Merge branch 'main' into refactoring

.gitignore

@@ -4,3 +4,6 @@
 __pycache__/
 strainy/.DS_Store
 .DS_Store
+build/
+dist/
+strainy.egg-info/

Dockerfile

@@ -0,0 +1,67 @@
+FROM ubuntu:22.04
+MAINTAINER Mikhail Kolmogorov, mikolmogorov@gmail.com
+
+# update and install dependencies
+RUN apt-get update && \
+	DEBIAN_FRONTEND="noninteractive" apt-get -y install tzdata && \
+    apt-get -y install cmake git make gcc g++ autoconf bzip2 lzma-dev zlib1g-dev tabix libbz2-dev && \
+	apt-get -y install libcurl4-openssl-dev libpthread-stubs0-dev liblzma-dev libhdf5-dev && \
+	apt-get -y install python3-pip python3-virtualenv virtualenv python3-dev && \
+	apt-get -y install wget libz-dev libncurses5-dev libgsl-dev && \
+	apt-get -y install graphviz libgraphviz-dev pkg-config && \
+	apt-get clean && \
+	apt-get purge && \
+	rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+RUN ln -s /usr/bin/python3 /usr/bin/python
+
+RUN python3 --version && \
+	python3 -m pip install --upgrade pip
+
+ARG MM_VER=2.28
+RUN wget https://github.com/lh3/minimap2/releases/download/v$MM_VER/minimap2-$MM_VER.tar.bz2 && \
+	tar xvf minimap2-$MM_VER.tar.bz2 && \
+	rm minimap2-$MM_VER.tar.bz2 && \
+	cd minimap2-$MM_VER && \
+	make && \
+	cp minimap2 /usr/bin/
+
+### samtools
+# 1.15
+WORKDIR /opt/samtools
+RUN wget https://github.com/samtools/samtools/releases/download/1.15/samtools-1.15.tar.bz2 && \
+    tar xvf samtools-1.15.tar.bz2 && \
+	rm -r /opt/samtools/samtools-1.15.tar.bz2 && \
+	cd samtools-1.15/ && \
+	autoheader && \
+	autoconf -Wno-header && \
+	./configure && \
+	make && \
+	cp samtools /usr/bin/samtools
+
+### bcftools
+WORKDIR /opt/bcftools
+RUN wget https://github.com/samtools/bcftools/releases/download/1.15/bcftools-1.15.tar.bz2 && \
+    tar xvf bcftools-1.15.tar.bz2 && \
+	cd bcftools-1.15/ && \
+	autoheader && \
+	autoconf -Wno-header && \
+	./configure --enable-libgsl && \
+	make && \
+	cp bcftools /usr/bin/bcftools
+
+#build and install Flye
+WORKDIR /opt/flye
+RUN git clone https://github.com/fenderglass/Flye && \
+	cd Flye && \
+	python setup.py install
+
+#Install strainy & dependencies
+WORKDIR /opt/strainy
+RUN git clone -b docker https://github.com/katerinakazantseva/strainy && \
+	cd strainy && \
+	python3 -m pip install -r requirements.txt && \
+	python3 setup.py install
+
+
+ENV PYTHONUNBUFFERED "1"

README.md

@@ -16,6 +16,7 @@ Third, Strainy enables assembly-based analysis, which is useful in the absence o
 ## Contents
 * [Installation](#installation)
 * [Quick Usage](#quick-usage)
+* [Docker container](#docker-container)
 * [Strainy input](#strainy-input)
 * [Preparing de novo metagenomic assemblies](#preparing-de-novo-metagenomic-assemblies)
 * [Parameters description](#parameters-description)
@@ -48,7 +49,7 @@ Find details [**here**](https://github.com/conda/conda/issues/11216)
 
