Merge branch 'release/0.1.0'

.gitignore

@@ -100,3 +100,10 @@ ENV/
 
 # mypy
 .mypy_cache/
+
+# Macbook 
+.DS_Store
+
+#VScode
+.vscode
+

.travis.yml

@@ -3,9 +3,6 @@
 language: python
 python:
   - 3.7
-  - 3.6
-  - 3.5
-  - 2.7
 
 # Command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
 install: pip install -U tox-travis
@@ -20,10 +17,10 @@ script: tox
 deploy:
   provider: pypi
   distributions: sdist bdist_wheel
-  user: rhshah
+  user: msk-access
   password:
-    secure: PLEASE_REPLACE_ME
+    secure: 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
   on:
     tags: true
-    repo: rhshah/merge_fastq
+    repo: msk-access/merge_fastq
     python: 3.7

README.rst

@@ -6,16 +6,16 @@ merge_fastq
 .. image:: https://img.shields.io/pypi/v/merge_fastq.svg
         :target: https://pypi.python.org/pypi/merge_fastq
 
-.. image:: https://img.shields.io/travis/rhshah/merge_fastq.svg
-        :target: https://travis-ci.org/rhshah/merge_fastq
+.. image:: https://img.shields.io/travis/msk-access/merge_fastq.svg
+        :target: https://travis-ci.com/msk-access/merge_fastq
 
 .. image:: https://readthedocs.org/projects/merge-fastq/badge/?version=latest
         :target: https://merge-fastq.readthedocs.io/en/latest/?badge=latest
         :alt: Documentation Status
 
 
-.. image:: https://pyup.io/repos/github/rhshah/merge_fastq/shield.svg
-     :target: https://pyup.io/repos/github/rhshah/merge_fastq/
+.. image:: https://pyup.io/repos/github/msk-access/merge_fastq/shield.svg
+     :target: https://pyup.io/repos/github/msk-access/merge_fastq/
      :alt: Updates
 
 
@@ -30,7 +30,33 @@ Package to merge multiple pair of pair-end fastq data
 Features
 --------
 
-* TODO
+* Given multiple pair-end fastq data merge them into single pair-end fastq w.r.t each READ1 and READ2 
+
+Usage
+-----
+
+> merge_fastq --help
+
+Usage: merge_fastq [OPTIONS]
+
+  Console script for merge_fastq.
+
+Options:
+  -fp1, --fastq1 PATH      Full path to gziped READ1 fastq files, can be
+                           specified multiple times for example: --fastq1
+                           test_part1_R1.fastq.gz --fastq1
+                           test_part2_R1.fastq.gz  [required]
+  -fp2, --fastq2 PATH      Full path to gziped READ2 fastq files, can be
+                           specified multiple times for example: --fastq2
+                           test_part1_R2.fastq.gz --fastq2
+                           test_part2_R2.fastq.gz  [required]
+  -op, --output-path PATH  Full path to write the output files (default:
+                           Current working directory)
+  -of1, --out-fastq1 TEXT  Name of the merged output READ1 fastq file
+                           (default: merged_fastq_R1.fastq.gz)
+  -of2, --out-fastq2 TEXT  Name of the merged output READ2 fastq file
+                           (default: merged_fastq_R2.fastq.gz)
+  --help                   Show this message and exit.
 
 Credits
 -------

docs/usage.rst

@@ -5,3 +5,58 @@ Usage
 To use merge_fastq in a project::
 
