ImGQfinder v2.2.0

A tool that searches G-quadruplexes and i-Motifs with buldges and mismatches.

Updates tracker

You can find the information about what's new in updates and versions of libraries via link.

Installation

1. Clone the repository.
2. Install the requirements. We recommend to create a new conda environment.

Via conda

conda env create -f environment.yml
conda activate imgqfinder_env  [windows]
source activate imgqfinder_env  [linux]

Via pip

pip install -r requirements.txt

Usage

python imgqfinder.py -i data.fasta -o test/,
where data.fasta is a fasta file, which can contain several sequences [REQUIRED],
-o test is a fold, where the output files will be stored [NOT REQUIRED].

At the output folder, by default, you will get the following files:

• %fasta_id%_quadruplets.csv: the full list of quadrupletes;
• %fasta_id%_quadruplexes.csv: the full list of quadruplexes;
• %fasta_id%_groups.csv: the non-redundant list of quadruplexes: without any intersections;
• %fasta_id%_ranges.bed: only start&end coordinates of the grouped quadruplexes in a BED-FORMAT;
• description.txt: the columns description file.

At this repository, you can find the test folder with the input and output example.

! Important !

While grouping, quadruplexes are not merging with the nearest, but the best possible quadruplex is chosen according to the next considerations.
If two quadruplexes intersect we prefer the one that: (the conditions are listed in their priority order)

• has less missmatches and buldges (by default, but you can abort this behavior);
• has less total length (this means the the space between quadruplets is less);
• meets first.

Big Files & Multiprocessing

By default, the output will contain the quadruplex sequences. In case of big fasta sequences, you will need significantly more time and space on the disk. To avoid overconsuming of the resources you can do the following:\

• If you do not need sequences you can turn off this behaviour with the tag --no-sequences.
• Also, you can reduce the time of computations by multiprocessing option. Just type the number of kernels the program may use, like --nthreads 4. Warning: there could be some issues with multiprocessing in Windows systems.
• By default, the program will generate 4 files, containing information about: quadruplets, quadruplexes, groups and ranges. You may request not all the files as output. Just type one or several names with the tag: --output_type 0 3, where 0 - quadruplets, 1 - quadruplexes, 2 - groups, 3 - ranges, 4 or all - all files.

Quadruplex Description

Full list of the options:

python imgqfinder.py --help                     
usage: ImGQFinder [-h] -i INPUT [-o OUTPUT] [-GC GC] [-L L] [-q Q]
                  [-mdef MDEF] [-bulgelen BULGELEN] [-maxbulge MAXBULGE] [-bp]
                  [-tetdef TETDEF] [-ns] [-r] [-v]

The tool for finding G-, C- quadruplexes. The output positions are represented
in a zero based counting.

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Assembly scaffolds/contigs or full genomes, required.
  -o OUTPUT, --output OUTPUT
                        Name/path of a folder for output files. Saves to the
                        current folder if not provided.
  -GC GC                Quad type, G- or C-. By default, G.
  -L L                  Maximum loop length. By default, 7.
  -q Q                  The length of a quadruplet.
  -mdef MDEF            Allowed number of defective tetrads. By default, 1.
  -bulgelen BULGELEN    Total length of bulges in one quadruplet. By default,
                        1.
  -maxbulge MAXBULGE    Maximum number of bulges per quadruplet. By default,
                        1.
  -bp, --bulge_priority
                        By default, quadrouplexes with shorter bulge or
                        without them are preferable while grouping. This
                        behaviour can be changed with this parameter.
  -tetdef TETDEF        Allowed number of defective nucleotides in tetrads. By
                        default, 1.
  -ns, --no-sequences   Not to include sequences to the output.
  -r, --repeats         To include soft-masked genome areas. By default, not
                        included.
  -v, --verbose         Show the status of procesing or not. By default print
                        stages info
  --nthreads NTHREADS   Number of kernels to use.
  --output_type OUTPUT_TYPE [OUTPUT_TYPE ...]
                        List the numbers of file types you need the tool to
                        generate or write all if you want all files. All - is
                        the default. 0 - quadruplets, 1 - quadruplexes, 2 -
                        groups, 3 - ranges. For example, --output_type 1 2
                        will generate only 2 files: quadruplexes and groups.