Commit 328b788216c93ab2ffac8552d89f5eac93d4d1bd

Authored by Jean-Michel Garant
1 parent ef444114
Exists in stable-0.3 and in 1 other branch master

Update Licensing towards v0.3

LICENSE
... ... @@ -632,7 +632,7 @@ state the exclusion of warranty; and each file should have at least
632 632 the "copyright" line and a pointer to where the full notice is found.
633 633  
634 634 Identification of potential RNA G-quadruplexes by G4RNA screener.
635   - Copyright (C) 2017 Jean-Michel Garant
  635 + Copyright (C) 2018 Jean-Michel Garant
636 636  
637 637 This program is free software: you can redistribute it and/or modify
638 638 it under the terms of the GNU General Public License as published by
... ... @@ -652,10 +652,10 @@ Also add information on how to contact you by electronic and paper mail.
652 652 If the program does terminal interaction, make it output a short
653 653 notice like this when it starts in an interactive mode:
654 654  
655   - G4RNA screener Copyright (C) 2017 Jean-Michel Garant
  655 + G4RNA screener Copyright (C) 2018 Jean-Michel Garant
656 656 This program comes with ABSOLUTELY NO WARRANTY. This is free
657 657 software, and you are welcome to redistribute it under certain
658   - conditions.
  658 + conditions <http://www.gnu.org/licenses/>.
659 659  
660 660 You should also get your employer (if you work as a programmer) or school,
661 661 if any, to sign a "copyright disclaimer" for the program, if necessary.
... ...
MANUAL.md
1 1 <Use a Markdown document viewer to display this file as an HTML file in your>
2   -<internet browser:>
3   -<Markdown Viewer 1.12 (Firefox extension) *recommended>
4   -<Markdown Reader 1.0.12 (Chrome extension)>
  2 +<internet browser>
5 3  
6 4 **G4RNA SCREENER MANUAL**
7 5 =========================
... ...
README.md
... ... @@ -19,7 +19,9 @@ gitlab username: _J-Michel_
19 19  
20 20 gitlab url: *gitlabscottgroup.med.usherbrooke.ca/J-Michel/g4rna_screener*
21 21  
22   -Version: G4RNA screener 0.2
  22 +Version: G4RNA screener 0.3
  23 +
  24 +**Please consider cloning/downloading a stable branch**
23 25  
24 26  
25 27 ## **DEPENDENCIES**
... ...
g4base.py
1 1 #!/usr/bin/env python
2 2  
  3 +# Identification of potential RNA G-quadruplexes by G4RNA screener.
  4 +# Copyright (C) 2018 Jean-Michel Garant
  5 +#
  6 +# This program is free software: you can redistribute it and/or modify
  7 +# it under the terms of the GNU General Public License as published by
  8 +# the Free Software Foundation, either version 3 of the License, or
  9 +# (at your option) any later version.
  10 +#
  11 +# This program is distributed in the hope that it will be useful,
  12 +# but WITHOUT ANY WARRANTY; without even the implied warranty of
  13 +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
  14 +# GNU General Public License for more details.
  15 +#
  16 +# You should have received a copy of the GNU General Public License
  17 +# along with this program. If not, see <http://www.gnu.org/licenses/>.
  18 +
3 19 from utils import *
4 20 from pybrain.datasets import ClassificationDataSet
5 21  
... ...
screen.py
1 1 #!/usr/bin/env python
2 2  
  3 +# Identification of potential RNA G-quadruplexes by G4RNA screener.
  4 +# Copyright (C) 2018 Jean-Michel Garant
  5 +#
  6 +# This program is free software: you can redistribute it and/or modify
  7 +# it under the terms of the GNU General Public License as published by
  8 +# the Free Software Foundation, either version 3 of the License, or
  9 +# (at your option) any later version.
  10 +#
  11 +# This program is distributed in the hope that it will be useful,
  12 +# but WITHOUT ANY WARRANTY; without even the implied warranty of
  13 +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
  14 +# GNU General Public License for more details.
  15 +#
  16 +# You should have received a copy of the GNU General Public License
  17 +# along with this program. If not, see <http://www.gnu.org/licenses/>.
  18 +
3 19 from g4base import *
4 20 import os
5 21  
... ... @@ -38,14 +54,8 @@ def apply_network(ann,
38 54 or str(fasta)[-4:] in ['.fas', '.txt']\
39 55 or str(fasta)[-6:] == '.fasta'\
40 56 or fasta == "/dev/stdin":
41   - ### without try/except since it catches most errors
42 57 RNome_df = gen_G4RNA_df(fasta_fetcher(fasta, 0, 0, verbose=verbose),
43 58 columns, 1, int(wdw_len), int(wdw_step), verbose=verbose)
44   -# try:
45   -# RNome_df = gen_G4RNA_df(fasta_fetcher(fasta, 0, 0, verbose=verbose),
46   -# columns, 1, int(wdw_len), int(wdw_step), verbose=verbose)
47   -# except:
48   -# screen_usage(52, 'fasta format not respected')
49 59 else:
50 60 screen_usage(52, 'fasta input not specified or not supported')
51 61 if 'G4NN' in columns:
... ... @@ -138,7 +148,7 @@ def main():
138 148 if arg in ["-?","--help"]:
139 149 screen_usage()
140 150 elif arg in ["-V","--version"]:
141   - print "Version: G4RNA screener 0.2"
  151 + print "Version: G4RNA screener 0.3"
142 152 sys.exit(0)
143 153 elif arg in ["-b","--bedgraph",
144 154 "-v","--verbose",
... ...
utils.py
1 1 #!/usr/bin/env python
2 2  
  3 +# Identification of potential RNA G-quadruplexes by G4RNA screener.
  4 +# Copyright (C) 2018 Jean-Michel Garant
  5 +#
  6 +# This program is free software: you can redistribute it and/or modify
  7 +# it under the terms of the GNU General Public License as published by
  8 +# the Free Software Foundation, either version 3 of the License, or
  9 +# (at your option) any later version.
  10 +#
  11 +# This program is distributed in the hope that it will be useful,
  12 +# but WITHOUT ANY WARRANTY; without even the implied warranty of
  13 +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
  14 +# GNU General Public License for more details.
  15 +#
  16 +# You should have received a copy of the GNU General Public License
  17 +# along with this program. If not, see <http://www.gnu.org/licenses/>.
  18 +
3 19 import time
4 20 import sys
5 21 import regex
... ...