[med-svn] [iva] 02/06: Imported Upstream version 1.0.5
Sascha Steinbiss
sascha at steinbiss.name
Thu May 5 09:35:02 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository iva.
commit 5fd942556e010821f93e31b73048167259ddc456
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Thu May 5 09:17:40 2016 +0000
Imported Upstream version 1.0.5
---
iva/__init__.py | 14 ++++++++++++++
iva/assembly.py | 14 ++++++++++++++
iva/common.py | 16 +++++++++++++++-
iva/contig.py | 14 ++++++++++++++
iva/contig_trim.py | 14 ++++++++++++++
iva/edge.py | 14 ++++++++++++++
iva/egg_extract.py | 14 ++++++++++++++
iva/external_progs.py | 18 ++++++++++++++++--
iva/graph.py | 14 ++++++++++++++
iva/kcount.py | 14 ++++++++++++++
iva/kmers.py | 14 ++++++++++++++
iva/kraken.py | 14 ++++++++++++++
iva/mapping.py | 20 +++++++++++++++++++-
iva/mummer.py | 14 ++++++++++++++
iva/qc.py | 14 ++++++++++++++
iva/qc_external.py | 28 ++++++++++++++++++++++------
iva/ratt/embl2gff.pl | 14 ++++++++++++++
iva/ratt/genbank2embl.pl | 15 +++++++++++++++
iva/ratt/main.ratt.pl | 21 ++++++++++++---------
iva/ratt/ratt_correction.pm | 19 ++++++++++++++-----
iva/ratt/start.ratt.sh | 15 ++++++++++++++-
iva/read_trim.py | 14 ++++++++++++++
iva/seed.py | 14 ++++++++++++++
iva/seed_processor.py | 14 ++++++++++++++
iva/test_data_runner.py | 16 +++++++++++++++-
iva/tests/assembly_test.py | 14 ++++++++++++++
iva/tests/contig_test.py | 14 ++++++++++++++
iva/tests/contig_trim_test.py | 14 ++++++++++++++
iva/tests/edge_test.py | 14 ++++++++++++++
iva/tests/egg_extract_test.py | 14 ++++++++++++++
iva/tests/external_progs_test.py | 14 ++++++++++++++
iva/tests/graph_test.py | 14 ++++++++++++++
iva/tests/kcount_test.py | 14 ++++++++++++++
iva/tests/kmers_test.py | 14 ++++++++++++++
iva/tests/kraken_test.py | 14 ++++++++++++++
iva/tests/mapping_test.py | 14 ++++++++++++++
iva/tests/mummer_test.py | 14 ++++++++++++++
iva/tests/qc_external_test.py | 14 ++++++++++++++
iva/tests/qc_test.py | 14 ++++++++++++++
iva/tests/read_trim_test.py | 14 ++++++++++++++
iva/tests/seed_processor_test.py | 14 ++++++++++++++
iva/tests/seed_test.py | 14 ++++++++++++++
scripts/iva | 20 +++++++++++++++++---
scripts/iva_qc | 14 ++++++++++++++
scripts/iva_qc_make_db | 14 ++++++++++++++
setup.py | 17 ++++++++++++++++-
46 files changed, 665 insertions(+), 30 deletions(-)
diff --git a/iva/__init__.py b/iva/__init__.py
index 47ee547..b1537dc 100644
--- a/iva/__init__.py
+++ b/iva/__init__.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
__all__ = [
'assembly',
'common',
diff --git a/iva/assembly.py b/iva/assembly.py
index 305c1d4..0ac45f9 100644
--- a/iva/assembly.py
+++ b/iva/assembly.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import os
import pysam
import tempfile
diff --git a/iva/common.py b/iva/common.py
index 271d35f..dfaed4d 100644
--- a/iva/common.py
+++ b/iva/common.py
@@ -1,8 +1,22 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import argparse
import os
import sys
import subprocess
-version = '1.0.4'
+version = '1.0.5'
class abspathAction(argparse.Action):
def __call__(self, parser, namespace, value, option_string):
diff --git a/iva/contig.py b/iva/contig.py
index e70d269..7a4eb83 100644
--- a/iva/contig.py
+++ b/iva/contig.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
from iva import kmers
class Contig:
diff --git a/iva/contig_trim.py b/iva/contig_trim.py
index 0ed33c9..5c28e9e 100644
--- a/iva/contig_trim.py
+++ b/iva/contig_trim.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import os
import sys
import shutil
diff --git a/iva/edge.py b/iva/edge.py
index 270e42d..f8e57c5 100644
--- a/iva/edge.py
+++ b/iva/edge.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import copy
from pyfastaq import intervals
diff --git a/iva/egg_extract.py b/iva/egg_extract.py
index b0dc057..443b10f 100644
--- a/iva/egg_extract.py
+++ b/iva/egg_extract.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import zipfile
import tempfile
import shutil
diff --git a/iva/external_progs.py b/iva/external_progs.py
index 8b42054..a63d84b 100644
--- a/iva/external_progs.py
+++ b/iva/external_progs.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import shutil
import subprocess
import re
@@ -23,10 +37,10 @@ prog_to_version_cmd = {
'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')),
'R': ('R --version', re.compile('^R version (.*) \(.*\) --')),
