rnftools 0.4.0.0__tar.gz

rnftools-0.4.0.0/LICENSE

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+The MIT License (MIT)
+
+Copyright (c) 2015 Karel Břinda
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+

rnftools-0.4.0.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: rnftools
+Version: 0.4.0.0
+Summary: RNF framework for NGS: simulation of reads, evaluation of mappers, conversion of RNF-compliant data.
+Home-page: http://karel-brinda.github.io/rnftools/
+Author: Karel Brinda
+Author-email: karel.brinda@univ-mlv.fr
+License: MIT
+Keywords: Bioinformatics,Computational Biology,Next-Generation Sequencing,Read Simulation,Mappers Evaluation
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Operating System :: Unix
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+License-File: LICENSE
+Requires-Dist: argparse
+Requires-Dist: beautifulsoup4
+Requires-Dist: pyfaidx
+Requires-Dist: pysam
+Requires-Dist: snakemake
+Requires-Dist: svg42pdf>=0.1.1
+
+RNFtools
+========
+
+.. image:: https://github.com/karel-brinda/rnftools/actions/workflows/ci.yml/badge.svg?branch=master
+	:target: https://github.com/karel-brinda/rnftools/actions/workflows/ci.yml
+
+.. image:: https://readthedocs.org/projects/rnftools/badge/?version=latest
+	:target: http://rnftools.rtfd.org
+
+.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square
+	:target: https://anaconda.org/bioconda/rnftools
+
+.. image:: https://badge.fury.io/py/RNFtools.svg
+	:target: https://badge.fury.io/py/RNFtools
+
+.. image:: https://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbtv524-brightgreen.svg
+	:target: http://dx.doi.org/10.1093/bioinformatics/btv524
+
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1066626.svg
+	:target: https://doi.org/10.5281/zenodo.1066626
+
+**Read Naming Format** is a generic format for assigning
+read names with encoded information about original positions.
+**RNFtools** is an associated
+software package which can:
+
+* simulate RNF-compliant reads using a wide class of integrated read simulators (Art, DwgSim, Mason, WgSim, etc.), either from a single genome (i.e., a whole genome sequencing) or multiple genomes (i.e., a metagenomic simulation);
+* evaluate mappers using RNF reads;
+* convert non-RNF simulated reads to RNF (e.g., from SAM format);
+* transform genomic coordinates of RNF reads between different coordinate systems (using chain LiftOver format).
+
+Links
+-----
+
+**Web of the project:** http://karel-brinda.github.io/rnftools/
+
+**RNF specification:** http://karel-brinda.github.io/rnf-spec/
+
+**Documentation:** http://rnftools.rtfd.org
+
+**Installation:** http://rnftools.readthedocs.org/en/latest/tutorial/00_installation.html
+
+**Examples of usage:** http://github.com/karel-brinda/rnftools/tree/master/examples/01_tutorial
+
+**Publication:** http://dx.doi.org/10.1093/bioinformatics/btv524

rnftools-0.4.0.0/README.rst

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+RNFtools
+========
+
+.. image:: https://github.com/karel-brinda/rnftools/actions/workflows/ci.yml/badge.svg?branch=master
+	:target: https://github.com/karel-brinda/rnftools/actions/workflows/ci.yml
+
+.. image:: https://readthedocs.org/projects/rnftools/badge/?version=latest
+	:target: http://rnftools.rtfd.org
+
+.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square
+	:target: https://anaconda.org/bioconda/rnftools
+
+.. image:: https://badge.fury.io/py/RNFtools.svg
+	:target: https://badge.fury.io/py/RNFtools
+
+.. image:: https://img.shields.io/badge/doi-10.1093%2Fbioinformatics%2Fbtv524-brightgreen.svg
+	:target: http://dx.doi.org/10.1093/bioinformatics/btv524
+
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1066626.svg
+	:target: https://doi.org/10.5281/zenodo.1066626
+
+**Read Naming Format** is a generic format for assigning
+read names with encoded information about original positions.
+**RNFtools** is an associated
+software package which can:
+
+* simulate RNF-compliant reads using a wide class of integrated read simulators (Art, DwgSim, Mason, WgSim, etc.), either from a single genome (i.e., a whole genome sequencing) or multiple genomes (i.e., a metagenomic simulation);
+* evaluate mappers using RNF reads;
+* convert non-RNF simulated reads to RNF (e.g., from SAM format);
+* transform genomic coordinates of RNF reads between different coordinate systems (using chain LiftOver format).
+
+Links
+-----
+
+**Web of the project:** http://karel-brinda.github.io/rnftools/
+
+**RNF specification:** http://karel-brinda.github.io/rnf-spec/
+
+**Documentation:** http://rnftools.rtfd.org
+
+**Installation:** http://rnftools.readthedocs.org/en/latest/tutorial/00_installation.html
+
+**Examples of usage:** http://github.com/karel-brinda/rnftools/tree/master/examples/01_tutorial
+
+**Publication:** http://dx.doi.org/10.1093/bioinformatics/btv524

