One-step genotyping tools for targeted long-read sequencing
Project description
⚠️ DAJIN2 is currently under development ⚠️
Expected to be available the stable version in August 2023 🤞
Installation (alpha-version)
pip install DAJIN2
Usage
Basics
You can run DAJIN2 for a single sample (one sample vs one control)
DAJIN2 [-h] [-s SAMPLE] [-c CONTROL] [-a ALLELE] [-n NAME] [-g GENOME] [-t THREADS] [-v]
options:
-h, --help show this help message and exit
-s SAMPLE, --sample SAMPLE
Full path to a sample FASTQ file
-c CONTROL, --control CONTROL
Full path to a control FASTQ file
-a ALLELE, --allele ALLELE
Full path to a FASTA file
-n NAME, --name NAME Output directory name
-g GENOME, --genome GENOME
Reference genome ID (e.g hg38, mm10) [default: '']
-t THREADS, --threads THREADS
Number of threads [default: 1]
-v, --version show program's version number and exit
Example
# Donwload example dataset
wget https://github.com/akikuno/DAJIN2/raw/main/examples/example-single.tar.gz
tar -xf example-single.tar.gz
# Run DAJIN2
DAJIN2 \
--name stx2-deletion \
--sample example-single/sample.fq.gz \
--control example-single/control.fq.gz \
--allele example-single/design.fa \
--genome mm39 \
--threads 10
# 2023-06-04 11:30:03: example-single/control.fq.gz is now processing...
# 2023-06-04 11:30:06: Preprocess example-single/control.fq.gz...
# 2023-06-04 11:30:06: Mapping example-single/control.fq.gz...
# 2023-06-04 11:30:21: Call MIDSV example-single/control.fq.gz...
# 2023-06-04 11:30:31: 🍵 example-single/control.fq.gz is finished!
# 2023-06-04 11:30:31: example-single/sample.fq.gz is now processing...
# 2023-06-04 11:30:35: Preprocess example-single/sample.fq.gz...
# 2023-06-04 11:34:13: Classify example-single/sample.fq.gz...
# 2023-06-04 11:34:18: Clustering example-single/sample.fq.gz...
# 2023-06-04 11:35:01: Consensus calling example-single/sample.fq.gz...
# 2023-06-04 11:35:08: 🍵 example-single/sample.fq.gz is finished!
# 🎉 Finished! Open DAJINResults/stx2-deletion to see the report.
Batch handling
DAJIN2 can handle many FASTQ files using the `batch' subcommand.
DAJIN2 batch [-h] -f FILE [-t THREADS]
options:
-h, --help Show this help message and exit
-f FILE, --file FILE CSV or Excel file
-t THREADS, --threads THREADS
Number of threads [default: 1]
Example
# Donwload example dataset
wget https://github.com/akikuno/DAJIN2/raw/main/examples/example-batch.tar.gz
tar -xf example-batch.tar.gz
# Run DAJIN2
DAJIN2 batch --file example-batch/batch.csv --threads 3
# 2023-07-31 17:01:10: example-batch/tyr_control.fq.gz is now processing...
# 2023-07-31 17:01:16: Preprocess example-batch/tyr_control.fq.gz...
# 2023-07-31 17:01:48: Output BAM files of example-batch/tyr_control.fq.gz...
# 2023-07-31 17:01:52: 🍵 example-batch/tyr_control.fq.gz is finished!
# 2023-07-31 17:01:52: example-batch/tyr_c230gt_50%.fq.gz is now processing...
# 2023-07-31 17:01:52: example-batch/tyr_c230gt_10%.fq.gz is now processing...
# 2023-07-31 17:01:52: example-batch/tyr_c230gt_01%.fq.gz is now processing...
# 2023-07-31 17:01:55: Preprocess example-batch/tyr_c230gt_01%.fq.gz...
# 2023-07-31 17:01:55: Preprocess example-batch/tyr_c230gt_50%.fq.gz...
# 2023-07-31 17:01:55: Preprocess example-batch/tyr_c230gt_10%.fq.gz...
# 2023-07-31 17:02:17: Classify example-batch/tyr_c230gt_50%.fq.gz...
# 2023-07-31 17:02:19: Clustering example-batch/tyr_c230gt_50%.fq.gz...
# 2023-07-31 17:02:34: Classify example-batch/tyr_c230gt_01%.fq.gz...
# 2023-07-31 17:02:35: Classify example-batch/tyr_c230gt_10%.fq.gz...
# 2023-07-31 17:02:39: Clustering example-batch/tyr_c230gt_01%.fq.gz...
# 2023-07-31 17:02:39: Clustering example-batch/tyr_c230gt_10%.fq.gz...
# 2023-07-31 17:02:53: Consensus calling of example-batch/tyr_c230gt_50%.fq.gz...
# 2023-07-31 17:02:59: Output reports of example-batch/tyr_c230gt_50%.fq.gz...
# 2023-07-31 17:03:04: 🍵 example-batch/tyr_c230gt_50%.fq.gz is finished!
# 2023-07-31 17:03:39: Consensus calling of example-batch/tyr_c230gt_01%.fq.gz...
# 2023-07-31 17:03:51: Output reports of example-batch/tyr_c230gt_01%.fq.gz...
# 2023-07-31 17:04:03: 🍵 example-batch/tyr_c230gt_01%.fq.gz is finished!
# 2023-07-31 17:04:08: Consensus calling of example-batch/tyr_c230gt_10%.fq.gz...
# 2023-07-31 17:04:16: Output reports of example-batch/tyr_c230gt_10%.fq.gz...
# 2023-07-31 17:04:24: 🍵 example-batch/tyr_c230gt_10%.fq.gz is finished!
# 🎉 Finished! Open DAJINResults/tyr-substitution to see the report.
References
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
DAJIN2-0.3.0.tar.gz
(51.7 kB
view hashes)
Built Distribution
DAJIN2-0.3.0-py3-none-any.whl
(66.4 kB
view hashes)