'smalt': ('smalt version', re.compile('^Version: (.*)$')),
- 'samtools': ('samtools', re.compile('^Version: (.*)$')),
+ 'samtools': ('samtools', re.compile('^Version: ([^ ]+)')),
}
-
+
minimum_versions = {
'samtools': '0.1.19'
}
diff --git a/iva/graph.py b/iva/graph.py
index a741c0c..9c289cb 100644
--- a/iva/graph.py
+++ b/iva/graph.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import networkx
from pyfastaq import intervals
from iva import edge
diff --git a/iva/kcount.py b/iva/kcount.py
index 1146c58..8f9a72d 100644
--- a/iva/kcount.py
+++ b/iva/kcount.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import os
import sys
import tempfile
diff --git a/iva/kmers.py b/iva/kmers.py
index a23d399..fed648a 100644
--- a/iva/kmers.py
+++ b/iva/kmers.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
from collections import Counter
class Kmers:
diff --git a/iva/kraken.py b/iva/kraken.py
index fc5bbda..9d96859 100644
--- a/iva/kraken.py
+++ b/iva/kraken.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import stat
import inspect
import sys
diff --git a/iva/mapping.py b/iva/mapping.py
index 681b5be..5da0fbb 100644
--- a/iva/mapping.py
+++ b/iva/mapping.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import os
import re
import subprocess
@@ -5,6 +19,7 @@ import collections
import pyfastaq
import pysam
from iva import common
+from iva import external_progs
class Error (Exception): pass
@@ -78,7 +93,10 @@ def map_reads(reads_fwd, reads_rev, ref_fa, out_prefix, index_k=15, index_s=3, t
if sort:
threads = min(4, threads)
thread_mem = int(500 / threads)
- sort_cmd = 'samtools sort -@' + str(threads) + ' -m ' + str(thread_mem) + 'M ' + intermediate_bam + ' ' + out_prefix
+ if str(external_progs.get_version('samtools')) >= '1.2':
+ sort_cmd = 'samtools sort -@' + str(threads) + ' -m ' + str(thread_mem) + 'M -o ' + final_bam + ' ' + intermediate_bam
+ else:
+ sort_cmd = 'samtools sort -@' + str(threads) + ' -m ' + str(thread_mem) + 'M ' + intermediate_bam + ' ' + out_prefix
index_cmd = 'samtools index ' + final_bam
if verbose >= 2:
print(' map reads. sort: ', sort_cmd)
diff --git a/iva/mummer.py b/iva/mummer.py
index 9f29fb8..98a6abd 100644
--- a/iva/mummer.py
+++ b/iva/mummer.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import os
import tempfile
import shutil
diff --git a/iva/qc.py b/iva/qc.py
index b97eb1b..4aaa4f1 100644
--- a/iva/qc.py
+++ b/iva/qc.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import os
import stat
import inspect
diff --git a/iva/qc_external.py b/iva/qc_external.py
index b04bbb1..e96d545 100644
--- a/iva/qc_external.py
+++ b/iva/qc_external.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import subprocess
import tempfile
import shutil
@@ -140,11 +154,13 @@ def run_ratt(embl_dir, assembly, outdir, config_file=None, transfer='Species', c
assembly = os.path.abspath(assembly)
cwd = os.getcwd()
- try:
- os.mkdir(outdir)
- os.chdir(outdir)
- except:
- raise Error('Error mkdir ' + outdir)
+ if os.path.exists(outdir):
+ if os.path.isdir(outdir):
+ shutil.rmtree(outdir)
+ else:
+ os.unlink(outdir)
+ os.mkdir(outdir)
+ os.chdir(outdir)
extractor = iva.egg_extract.Extractor(os.path.abspath(os.path.join(os.path.dirname(iva.__file__), os.pardir)))
ratt_code_indir = os.path.join('iva', 'ratt')
@@ -200,7 +216,7 @@ def run_ratt(embl_dir, assembly, outdir, config_file=None, transfer='Species', c
except:
pass
- iva.common.syscall('rm query.* Reference.* nucmer.* out.*')
+ iva.common.syscall('rm -f query.* Reference.* nucmer.* out.*')
os.chdir(cwd)
return stats
diff --git a/iva/ratt/embl2gff.pl b/iva/ratt/embl2gff.pl
index 2e2018c..96e21ec 100755
--- a/iva/ratt/embl2gff.pl
+++ b/iva/ratt/embl2gff.pl
@@ -1,4 +1,18 @@
#!/usr/bin/env perl
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
use strict;
use warnings;
diff --git a/iva/ratt/genbank2embl.pl b/iva/ratt/genbank2embl.pl
index a6f29b4..325035e 100755
--- a/iva/ratt/genbank2embl.pl
+++ b/iva/ratt/genbank2embl.pl
@@ -1,4 +1,19 @@
#!/usr/bin/env perl
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
+
use strict;
use warnings;
use Bio::SeqIO;
diff --git a/iva/ratt/main.ratt.pl b/iva/ratt/main.ratt.pl
index 8743c64..a18ab00 100644
--- a/iva/ratt/main.ratt.pl
+++ b/iva/ratt/main.ratt.pl
@@ -1,15 +1,18 @@
#! /usr/bin/perl -w
+# Copyright (c) 2014-2016 Genome Research Ltd.
