diff --git a/non-regression-tests/run_nrt.sh b/non-regression-tests/run_nrt.sh deleted file mode 100755 index e1c477d11f1a3367341ccb1f908a4d8605de0a90..0000000000000000000000000000000000000000 --- a/non-regression-tests/run_nrt.sh +++ /dev/null @@ -1,97 +0,0 @@ -#/bin/bash -DATA_PATH=./data -REF_RES_PATH=./reference_results - -## VL: decided to write the checking of results in python scripts rather than shel script for portability. - - -echo "running non regression tests with default options" -./run_HK97.sh || exit 1 -./run_lamda.sh || exit 1 -./run_P1.sh ||exit 1 -./run_N1.sh ||exit 1 -#./run_T4.sh || exit 1 -./run_T7.sh || exit 1 - - - - -#echo " running PhageTerm on lamda genome" -#python ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/Lambda_assembly.fasta -#check_lamda_T7_res -#ret_code=$? -#if [ "$ret_code" -ne "0" ]; then -# exit $ret_code -#fi -#copy_lamda_T7_res res_lamda.20 - -#echo "running PhageTerm on T7 genome" -#python ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/T7_assembly.fasta -#check_StaphN1_T7_res -#ret_code=$? -#echo "ret_code="$ret_code -#if [ "$ret_code" -ne "0" ]; then -# exit $ret_code -#fi -#copy_StaphN1_T7_res res_T7.20 - -#echo "running PhageTerm on P1 genome" -#python ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/P1_assembly.fasta -#check_HK97_P1_T4_res -#ret_code=$? -#echo "ret_code="$ret_code -#if [ "$ret_code" -ne "0" ]; then -# exit $ret_code -#fi -#copy_HK97_P1_T4_res res_P1.20 - -#echo "running PhageTerm on Staph1N genome" -#python ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/Staph1N_assembly.fasta -#check_StaphN1_T7_res -#ret_code=$? -#if [ "$ret_code" -ne "0" ]; then -# exit $ret_code -#fi -#copy_StaphN1_T7_res res_1N.20 -# -#echo "running PhageTerm on T4 genome" -#python ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/T4_assembly.fasta -#check_HK97_P1_T4_res -#ret_code=$? -#if [ "$ret_code" -ne "0" ]; then -# exit $ret_code -#fi -#copy_HK97_P1_T4_res res_T4.20 -# -#echo "running PhageTerm on Virome" -#python ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/virome_assembly_raw.fa - - - - -#echo "Performing non regression tests with -l option" -#python -l 10000 ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/HK97_assembly.fasta -#if [ ! -f NA_cohesive-sequence.fasta ]; then -# echo "NA_cohesive-sequence.fasta does not exist!" -# exit 11 -#fi -#if [ ! -f NA_PhageTerm_report.pdf ]; then -# echo "NA_PhageTerm_report.pdf does not exist!" -# exit 12 -#fi -#if [ ! -f NA_cohesive-sequence.fasta ]; then -# echo "NA_cohesive-sequence.fasta does not exist!" -# exit 13 -#fi -#if [ ! -f NA_statistics.csv ]; then -# echo "NA_statistics.csv does not exist!" -# exit 14 -#fi -#python -l 10000 ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/Lambda_assembly.fasta -#python -l 10000 ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/T7_assembly.fasta -#python -l 10000 ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/P1_assembly.fasta -#python -l 10000 ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/Staph1N_assembly.fasta -#python -l 10000 ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/Staph1N_assembly.fasta -#python -l 10000 ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/T4_assembly.fasta -#python -l 10000 ../PhageTerm.py -f $DATA_PATH/R1_1M_READS_EACH_PHAGE.fastq.20 -p $DATA_PATH/R2_1M_READS_EACH_PHAGE.fastq.20 -r $DATA_PATH/virome_assembly_raw.fa -#exit 0 diff --git a/pyproject.toml b/pyproject.toml index fa7093a33c048d9db6e0eb3b4d8daa57426754e3..8aa788b7a4c853f91b63c2d59e4a2b54ca4d061a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,3 +1,27 @@ [build-system] requires = ["setuptools>=42"] -build-backend = "setuptools.build_meta" \ No newline at end of file +build-backend = "setuptools.build_meta" + +[project] +name = "phageTermVirome" +version = "4.1" +authors = [ +{name="Marc Monot", email="marc.monot@pasteur.fr"}, +{name="Julian Garneau", email="julian.garneau@pasteur.fr"}, +{name="David Bikard", email="david.bikard@pasteur.fr"}, +{name="Véronique Legrand", email="vlegrand@pasteur.fr"} +] +description ="PhageTermVirome software is a tool to determine phage genome termini and genome packaging mode on single phage or multiple contigs at once." +readme = "README.txt" + +license = { file="LICENSE" } +requires-python = ">=3.7.8" +classifiers = [ + "Programming Language :: Python :: 3", + "License :: OSI Approved :: GNU Affero General Public License v3", + "Operating System :: OS Independent", +] + +[project.urls] +"Homepage" = "https://gitlab.pasteur.fr/vlegrand/ptv" +"Bug Tracker" = "https://gitlab.pasteur.fr/vlegrand/ptv/-/issues" \ No newline at end of file diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..a06b7a6debe656435c7be37a8cc056bda5b941ce --- /dev/null +++ b/requirements.txt @@ -0,0 +1,25 @@ +backports +backports.functools_lru_cache +backports_abc +cycler +libwebp-base +lz4-c +matplotlib +numpy +openssl +pandas +patsy +pillow +pip +pyparsing +python3.6 +python-dateutil +python_abi +pytz +readline +reportlab +scikit-learn +scipy +setuptools +statsmodels +tk \ No newline at end of file diff --git a/setup.cfg b/setup.cfg index 98c4b582c569fbe1126d8d0cbe66e0202a0a474a..5ab250f58e558274234932761e131074cb2c725c 100644 --- a/setup.cfg +++ b/setup.cfg @@ -1,18 +1,20 @@ [metadata] -name = phageTerm -version = 4.1 +name = phageTermVirome +version = 2.0 author = Marc Monot author_email = marc.monot@pasteur.fr description = Using sequencing bias to identify phages terminii and phage genome packaging. long_description = file: README.txt -long_description_content_type = text +long_description_content_type = text/plain url = https://gitlab.pasteur.fr/vlegrand/ptv project_urls = Bug Tracker = https://gitlab.pasteur.fr/vlegrand/ptv/-/issues classifiers = Programming Language :: Python :: 3 - License :: OSI Approved :: GNU AFFERO GENERAL PUBLIC LICENSE, Version 3, 19 November 2007 + License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+) Operating System :: OS Independent + Development Status :: 5 - Production/Stable +platforms=any [options] package_dir = @@ -21,4 +23,47 @@ packages = find: python_requires = >=3.6 [options.packages.find] -where = . \ No newline at end of file +where = . + +install_requires = + backports + backports.functools_lru_cache + backports_abc + cycler + libwebp-base + lz4-c + matplotlib + numpy + openssl + pandas + patsy + pillow + pip + pyparsing + python3.6 + python-dateutil + python_abi + pytz + readline + reportlab + scikit-learn + scipy + setuptools + statsmodels + tk + +[options.package_data]= + test-data=test-data/COS-3.500.fastq,test-data/COS-3.fasta,test-data/COS-3.fastq,test-data/COS-5.fasta + test-data/COS-5.fastq,test-data/DTR-long.fasta,test-data/DTR-long.fastq,test-data/DTR-short.fasta + test-data/DTR-short.fastq,test-data/Headful.fasta,test-data/Headful.fastq,test-data/Mu-like.fasta + test-data/Mu-like_R1.fastq,test-data/Mu-like_R2.fastq,test-data/Virome.fasta + test-data/Virome.fastq,test-data/chk_0_2_10_0.npz + data-virome=data-virome/Contigs_30min.fasta,data-virome/SRR4295172_2_div6.fastq,data-virome/SRR4295172_1_div6.fastq + unit-tests-data=unit-tests/data/G-janv_S2_R1_001.fastq.500,unit-tests/data/G-janv_S2_R2_001.fastq.500 + unit-tests/data/chk_0_0_38_863.npz,unit-tests/data/coverage0_0.npz,unit-tests/data/seq1_2_3.fasta + non-regression-tests-data=non-regression-tests/data/HK97_assembly.fasta,non-regression-tests/data/Lambda_assembly.fasta + non-regression-tests/data/P1_assembly.fasta,non-regression-tests/data/R1_1M_READS_EACH_PHAGE(1).fastq.4 + non-regression-tests/data/R1_1M_READS_EACH_PHAGE.fastq.20,non-regression-tests/data/R2_1M_READS_EACH_PHAGE(1).fastq.4 + non-regression-tests/data/R2_1M_READS_EACH_PHAGE.fastq.20,non-regression-tests/data/Staph1N_assembly.fasta + non-regression-tests/data/T4_assembly.fasta,non-regression-tests/data/T7_assembly.fasta + non-regression-tests/data/virome_6seq.fa diff --git a/setup.py b/setup.py new file mode 100644 index 0000000000000000000000000000000000000000..0407ad7928fd4da073f06236c39237e1abee34e6 --- /dev/null +++ b/setup.py @@ -0,0 +1,17 @@ +"""A setuptools based setup module. +See: +https://packaging.python.org/guides/distributing-packages-using-setuptools/ +https://github.com/pypa/sampleproject +""" + +# Always prefer setuptools over distutils +from setuptools import setup, find_packages +import pathlib + +here = pathlib.Path(__file__).parent.resolve() + +# Get the long description from the README file +# long_description = (here / "README.md").read_text(encoding="utf-8") +#long_description = (here / "README.txt").read_text(encoding="utf-8") + +setup() \ No newline at end of file