convert to python pkg

Author: trvinh

MANIFEST.in

@@ -0,0 +1 @@
+recursive-include hamstr1s *

bin/Filehandler.pm renamed to hamstr1s/Filehandler.pm

@@ -144,7 +144,7 @@ def main():
                 index = index + 1
                 id = str(id) + '_' + str(index)
                 tmpDict[id] = 1
-            id = re.sub('\|', '_', seq)
+            id = re.sub('\|', '_', id)
             seq = str(inSeq[id].seq)
             specialChr = 'no'
             if any(c for c in seq if not c.isalpha()):

hamstr1s/__init__.py

@@ -0,0 +1,72 @@
+# -*- coding: utf-8 -*-
+
+#######################################################################
+# Copyright (C) 2020 Vinh Tran
+#
+#  This script is used to run HaMStR oneSeq.
+#
+#  This script is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License <http://www.gnu.org/licenses/> for
+#  more details
+#
+#  Contact: [email protected]
+#
+#######################################################################
+
+import sys
+import os
+import argparse
+import subprocess
+
+def runOneseq(args):
+    (f,n,i,o,c,v,a,cpus,replace,oldFAS) = args
+    script = os.path.realpath(__file__).replace('addTaxaHamstr', 'addTaxonHamstr')
+    cmd = 'python3 %s -f %s -n %s -i %s -o %s -v %s --cpus %s' % (script, f,n,i,o,v,cpus)
+    if c == True:
+        cmd = cmd + ' -c'
+    if a == True:
+        cmd = cmd + ' -a'
+    if oldFAS == True:
+        cmd = cmd + ' --oldFAS'
+    if replace == True:
+        cmd = cmd + ' --replace'
+    # print(cmd)
+    logFile = o + '/addTaxaHamstr.log'
+    cmd = cmd + ' >> ' + logFile
+    try:
+        subprocess.call([cmd], shell = True)
+    except:
+        sys.exit('Problem running\n%s' % (cmd))
+
+def main():
+    version = '0.0.1'
+    parser = argparse.ArgumentParser(description='You are running runOneseq version ' + str(version) + '.')
+    required = parser.add_argument_group('required arguments')
+    optional = parser.add_argument_group('optional arguments')
+    required.add_argument('-i', '--input', help='Input fasta file', action='store', default='', required=True)
+    optional.add_argument('--setup', help='Setup HaMStR-oneSeq', action='store_true', default=False)
+    optional.add_argument('--oneseqHelp', help='Print help of oneseq', action='store_true', default=False)
+
+    ### get arguments
+    args = parser.parse_args()
+    input = args.input
+    help = args.oneseqHelp
+    setup = args.setup
+
+    oneseqPath = os.path.realpath(__file__).replace('/runOneseq.py','')
+    if help:
+        if os.path.exists(oneseqPath + '/oneSeq.pl'):
+            helpMsgCmd = subprocess.Popen([oneseqPath + '/hamstr.pl', '-h'], stdin=subprocess.PIPE, stdout=subprocess.PIPE, stderr=subprocess.PIPE)
+            helpMsg, helpErr = helpMsgCmd.communicate()
+            print(helpMsg.decode('UTF-8'))
+            print(helpErr.decode('UTF-8'))
+
+    if setup:
+        setupFile = oneseqPath + '/setup.sh'
+        subprocess.call([setupFile], shell = True)
+
+
+if __name__ == '__main__':
+    main()

hamstr1s/__pycache__/__init__.cpython-37.pyc

@@ -0,0 +1,58 @@
+#!/bin/env python
+
+#######################################################################
+# Copyright (C) 2019 Julian Dosch
+#
+# This file is part of greedyFAS.
+#
+#  greedyFAS is free software: you can redistribute it and/or modify
+#  it under the terms of the GNU General Public License as published by
+#  the Free Software Foundation, either version 3 of the License, or
+#  (at your option) any later version.
+#
+#  greedyFAS is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with greedyFAS.  If not, see <http://www.gnu.org/licenses/>.
+#
+#######################################################################
+
+from setuptools import setup, find_packages
+
+with open("README.md", "r") as input:
+    long_description = input.read()
+
+setup(
+    name="hamstr1s",
+    version="2.0.0",
+    python_requires='>=3.7.0',
+    description="Feature-aware orthology prediction tool",
+    long_description=long_description,
+    author="Vinh Tran",
+    author_email="[email protected]",
+    url="https://github.com/BIONF/HaMStR",
+    packages=find_packages(),
+    package_data={'': ['*']},
+    install_requires=[
+        'biopython',
+        'tqdm',
+        'ete3'
+    ],
+    entry_points={
+        'console_scripts': ["1s = hamstr1s.runOneseq:main",
+                            "addTaxonHamstr = hamstr1s.addTaxonHamstr:main",
+                            "addTaxaHamstr = hamstr1s.addTaxaHamstr:main",
+                            "mergeHamstrOutput = hamstr1s.mergePhyloprofileData:main"],
+    },
+    license="GPL-3.0",
+    classifiers=[
+        "Environment :: Console",
+        "Intended Audience :: End Users/Desktop",
+        "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
+        "Natural Language :: English",
+        "Programming Language :: Python :: 3",
+    ],
+)