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update copyright/licence notices
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@widdowquinn
widdowquinn committed Feb 8, 2019
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2 changes: 1 addition & 1 deletion LICENSE
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@@ -1,6 +1,6 @@
The MIT License

Copyright (c) 2016 The James Hutton Institute
Copyright (c) 2016-2019 The James Hutton Institute

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
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4 changes: 2 additions & 2 deletions bin/pdp_mafft_wrapper.py
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This wrapper is not very robust, but will be improved in later
versions of pdp.
(c) The James Hutton Institute 2018
(c) The James Hutton Institute 2018-2019
Author: Leighton Pritchard
Contact:
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Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
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2 changes: 1 addition & 1 deletion diagnostic_primers/blast.py
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Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
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2 changes: 1 addition & 1 deletion diagnostic_primers/classify.py
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Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
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2 changes: 1 addition & 1 deletion diagnostic_primers/config.py
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Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
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2 changes: 1 addition & 1 deletion diagnostic_primers/eprimer3.py
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Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
Expand Down
2 changes: 1 addition & 1 deletion diagnostic_primers/extract.py
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Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
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86 changes: 42 additions & 44 deletions diagnostic_primers/multiprocessing.py
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@@ -1,51 +1,49 @@
#!/usr/bin/env python3
#
# prodigal.py
#
# Code to conduct CDS prediction with Prodigal
#
# (c) The James Hutton Institute 2016
# Author: Leighton Pritchard
#
# Contact:
# leighton.pritchard@hutton.ac.uk
#
# Leighton Pritchard,
# Information and Computing Sciences,
# James Hutton Institute,
# Errol Road,
# Invergowrie,
# Dundee,
# DD6 9LH,
# Scotland,
# UK
#
# The MIT License
#
# Copyright (c) 2016 The James Hutton Institute
#
# 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.

"""Code to run a set of command-line jobs using multiprocessing.
# -*- coding: utf-8 -*-
"""multiprocessing.py
Code to run a set of command-line jobs using multiprocessing.
For parallelisation on multi-core desktop/laptop systems, etc. we use
Python's multiprocessing module to distribute command-line jobs.
(c) The James Hutton Institute 2016-2019
Author: Leighton Pritchard
Contact:
leighton.pritchard@hutton.ac.uk
Leighton Pritchard,
Information and Computing Sciences,
James Hutton Institute,
Errol Road,
Invergowrie,
Dundee,
DD2 5DA,
Scotland,
UK
The MIT License
Copyright (c) 2016-2019 The James Hutton Institute
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.
"""

import multiprocessing
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2 changes: 1 addition & 1 deletion diagnostic_primers/nucmer.py
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Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
Expand Down
2 changes: 1 addition & 1 deletion diagnostic_primers/plot.py
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Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
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2 changes: 1 addition & 1 deletion diagnostic_primers/primersearch.py
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Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
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2 changes: 1 addition & 1 deletion diagnostic_primers/prodigal.py
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Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
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4 changes: 2 additions & 2 deletions diagnostic_primers/scripts/logger.py
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Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
The MIT License
Copyright (c) 2017 The James Hutton Institute
Copyright (c) 2017-2019 The James Hutton Institute
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
Expand Down
2 changes: 1 addition & 1 deletion diagnostic_primers/scripts/parsers/blastscreen_parser.py
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Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
Expand Down
2 changes: 1 addition & 1 deletion diagnostic_primers/scripts/parsers/classify_parser.py
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Expand Up @@ -12,7 +12,7 @@
Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
Expand Down
2 changes: 1 addition & 1 deletion diagnostic_primers/scripts/parsers/common_parser.py
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Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
Expand Down
2 changes: 1 addition & 1 deletion diagnostic_primers/scripts/parsers/config_parser.py
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Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
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2 changes: 1 addition & 1 deletion diagnostic_primers/scripts/parsers/dedupe_parser.py
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Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
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2 changes: 1 addition & 1 deletion diagnostic_primers/scripts/parsers/eprimer3_parser.py
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Expand Up @@ -12,7 +12,7 @@
Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
Expand Down
2 changes: 1 addition & 1 deletion diagnostic_primers/scripts/parsers/extract_parser.py
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Expand Up @@ -12,7 +12,7 @@
Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
Expand Down
2 changes: 1 addition & 1 deletion diagnostic_primers/scripts/parsers/filter_parser.py
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Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
Expand Down
2 changes: 1 addition & 1 deletion diagnostic_primers/scripts/parsers/nucmer_parser.py
View file
Expand Up @@ -12,7 +12,7 @@
Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
Expand Down
2 changes: 1 addition & 1 deletion diagnostic_primers/scripts/parsers/plot_parser.py
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Expand Up @@ -12,7 +12,7 @@
Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
Expand Down
2 changes: 1 addition & 1 deletion diagnostic_primers/scripts/parsers/primersearch_parser.py
View file
Expand Up @@ -12,7 +12,7 @@
Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
Expand Down
2 changes: 1 addition & 1 deletion diagnostic_primers/scripts/parsers/scheduler_parser.py
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Expand Up @@ -12,7 +12,7 @@
Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
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6 changes: 3 additions & 3 deletions diagnostic_primers/scripts/pdp_script.py
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Implements the pdp script for finding differential primers
(c) The James Hutton Institute 2017-2018
(c) The James Hutton Institute 2017-2019
Author: Leighton Pritchard
Contact: leighton.pritchard@hutton.ac.uk
Expand All @@ -15,13 +15,13 @@
Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
The MIT License
Copyright (c) 2017 The James Hutton Institute
Copyright (c) 2017-2019 The James Hutton Institute
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
Expand Down
8 changes: 4 additions & 4 deletions diagnostic_primers/scripts/subcommands/subcmd_blastscreen.py
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# -*- coding: utf-8 -*-
"""subcmd_blastscreen.py
Provides the blastscreen subcommand for pdp.py
Provides the blastscreen subcommand for pdp
(c) The James Hutton Institute 2017-18
(c) The James Hutton Institute 2017-19
Author: Leighton Pritchard
Contact: leighton.pritchard@hutton.ac.uk
Expand All @@ -15,13 +15,13 @@
Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
The MIT License
Copyright (c) 2017-18 The James Hutton Institute
Copyright (c) 2017-19 The James Hutton Institute
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
Expand Down
6 changes: 3 additions & 3 deletions diagnostic_primers/scripts/subcommands/subcmd_classify.py
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Expand Up @@ -2,9 +2,9 @@
# -*- coding: utf-8 -*-
"""subcmd_classify.py
Provides the classify subcommand for pdp.py
Provides the classify subcommand for pdp
(c) The James Hutton Institute 2017-18
(c) The James Hutton Institute 2017-19
Author: Leighton Pritchard
Contact: leighton.pritchard@hutton.ac.uk
Expand All @@ -15,7 +15,7 @@
Errol Road,
Invergowrie,
Dundee,
DD6 9LH,
DD2 5DA,
Scotland,
UK
Expand Down

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