rnftools-0.4.0.0/rnftools/__init__.py

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+import builtins
+import sys
+import snakemake
+import os
+import re
+
+import rnftools.mishmash
+import rnftools.lavender
+import rnftools.rnfformat
+import rnftools.utils
+
+# version detection
+try:
+    from importlib.metadata import version, PackageNotFoundError
+    __version__ = version("rnftools")
+except (ImportError, PackageNotFoundError):
+    __version__ = ""
+
+DEFAULT_RNFTOOLS_CONF = {
+    'print_info': sys.argv[0] == "snakemake",
+}
+
+# default configuration
+try:
+    RNFTOOLS_CONF = builtins.RNFTOOLS_CONF
+except AttributeError:
+    RNFTOOLS_CONF = {}
+
+assert type(RNFTOOLS_CONF) is dict, "builtins.RNFTOOLS_CONF must be a dictionary"
+for key in DEFAULT_RNFTOOLS_CONF.keys():
+    if not key in RNFTOOLS_CONF:
+        RNFTOOLS_CONF[key] = DEFAULT_RNFTOOLS_CONF[key]
+
+# print info
+if RNFTOOLS_CONF["print_info"]:
+    message("", program="RNFtools")
+    message("RNFtools", program="RNFtools")
+    message("~~~~~~~~", program="RNFtools")
+    message("Version:     {}".format(__version__), program="RNFtools")
+    message("Web:         http://karel-brinda.github.io/rnftools/", program="RNFtools")
+    message("Contact:     Karel Brinda, karel.brinda@univ-mlv.fr", program="RNFtools")
+    message("Publication: K. Brinda, V. Boeva, G. Kucherov. RNF: a general framework to evaluate", program="RNFtools")
+    message(
+        "             NGS read mappers, Bioinformatics 32(1), 2016 [DOI:10.1093/bioinformatics/btv524].",
+        program="RNFtools"
+    )
+    message("", program="RNFtools")
+
+
+def include():
+    return os.path.join(
+        os.path.dirname(__file__),
+        "include_all.snake",
+    )
+
+
+def input():
+    return [
+        rnftools.lavender.input(),
+        rnftools.mishmash.input(),
+    ]
+
+
+def message(message, program=None, subprogram=None):
+    if program == None:
+        program_part = ""
+        subprogram_part = ""
+    else:
+        program_part = "[{}] ".format(program)
+        if subprogram == None:
+            subprogram_part = ""
+        else:
+            subprogram_part = "{}: ".format(subprogram)
+
+    print(
+        "".join([program_part, subprogram_part, message]),
+        file=sys.stderr,
+    )
+
+    #cprint(
+    #	"".join([program_part, subprogram_part, message]),
+    #	"blue",
+    #	attrs=['bold'],
+    #)
+
+
+def error(message, program=None, subprogram=None, exception=None):
+    if exception != None:
+        assert issubclass(exception, Exception)
+
+    if program == None:
+        program_part = ""
+        subprogram_part = ""
+    else:
+        program_part = "[{}] ".format(program)
+        if subprogram == None:
+            subprogram_part = ""
+        else:
+            subprogram_part = "{}: ".format(subprogram)
+
+    print(
+        "".join([program_part, subprogram_part, "Error: ", message]),
+        file=sys.stderr,
+    )
+    #cprint(
+    #	"".join([program_part, subprogram_part, "Error: ", message]),
+    #	"red",
+    #	attrs=['bold'],
+    #)
+
+    if exception != None:
+        raise exception(message)
+
+
+def shell(
+    cmd,
+    remove_spaces=True,
+    iterable=False,
+    read=False,
+):
+    if remove_spaces:
+        # print("removing spaces from command")
+        cmd = re.sub(r'[ \t\f\v]+', ' ', cmd).strip()
+
+    return snakemake.shell(
+        cmd=cmd,
+        iterable=iterable,
+        read=read,
+    )

rnftools-0.4.0.0/rnftools/include_all.snake

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+from snakemake.utils import min_version
+
+include: "mishmash/mishmash.snake"
+include: "lavender/lavender.snake"
+
+rule index_fasta:
+	output:
+		"{filename}.{suffix}.fai"
+	input:
+		"{filename}.{suffix}"
+	message:
+		"Creating index for a FASTA file ({input})."
+	shell:
+		"""
+			(
+		 		samtools faidx "{input}"
+			) > /dev/null
+		"""
+
+