     import merge_fastq
+    merge_fastq(fastq1,fastq2)
+
+To use merge_fastq for command line::
+
+    > merge_fastq --help
+
+    Usage: merge_fastq [OPTIONS]
+
+    Console script for merge_fastq.
+
+    Options:
+    -fp1, --fastq1 PATH      Full path to gziped READ1 fastq files, can be
+                            specified multiple times for example: --fastq1
+                            test_part1_R1.fastq.gz --fastq1
+                            test_part2_R1.fastq.gz  [required]
+    -fp2, --fastq2 PATH      Full path to gziped READ2 fastq files, can be
+                            specified multiple times for example: --fastq2
+                            test_part1_R2.fastq.gz --fastq2
+                            test_part2_R2.fastq.gz  [required]
+    -op, --output-path PATH  Full path to write the output files (default:
+                            Current working directory)
+    -of1, --out-fastq1 TEXT  Name of the merged output READ1 fastq file
+                            (default: merged_fastq_R1.fastq.gz)
+    -of2, --out-fastq2 TEXT  Name of the merged output READ2 fastq file
+                            (default: merged_fastq_R2.fastq.gz)
+    --help                   Show this message and exit.
+
+Example commandline:
+
+* Using default option for multiple fastq1 and fastq2 files
+
+    .. code-block:: console
+    
+       $ merge_fastq \
+       --fastq1 test_part1_R1.fastq.gz \
+       --fastq1 test_part2_R1.fastq.gz \
+       --fastq2 test_part1_R2.fastq.gz \
+       --fastq2 test_part2_R2.fastq.gz \    
+    
+    .. code
+
+* Using custom option for multiple fastq1 and fastq2 files
+
+    .. code-block:: console
+    
+       $ merge_fastq \
+       --fastq1 test_part1_R1.fastq.gz \
+       --fastq1 test_part2_R1.fastq.gz \
+       --fastq2 test_part1_R2.fastq.gz \
+       --fastq2 test_part2_R2.fastq.gz \ 
+       --output-path /path/to/where/you/want/output
+       --out-fastq1 test_merged_R1.fastq.gz
+       --out-fastq2 test_merged_R2.fastq.gz   
+    
+    .. code

merge_fastq/cli.py

@@ -1,18 +1,126 @@
 # -*- coding: utf-8 -*-
 
-"""Console script for merge_fastq."""
+import os
 import sys
-import click
+import logging
+import time
+import pathlib
+try:
+    import click
+except ImportError as e:
+    print(
+        "cli: click is not installed, please install click as it is one of the requirements. \n", e
+    )
+    exit(1)
+try:
+    import click_log
+except ImportError as e:
+    print(
+        "cli: click-log is not installed, please install click_log as it is one of the requirements.\n", e
+    )
+    exit(1)
+try:
+    import merge_fastq.merge_fastq as mf
+except ImportError as e:
+    print(
+        "cli: merge_fastq module could not be loaded, please install package correctly to get this running. \n", e
+    )
+    exit(1)
+
+"""
+cli
+~~~~~~~~~~~~~~~
+:Description: console script for running merge_fastq
+"""
+"""
+Created on October 10, 2019
+Description: console script for running merge_fastq
+@author: Ronak H Shah
+"""
+
+version = None
+scriptpath = os.path.realpath(__file__)
+p_scriptpath = pathlib.Path(scriptpath)
+with open(os.path.join(p_scriptpath.parent, "__init__.py"), "r") as f:
+    for line in f.readlines():
+        line = line.strip()
+        if line.startswith("__version__"):
+            version = line.split("=")[-1].strip()
+__all__ = []
+__version__ = version
+__date__ = "2019-10-21"
+__updated__ = "2019-10-21"
+# Making logging possible
+logger = logging.getLogger("merge_fastq")
+click_log.basic_config(logger)
+click_log.ColorFormatter.colors["info"] = dict(fg="green")
 
 
 @click.command()
-def main(args=None):
+@click.option(
+    "--fastq1",
+    "-fp1",
+    required=True,
+    multiple=True,
+    type=click.Path(exists=True),
+    help="Full path to gziped READ1 fastq files, can be specified multiple times for example: --fastq1 test_part1_R1.fastq.gz --fastq1 test_part2_R1.fastq.gz",
+)
+@click.option(
+    "--fastq2",
+    "-fp2",
+    required=True,
+    multiple=True,
+    type=click.Path(exists=True),
+    help="Full path to gziped READ2 fastq files, can be specified multiple times for example: --fastq2 test_part1_R2.fastq.gz --fastq2 test_part2_R2.fastq.gz",
+)
+@click.option(
+    "--output-path",
+    "-op",
+    required=False,
+    default=os.getcwd(),
+    type=click.Path(exists=True),
+    help="Full path to write the output files (default: Current working directory)",
+)
+@click.option(
+    "--out-fastq1",
+    "-of1",
+    required=False,
+    default="merged_fastq_R1.fastq.gz",
+    type=click.STRING,
+    help="Name of the merged output READ1 fastq file (default: merged_fastq_R1.fastq.gz)",
+)
+@click.option(
+    "--out-fastq2",
+    "-of2",
+    required=False,
+    default="merged_fastq_R2.fastq.gz",
+    type=click.STRING,
+    help="Name of the merged output READ2 fastq file (default: merged_fastq_R2.fastq.gz)",
+)
+def main(fastq1, fastq2, output_path, out_fastq1, out_fastq2):
     """Console script for merge_fastq."""
-    click.echo("Replace this message by putting your code into "
-               "merge_fastq.cli.main")
-    click.echo("See click documentation at https://click.palletsprojects.com/")
+    logger_output = os.path.join(output_path, "merge_fastq.log")
+    fh = logging.FileHandler(logger_output)
+    formatter = logging.Formatter(
+        fmt="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
+        datefmt="%m/%d/%Y %I:%M:%S %p",
+    )
+    fh.setFormatter(formatter)
+    logger.addHandler(fh)
+    logger.info("==================================================")
+    logger.info(">>> Running merge_fastq for <<<")
+    logger.info("==================================================")
+    t1_start = time.perf_counter()
+    t2_start = time.process_time()
+    mf.run(fastq1, fastq2, output_path, out_fastq1, out_fastq2)
+    t1_stop = time.perf_counter()
+    t2_stop = time.process_time()
+    logger.info("--------------------------------------------------")
+    logger.info("Elapsed time: %.1f [min]" % ((t1_stop - t1_start) / 60))
+    logger.info("CPU process time: %.1f [min]" % ((t2_stop - t2_start) / 60))
+    logger.info("--------------------------------------------------")
     return 0
 
