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setup.py
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import os
import sys
from setuptools import setup, find_packages
sys.path.append(os.path.dirname(os.path.abspath(__file__)) + '/pavfinder')
from pavfinder import __version__
setup(
name='pavfinder',
version=__version__,
description='Post Assembly Variant Finder',
long_description='Identifies genomic structural variants or transcriptomic splice variants given the alignments of assembly contigs',
url='https://github.com/bcgsc/pavfinder.git',
author='Readman Chiu',
author_email='[email protected]',
license='GPL',
classifiers=[
'Development Status :: 5 - Production/Stable',
'Programming Language :: Python :: 3.8',
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering :: Bio-Informatics',
],
packages=find_packages(),
install_requires = [
'pysam>=0.8.1',
'pybedtools>=0.7.0',
'intspan>=0.701',
'biopython',
'ruffus',
],
package_data = {'pavfinder': ['test/*', 'scripts/*']},
data_files = [('config', ['pavfinder/cfg/tap.cfg',
'pavfinder/cfg/fusion-bloom.profile']),
('test/genome', ["pavfinder/test/genome/c2g.bam",
"pavfinder/test/genome/r2c.bam",
"pavfinder/test/genome/r2c.bam.bai",
"pavfinder/test/genome/test.fa"]),
('test/genome/expected_output', ["pavfinder/test/genome/expected_output/adjacencies.bedpe",
"pavfinder/test/genome/expected_output/variants.vcf",
"pavfinder/test/genome/expected_output/adjacencies_filtered.bedpe",
"pavfinder/test/genome/expected_output/variants_filtered.vcf",
"pavfinder/test/genome/expected_output/coords.tsv",
"pavfinder/test/genome/expected_output/support.tsv"]),
('test/transcriptome', ["pavfinder/test/transcriptome/c2g.bam",
"pavfinder/test/transcriptome/c2t.bam",
"pavfinder/test/transcriptome/r2c.bam",
"pavfinder/test/transcriptome/r2c.bam.bai",
"pavfinder/test/transcriptome/refGene.fa",
"pavfinder/test/transcriptome/refGene.fa.amb",
"pavfinder/test/transcriptome/refGene.fa.ann",
"pavfinder/test/transcriptome/refGene.fa.bwt",
"pavfinder/test/transcriptome/refGene.fa.fai",
"pavfinder/test/transcriptome/refGene.fa.pac",
"pavfinder/test/transcriptome/refGene.fa.sa",
"pavfinder/test/transcriptome/refGene.sorted.gtf.gz",
"pavfinder/test/transcriptome/refGene.sorted.gtf.gz.tbi",
"pavfinder/test/transcriptome/ensGene.sorted.gtf.gz",
"pavfinder/test/transcriptome/ensGene.sorted.gtf.gz.tbi",
"pavfinder/test/transcriptome/test_1.fastq.gz",
"pavfinder/test/transcriptome/test_2.fastq.gz",
"pavfinder/test/transcriptome/test.cfg",
"pavfinder/test/transcriptome/test.fa",
"pavfinder/test/transcriptome/test_genes.bf",
"pavfinder/test/transcriptome/test_genes.bf.sdsl",
"pavfinder/test/transcriptome/test_genes_ids.txt",
"pavfinder/test/transcriptome/test.profile"]),
('test/transcriptome/expected_output/pavfinder', ["pavfinder/test/transcriptome/expected_output/pavfinder/junctions.bed",
"pavfinder/test/transcriptome/expected_output/pavfinder/mappings.tsv",
"pavfinder/test/transcriptome/expected_output/pavfinder/novel_splicing.bedpe",
"pavfinder/test/transcriptome/expected_output/pavfinder/sv.bedpe"]),
('test/transcriptome/expected_output', ["pavfinder/test/transcriptome/expected_output/tap.tar.gz",
"pavfinder/test/transcriptome/expected_output/fusion-bloom.tar.gz"]),
('test/transcriptome/test_genes', ["pavfinder/test/transcriptome/test_genes/ATXN3.fa",
"pavfinder/test/transcriptome/test_genes/CEBPA.fa",
"pavfinder/test/transcriptome/test_genes/FLT3.fa",
"pavfinder/test/transcriptome/test_genes/FOXP1.fa",
"pavfinder/test/transcriptome/test_genes/KMT2A.fa",
"pavfinder/test/transcriptome/test_genes/NPM1.fa",
"pavfinder/test/transcriptome/test_genes/NSD1.fa",
"pavfinder/test/transcriptome/test_genes/NUP98.fa"]),
],
scripts = ['pavfinder/scripts/pavfinder',
'pavfinder/scripts/check_support.py',
'pavfinder/scripts/find_sv_genome.py',
'pavfinder/scripts/find_sv_transcriptome.py',
'pavfinder/scripts/map_splice.py',
'pavfinder/scripts/extract_transcript_sequence.py',
'pavfinder/scripts/tap',
'pavfinder/scripts/rescue_fusion.py',
'pavfinder/scripts/fusion-bloom',
'pavfinder/scripts/fusion-bloom.makefile',
'pavfinder/scripts/tap2',
'pavfinder/scripts/filter_fasta.py',
'pavfinder/scripts/link_ssv.py',
],
)