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.travis.yml
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.travis.yml
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language: python
python:
- "3.6" # current default Python on Travis CI
- "3.7"
- "3.8"
# install dependencies
install:
- pip install -r requirements.txt
- pip install .
- pip install coveralls
- pip install coverage
- wget ftp://emboss.open-bio.org/pub/EMBOSS/emboss-latest.tar.gz -O /tmp/emboss.tar.gz
- tar -xvzf /tmp/emboss.tar.gz
- cd EMBOSS-6.6.0
- ./configure --without-x
- make
- cd ..
- export PATH=$PATH:$PWD/EMBOSS-6.6.0/emboss
#install ORFm
- wget https://github.com/wwood/OrfM/releases/download/v0.7.1/orfm-0.7.1_Linux_x86_64.tar.gz -O /tmp/orfm.tar.gz
- tar -xvzf /tmp/orfm.tar.gz
- export PATH=$PATH:$PWD/orfm-0.7.1_Linux_x86_64
# command to run tests
script:
- ls
#run getorf comparison
- getorf -find 3 -outseq ec3.fa -sequence tests/testseq/ecoli.fa -min 120
- getorf -find 1 -outseq ecp3.fa -sequence tests/testseq/ecoli.fa -min 120
- getorf -find 2 -outseq ec.fa -sequence tests/testseq/ecoli.fa -min 120
- getorf -find 0 -outseq ecp.fa -sequence tests/testseq/ecoli.fa -min 120
- orfipy --single --partial-3 --start ATG --min 120 --outdir ofout --dna d3 --pep p3 tests/testseq/ecoli.fa
- orfipy --single --between-stops --min 120 --outdir ofout --dna d --pep p tests/testseq/ecoli.fa
- python scripts/compare_fasta_files.py ec3.fa ofout/d3
- python scripts/compare_fasta_files.py ecp3.fa ofout/p3
- python scripts/compare_fasta_files.py ec.fa ofout/d
- python scripts/compare_fasta_files.py ecp.fa ofout/p
#test run some parameters
- orfipy --single --between-stops --min 120 --outdir ofout --dna d --pep p tests/testseq/ecoli.fa --include-stop
- orfipy --single --min 120 --outdir ofout --dna d --pep p tests/testseq/ecoli.fa --include-stop --partial-3 --partial-5
- orfipy --single --min 120 --outdir ofout --dna d --pep p tests/testseq/ecoli.fa --include-stop --partial-5
- orfipy --single --min 120 --outdir ofout --dna d --pep p tests/testseq/ecoli.fa --include-stop --partial-5 --start ACG --stop TGC
#test gzipped
- gzip tests/testseq/ecoli.fa
- orfipy --single --partial-3 --start ATG --min 120 --outdir ofout --dna d3 --pep p3 tests/testseq/ecoli.fa.gz
- orfipy --single --between-stops --min 120 --outdir ofout --dna d --pep p tests/testseq/ecoli.fa.gz
- python scripts/compare_fasta_files.py ec3.fa ofout/d3
- python scripts/compare_fasta_files.py ecp3.fa ofout/p3
- python scripts/compare_fasta_files.py ec.fa ofout/d
- python scripts/compare_fasta_files.py ecp.fa ofout/p
#test fq
- orfipy --single --between-stops --min 36 --outdir fqout --dna d --pep p tests/testseq/sample.fq
- orfm -m 36 -t orfm_dna tests/testseq/sample.fq > orfm_pep
- python scripts/compare_fasta_files.py orfm_dna fqout/d
- python scripts/compare_fasta_files.py orfm_pep fqout/p
#test fq.gzip
- gzip tests/testseq/sample.fq
- orfipy --single --between-stops --min 36 --outdir fqoutgz --dna d --pep p tests/testseq/sample.fq.gz
- python scripts/compare_fasta_files.py orfm_dna fqoutgz/d
- python scripts/compare_fasta_files.py orfm_pep fqoutgz/p
#see logs
- cat ofout/*.log
#- coverage run -m pytest tests/
#- coverage report --show-missing
#after_success:
# - coveralls