 
 if __name__ == "__main__":
-    sys.exit(main())  # pragma: no cover
+    sys.exit(main())

merge_fastq/merge_fastq.py

@@ -1,3 +1,56 @@
 # -*- coding: utf-8 -*-
 
-"""Main module."""
+import os
+import logging
+import shutil
+
+"""
+merge_fastq
+~~~~~~~~~~~~~~~
+:Description: main module for merge_fastq
+"""
+"""
+Created on October 21, 2019
+Description: main module for merge_fastq
+@author: Ronak H Shah
+"""
+
+# Making logging possible
+logger = logging.getLogger("merge_fastq")
+
+
+def run(fastq1, fastq2, output_path, out_fastq1, out_fastq2):
+    out_file1 = os.path.join(output_path, out_fastq1)
+    out_file2 = os.path.join(output_path, out_fastq2)
+    if(len(fastq1) == len(fastq2)):
+        if len(fastq1) == 1:
+            try:
+                shutil.copyfile(fastq1[0], out_file1)
+            except IOError as e:
+                logging.error(
+                    "Could not copy file %s to %s, please see the execution error. \n %s \n", fastq1[0], out_file1, e)
+                exit(1)
+            try:
+                shutil.copyfile(fastq2[0], out_file2)
+            except IOError as e:
+                logging.error(
+                    "Could not copy file %s to %s, please see the execution error. \n %s \n", fastq2[0], out_file2, e)
+                exit(1)
+        else:
+            merge_fastq(fastq1, fastq2, out_file1, out_file2)
+            logging.info("Done merging fastq file in %s and %s", out_file1, out_file2)
+
+    else:
+        logger.error("The program expects that the same number of fastq are provided for READ1 and READ2, current they dont match. \n\n ### READ1 ### \n %s \n ### READ2 ### \n %s \n", fastq1, fastq2)
+        exit(1)
+
+
+def merge_fastq(fastq_list_R1, fastq_list_R2, out_file1, out_file2):
+    with open(out_file1, 'wb') as outfile:
+        for fastq in fastq_list_R1:
+            with open(fastq, 'rb') as infile:
+                shutil.copyfileobj(infile, outfile)
+    with open(out_file2, 'wb') as outfile:
+        for fastq in fastq_list_R2:
+            with open(fastq, 'rb') as infile:
+                shutil.copyfileobj(infile, outfile)

requirements_dev.txt → requirements.txt

@@ -1,12 +1,13 @@
-pip==19.2.3
+pip==19.3.1
 bump2version==0.5.11
 wheel==0.33.6
 watchdog==0.9.0
 flake8==3.7.8
 tox==3.14.0
 coverage==4.5.4
-Sphinx==1.8.5
-twine==1.14.0
+Sphinx==2.2.0
+twine==2.0.0
 Click==7.0
-pytest==4.6.5
+click-log==0.3.2
+pytest==5.2.1
 pytest-runner==5.1

setup.py

@@ -26,11 +26,6 @@
         'Intended Audience :: Developers',
         'License :: OSI Approved :: Apache Software License',
         'Natural Language :: English',
-        "Programming Language :: Python :: 2",
-        'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.5',
-        'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
     ],
     description="Package to merge multiple pair of pair-end fastq data",