 ## Quick usage
 
-After successful installation, you should be able to run:
+After repository cloning/installation, you should be able to run:
 
 ```
 conda activate strainy
@@ -65,6 +66,15 @@ See below for the details on how to interpret strainy output.
 
 Also see a more detailed [tutorial](#strainy-tutorial) for the example of how to use Strainy.
 
+## Docker container
+
+Alternatively, you can use a Docker container (using the example provided in `test_set` Strainy directory):
+
+```
+ST_DIR=`pwd`
+docker run -v $ST_DIR:$ST_DIR -u `id -u`:`id -g` mkolmogo/strainy:1.0 strainy --gfa $ST_DIR/test_set/toy.gfa --fastq $ST_DIR/test_set/toy.fastq.gz -o $ST_DIR/out_strainy --threads 8 --mode hifi
+```
+
 ## Strainy input
 
 Strainy supports PacBio HiFi, Nanopore R9 (Guppy5+) and R10 sequencing. 

requirements.txt

@@ -1,10 +1,11 @@
+networkx>=2.6,<3.4
+numpy>=1.24,<1.27
+pandas>=1.3,<3
+pysam>=0.20,<0.23
+scipy>=1.8,<1.13
 biopython
 gfapy
 karateclub
 matplotlib
-networkx
-numpy
-pandas
 pygraphviz
-pysam
 edlib

setup.py

@@ -0,0 +1,31 @@
+import os
+import sys
+import subprocess
+import shutil
+
+try:
+    import setuptools
+except ImportError:
+    sys.exit("setuptools package not found. "
+             "Please use 'pip install setuptools' first")
+
+from setuptools import setup
+
+# Make sure we're running from the setup.py directory.
+script_dir = os.path.dirname(os.path.realpath(__file__))
+if script_dir != os.getcwd():
+    os.chdir(script_dir)
+
+from strainy.__version__ import __version__
+
+
+setup(name='strainy',
+      version=__version__,
+      description='Metagenomic strain phasing and assmebly using long reads',
+      url='https://github.com/katerinakazantseva/strainy',
+      author='Ekaterina Kazantseva & Ataberk Donmez',
+      author_email = 'ekaterina.v.kazantseva@gmail.com',
+      license='CC BY-NC-SA 4.0',
+      packages=['strainy', 'strainy/clustering', 'strainy/gfa_operations', 'strainy/reports', 'strainy/simplification'],
+      entry_points={'console_scripts': ['strainy = strainy.main:main']},
+      )

strainy.py

@@ -1,15 +1,12 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
+
+"""
+This script sets up environment paths
+and invokes Strainy without installation.
+"""
 
-import sys
 import os
-import platform
-import re
-import subprocess
-import argparse
-import logging
-import shutil
-import cProfile
-import gfapy
+import sys
 
 
 #Setting executable paths and additional import dirs
@@ -23,126 +20,13 @@
 os.environ["PATH"] = bin_absolute + os.pathsep + os.environ["PATH"]
 ###
 
-
-from strainy.phase import phase_main
-from strainy.transform import transform_main
-from strainy.params import StRainyArgs, init_global_args_storage
-from strainy.logging import set_thread_logging
-from strainy.preprocessing import preprocess_cmd_args
-
-
-logger = logging.getLogger()
-
-def get_processor_name():
-    if platform.system() == "Windows":
-        return platform.processor()
-    elif platform.system() == "Darwin":
-        os.environ['PATH'] = os.environ['PATH'] + os.pathsep + '/usr/sbin'
-        command ="sysctl -n machdep.cpu.brand_string"
-        return subprocess.check_output(command).strip()
-    elif platform.system() == "Linux":
-        command = "cat /proc/cpuinfo"
-        all_info = subprocess.check_output(command, shell=True).decode().strip()
-        for line in all_info.split("\n"):
-            if "model name" in line:
-                return re.sub( ".*model name.*:", "", line,1)
-    return ""
-
-
 def main():
-    parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
-    requiredNamed = parser.add_argument_group('Required named arguments')
-    requiredNamed.add_argument("-o", "--output", help="output directory",required=True)
-    requiredNamed.add_argument("-g", "--gfa", help="input gfa to uncollapse",required=True)
-    requiredNamed.add_argument("-m", "--mode", help="type of reads", choices=["hifi", "nano"],
-                               required=True)
-    requiredNamed.add_argument("-q", "--fastq",help="fastq file with reads to phase / assemble",
-                               required=True)
-    parser.add_argument("-s", "--stage", help="stage to run: either phase, transform or e2e (phase + transform)",
-                        choices=["phase", "transform", "e2e"], default="e2e")
