PicklSeq

A python command line tool to turn a fastq and fasta to a pickle file for ML or other stuff. Currently, only mac is fully supported, unix based os should also work as well but no tests have been done on it.

Current implement implementation only allow the following clones:

1. CRT
2. DHFR
3. DHPS

Future implementation will allow any fasta file as the input.

Installation

1. Clone this repo.
2. install minimap2: https://github.com/lh3/minimap2
3. install samtools: http://www.htslib.org/
4. install chopper: https://github.com/wdecoster/chopper

tip: Use homebrew for Mac

*you could also alias the python picklseq.py command in your bash profile for ease of use.

Version used during development:

1. Python 3.11.3
2. minimap2 2.26-r1175
3. samtools 1.17 Using htslib 1.17
4. chopper 0.5.0

Run

Run picklseq.py to trim sequences to a pickl file

usage: picklseq.py [-h] [-f FILE] [-o FILEOUT] [-t TYPE] [-m MINLENGTH] [-M MAXLENGTH] [-q QUALITY]
                   [-T THREADS] [-c MATCHCOUNT] [-p] [-k]

A script to trim DNA sequences

options:
  -h, --help            show this help message and exit
  -f FILE, --file FILE  The file name of the fastq
  -o FILEOUT, --fileout FILEOUT
                        The file name of the file output
  -t TYPE, --type TYPE  The type of the DNA sequence. Could be CRT, DHPS, or DHFR. Alternatively, you could
                        provide a .fasta file.
  -m MINLENGTH, --minlength MINLENGTH
                        min length of acceptable DNA sequence
  -M MAXLENGTH, --maxlength MAXLENGTH
                        max length of acceptable DNA sequence
  -q QUALITY, --quality QUALITY
                        quality of Chopper reads
  -T THREADS, --threads THREADS
                        number of CPU threads
  -c MATCHCOUNT, --matchcount MATCHCOUNT
                        number of the number of CIGAR matches
  -p, --pad             pad the start of the DNA sequence when pos is not 1
  -k, --keep            keep subprocess file output