h for more options.

Dependencies

• plotly - pip install plotly
• termcolor
• bowtie2 (tested for version 2.2.9)
• samtools (tested for version 1.3.1)

You can now simply: pip3 install -r requirements.txt

Important note regarding the parsing of argument -r

You should provide the path to the directory containing the directories with the reads (.fastq files). For instance if you have something like ~/Reads/sample1/example.fastq and ~/Reads/sample2/example2.fastq, you should provide ~/Reads as the argument for -r option.

Options for PlasmidUNCoverage.py:

**'-p'**,**'--plasmid'**, dest='plasmid_dir', required=True, help='Provide the path to the directory containing plasmid fastas.'

**-idx**, **"--bowtie-index"**, dest="bowtie_index", help="Provide the path to bowtie index file"

**'-r'**,**'--read'**, dest='read_dir', required=True, help='Provide the path to the directory containing reads fastas.'

**'-t'**, **'--threads'**, dest='threads', default="1", help="Specify the number of threads to be used by bowtie2."

**'-2'**, **'--pair'**, dest='paired', action='store_true', help='Use this 
option if you have paired end reads. Paired end reads just have to be inside 
the same folder, without any other files inside it. Structure to read files 
should be something like: ./reads/read_folder/<with pairs inside it>.')

**'-k'**, **"--max_align"**, dest="max_align", help="Specify the maximum number of alignments possible for each read. This option changes -k parameter of Bowtie2. By default this script will set -k to the number of fasta files in reference directory (e.g. if you have 3 reference sequences the number of max_align allowed will automatically be set to 3). So, if you have a single multi-fasta -k will be set to 1."

**'-o'**,**'--output'**, dest='output_name', default="plasmid_db_out", help='Specify the output name you wish. There is no need of file extension.')

**'-c'**,**'--cutoff'**, dest='cutoff_number', help='Specify the cutoff for percentage of plasmid coverage that reads must have to be in the output. This should be a number between 0-1.')

- Accessory tools

plasmid_or_not.py

Currently this tool is separated from the main script (PlasmidCoverage_Sdb.py). This script is intended to separate reads from plasmids (or other type of sequences that have a database in fasta format) from reads for mixed libraries of chromosomal + plasmid reads.

Options for plasmid_or_not.py

**'-p'**,**'--plasmid'**, dest='plasmid', nargs='+', required=True, help='Provide the plasmid fastas'

**'-r'**,**'--read'**, dest='reads', nargs='+', required=True, help='Provide the path to the directory containing reads fastas'

**'-t'**, **'--threads'**, dest='threads', default="1", help="Specify the number of threads to be used by bowtie2"

**'-o'**,**'--output'**, dest='output_name', required=True, help='Specify the output name you wish. No need for file extension! Output file will be a fasta.'

**'-unmap'**,**'--unmapped'**, dest='unmapped_reads', action='store_true', help='By default this script attempts to save sequences available in the provided read files. If you want to save the reads that do not belong to plasmids, use this option.'

diffs_json.py

Currently this tool is separated from the main script (PlasmidCoverage_Sdb.py). This script compares two json files with coverage percentage per gi (json files retrieved by PlasmidCoverage_Sdb.py.

Options for diffs_json.py

**-i**,**--input_jsons** - Provide the input json files of interest.

**-c**,**--cutoff** - Provide the cutoff value used for the minimum coverage allowed to be outputed to json files. This value should be equal in both files to compare.