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/ __ \/ | / __ \ | / / _/ | / /
/ / / / /| | / /_/ / | /| / // // |/ /
/ /_/ / ___ |/ _, _/| |/ |/ // // /| /
/_____/_/ |_/_/ |_| |__/|__/___/_/ |_/
---------------------------------------------------------------------------
- Thread : 32
- Index Path : 2.HISAT2REF/
- Sample Path : 3.SAMPLE/
- Sample % : r10
- Save Result csv : True
---------------------------------------------------------------------------
©️ ABCLab Jongheon Lee
$ pip install glob2
$ pip install figlet
.
├── 1.ENSEMBL # FASTA DATA FROM ENSEMBL
│ ├── Acanthochromis_polyacanthus.ASM210954v1.dna.toplevel.fa
│ ├── ...
│ └── Zosterops_lateralis_melanops.ASM128173v1.dna.toplevel.fa
├── 2.HISAT2REF # INDEX DIR
│ ├── Acanthochromis_polyacanthus
│ ├── ...
│ └── Zosterops_lateralis_melanops
├── 3.SAMPLE # SAMPLE DIR
│ ├── r10_sample_1.fastq
│ └── r10_sample_2.fastq
├── 4.HISAT2MAP # MAP DIR
│ ├── logs
│ ├── results.csv
│ └── SAM
├── hisat2map.py # HISAT2 MAPPING
├── darwin.py # HISAT2 MAPPING - main script
├── hisat2ref.py # HISAT2 INDEX
├── taxonomy.py # TAXONOMY SPECIES INFO
├── LICENSE
├── seqchop.py # CLIENT S/W PyQt5
├── preprocessing_fastq.ipynb # BIOPYTHON SAMPLING Fastq SAMPLE
├── __pycache__
├── README.md
└── tidydata.py # To build CSV result file.
- hisat2ref.py
$ python3 hisat2ref.py -t 4 -p 1.NCBI/ -o 2.HISAT2REF/
$ python3 hisat2ref.py -h
usage: hisat2ref.py [-h] [-t THREAD] [-p PATH] [-o OUTDIR]
HISAT2 INDEXING ENSEMBL ENTIRE SPECIES SCRIPT
optional arguments:
-h, --help show this help message and exit
-t THREAD, --thread THREAD
Launch NTHREADS parallel build threads
-p PATH, --path PATH Directory path ENSEMBL Refernce fasta files stored
-o OUTDIR, --outdIr OUTDIR
HISAT2 Output Directory path
- darwin.py
$ python3 darwin.py -t 32 --name Homo_sapiens --per r10 #example
$ python3 darwin.py -h
usage: darwin.py [-h] [-t THREAD] [-i INDEX_PATH] [-s SAMPLE_PATH] --name SAMPLE_NAME --per SAMPLE_RATE [--save] [--no-save] [--version]
DARWIN : Data Alignment of RNA-seq for Web-based Interspecies Navigator - HISAT2 MAPPING ENSEMBL ENTIRE SPECIES SCRIPT
optional arguments:
-h, --help show this help message and exit
-t THREAD, --thread THREAD
Launch NTHREADS parallel build threads
-i INDEX_PATH, --index INDEX_PATH
Directory path HISAT2 index files stored
-s SAMPLE_PATH, --sample SAMPLE_PATH
Directory path Sample files stored
--name SAMPLE_NAME Sample file name
--per SAMPLE_RATE the number of reads ( e.g. r50, r10, r1 )
--save Mapping Rate Result CSV file save (Default : save)
--no-save Mapping Rate Result CSV file do not save
--version show program's version number and exit
- tidydata.py # result.csv
- seqchop.py