-    parser.add_argument("--snp", help="path to vcf file with SNP calls to use", default=None)
-    parser.add_argument("-t", "--threads", help="number of threads to use", type=int, default=4)
-    parser.add_argument("-f", "--fasta", required=False, help=argparse.SUPPRESS)
-    parser.add_argument("-b", "--bam", help="path to indexed alignment in bam format",required=False)
-    parser.add_argument("--link-simplify", required=False, action="store_true", default=False,
-                        dest="link_simplify",help="Enable agressive graph simplification")
-    parser.add_argument("--debug", required=False, action="store_true", default=False,
-                        help="Generate extra output for debugging")
-    parser.add_argument("--unitig-split-length",
-                        help="The length (in kb) which the unitigs that are longer will be split, set 0 to disable",
-                        required=False,
-                        type=int,
-                        default=50)
-    parser.add_argument("--only-split",help="Do not run stRainy, only split long gfa unitigs", default='False',
-                        required=False)
-    parser.add_argument("-d","--cluster-divergence",help="cluster divergence", type=float, default=0, required=False)  
-    parser.add_argument("-a","--allele-frequency",help="Set allele frequency for internal caller only (pileup)",
-                        type=float, default=0.2, required=False)
-    parser.add_argument("--min-unitig-length",
-                        help="The length (in kb) which the unitigs that are shorter will not be phased",
-                        required=False,
-                        type=float,
-                        default=1)
-    parser.add_argument("--min-unitig-coverage",
-                        help="The minimum coverage threshold for phasing unitigs, unitigs with lower coverage will not be phased",
-                        required=False,
-                        type=int,
-                        default=20)
-    parser.add_argument("--max-unitig-coverage",
-                        help="The maximum coverage threshold for phasing unitigs, unitigs with higher coverage will not be phased",
-                        required=False,
-                        type=int,
-                        default=500)
-
-    args = parser.parse_args()
-    args.strainy_root = strainy_root
-    #setting up global arguments storage
-    input_graph = gfapy.Gfa.from_file(args.gfa)
-    args.graph_edges = input_graph.segment_names
-    args.edges_to_phase = []
-    init_global_args_storage(args)
-    BIN_TOOLS = ["samtools", "bcftools", "minimap2", StRainyArgs().flye]
-    for tool in BIN_TOOLS:
-        if not shutil.which(tool):
-            print("{} not installed".format(tool), file=sys.stderr)
-            return 1
-
-    os.makedirs(StRainyArgs().output, exist_ok=True)
-    os.makedirs(StRainyArgs().output_intermediate, exist_ok=True)
-    if os.path.isdir(StRainyArgs().log_phase):
-        shutil.rmtree(StRainyArgs().log_phase)
-    os.makedirs(StRainyArgs().log_phase, exist_ok=True)
-    set_thread_logging(StRainyArgs().log_phase, "phase_root", None)
+    #Strainy entry point
+    import strainy.main
+    sys.exit(strainy.main.main())
 
-    preprocess_cmd_args(args)
 
-    if StRainyArgs().debug:
-        print(f'Using processor(s): {get_processor_name()}')
-
-    # set one more time for the modified args
-    init_global_args_storage(args)
-    if args.only_split=='True':
-        sys.exit()
-    elif args.stage == "phase":
-        sys.exit(phase_main(args))
-    elif args.stage == "transform":
-        sys.exit(transform_main(args))
-    elif args.stage == "e2e":
-        pr_phase = cProfile.Profile()
-        pr_phase.enable()
-        phase_main(args)
-        logger.info("Phase stage completed, starting transform now...")
-        pr_phase.disable()
-        pr_phase.dump_stats(f'{StRainyArgs().output_intermediate}/phase.prof')
-
-        pr_transform = cProfile.Profile()
-        pr_transform.enable()
-        transform_main(args)
-        logger.info("Transform stage completed, exiting...")
-        pr_transform.disable()
-        pr_transform.dump_stats(f'{StRainyArgs().output_intermediate}/transform.prof')
 
 
 if __name__ == "__main__":
     main()
-

strainy/__version__.py

@@ -0,0 +1 @@
+__version__ = "1.1"