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Project description
pybiotk: A python toolkit for bioinformatics analysis
Install
SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
use PyPi(official)
pip install pybiotk
An older version may be installed
use build frontend(build: A simple, correct PEP 517 build frontend.)
git clone https://gitee.com/liqiming_whu/pybiotk.git
cd pybiotk
pip install build
python -m build
pip install dist/*tar.gz
use setup.py sdist
git clone https://gitee.com/liqiming_whu/pybiotk.git
cd pybiotk
pip install cython
python setup.py sdist
pip install dist/*tar.gz
Modules
console_scripts =
gtf2bed = pybiotk.convert.gtf2bed:run
bed2bedgraph = pybiotk.convert.bed2bedgraph:run
fq2fasta = pybiotk.convert.fq2fasta:run
bam2fastx = pybiotk.convert.bam2fastx:run
bampe_order_by_name = pybiotk.convert.bampe_order_by_name:run
bam_random = pybiotk.utils.bam_random:run
gtf_filter = pybiotk.utils.gtf_filter:run
fasta_filter = pybiotk.utils.fasta_filter:run
fastq_uniq = pybiotk.utils.fastq_uniq:run
seq_random = pybiotk.utils.seq_random:run
merge_row = pybiotk.utils.merge_row:run
read_tables = pybiotk.utils.read_tables:run
rmats_filter = pybiotk.utils.rmats_filter:run
count_normalize = pybiotk.utils.normalize:run
reference_count = pybiotk.utils.reference_count:run
pyanno = pybiotk.utils.pyanno:run
rna_fragment_size = pybiotk.utils.fragment_size:run
merge_subseq = pybiotk.utils.merge_subseq:run
subseq_analysis = pybiotk.utils.subseq_analysis:run
Usage
usage: pyanno [-h] -i INPUT -o OUTPUT -g GTF [-l {transcript,gene}] [--tss_region TSS_REGION [TSS_REGION ...]] [--downstream DOWNSTREAM] [-s]
[--rule {1+-,1-+,2++,2--,1++,1--,2+-,2-+,+-,-+,++,--}] [-p] [--ordered_by_name]
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
input file, bam or bed. The file type will be inferred from the filename suffix ['*.bam', '*.bed']. (default: None)
-o OUTPUT, --output OUTPUT
output file name. (default: None)
-g GTF, --gtf GTF gtf file download from Genecode, or a sorted gtf file. (default: None)
-l {transcript,gene}, --level {transcript,gene}
annotation level, transcript or gene. (default: transcript)
--tss_region TSS_REGION [TSS_REGION ...]
choose region from tss. (default: [-1000, 1000])
--downstream DOWNSTREAM
downstream length from tes. (default: 3000)
-s, --strand require same strandedness. (default: False)
--rule {1+-,1-+,2++,2--,1++,1--,2+-,2-+,+-,-+,++,--}
how read(s) were stranded during sequencing. only for bam. (default: 1+-,1-+,2++,2--)
-p, --pair annotate fragments instead of reads. (default: False)
--ordered_by_name if input bam is ordered by name, only for pair-end bam. (default: False)
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