#
-# File: annotation.correctString.pl
-# Time-stamp: <08-Oct-2010 14:39:38 tdo>
-# $Id: $
-#
-# Copyright (C) 2010 by Pathogene Group, Sanger Center
-#
-# Author: Thomas Dan Otto tdo at sanger.ac.uk and Gary Dilon
-#
-# Description: Please see http://ratt.sourceforge.net for information
+# This file is part of IVA.
#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
use strict;
use Data::Dumper;
diff --git a/iva/ratt/ratt_correction.pm b/iva/ratt/ratt_correction.pm
index 340d7e2..d34099a 100644
--- a/iva/ratt/ratt_correction.pm
+++ b/iva/ratt/ratt_correction.pm
@@ -1,10 +1,19 @@
package ratt_correction;
-# tdo 01.11.09: include that when new contig, the contig with max
-# overhang left, is take
-
-#To DO lkist
-# inlcude %lefthandPosContig
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
use 5.008008;
use strict;
diff --git a/iva/ratt/start.ratt.sh b/iva/ratt/start.ratt.sh
index a601e98..f910794 100755
--- a/iva/ratt/start.ratt.sh
+++ b/iva/ratt/start.ratt.sh
@@ -1,5 +1,18 @@
#!/bin/bash
-
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
refembl=$1
query=$2
diff --git a/iva/read_trim.py b/iva/read_trim.py
index 3f253e8..8a8605a 100644
--- a/iva/read_trim.py
+++ b/iva/read_trim.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import os
from iva import common
diff --git a/iva/seed.py b/iva/seed.py
index 993e31f..405b18a 100644
--- a/iva/seed.py
+++ b/iva/seed.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import copy
import os
import shutil
diff --git a/iva/seed_processor.py b/iva/seed_processor.py
index d62d6b3..4607da8 100644
--- a/iva/seed_processor.py
+++ b/iva/seed_processor.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import tempfile
import os
import sys
diff --git a/iva/test_data_runner.py b/iva/test_data_runner.py
index 6585899..3534d66 100644
--- a/iva/test_data_runner.py
+++ b/iva/test_data_runner.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import os
import iva
@@ -7,7 +21,7 @@ class Tester:
def __init__(self, outdir, iva_script, trimmo_jar=None, threads=1):
self.outdir = os.path.join(outdir)
if os.path.exists(self.outdir):
- raise Error('Output directory alread exists. Cannot continue')
+ raise Error('Output directory already exists. Cannot continue')
self.iva_script = iva_script
self.trimmo_jar = trimmo_jar
diff --git a/iva/tests/assembly_test.py b/iva/tests/assembly_test.py
index 21d5b33..5965650 100644
--- a/iva/tests/assembly_test.py
+++ b/iva/tests/assembly_test.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import unittest
import sys
import os
diff --git a/iva/tests/contig_test.py b/iva/tests/contig_test.py
index c3a136a..840c54d 100644
--- a/iva/tests/contig_test.py
+++ b/iva/tests/contig_test.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
#!/usr/bin/env python3
import unittest
diff --git a/iva/tests/contig_trim_test.py b/iva/tests/contig_trim_test.py
index cda5f22..9300930 100644
--- a/iva/tests/contig_trim_test.py
+++ b/iva/tests/contig_trim_test.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import unittest
import filecmp
import os
diff --git a/iva/tests/edge_test.py b/iva/tests/edge_test.py
index d037a88..3b45fea 100644
--- a/iva/tests/edge_test.py
+++ b/iva/tests/edge_test.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import unittest
import copy
from iva import edge
diff --git a/iva/tests/egg_extract_test.py b/iva/tests/egg_extract_test.py
index 65b7c57..e26d3e6 100644
--- a/iva/tests/egg_extract_test.py
+++ b/iva/tests/egg_extract_test.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import unittest
import sys
import shutil
diff --git a/iva/tests/external_progs_test.py b/iva/tests/external_progs_test.py
index b5ceb13..8795f33 100644
--- a/iva/tests/external_progs_test.py
+++ b/iva/tests/external_progs_test.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import unittest
from iva import external_progs
diff --git a/iva/tests/graph_test.py b/iva/tests/graph_test.py
index 7ba446e..ab7b1f5 100644
--- a/iva/tests/graph_test.py
+++ b/iva/tests/graph_test.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import unittest
import os
import filecmp
diff --git a/iva/tests/kcount_test.py b/iva/tests/kcount_test.py
index 65ae02a..d6aeeb7 100644
--- a/iva/tests/kcount_test.py
+++ b/iva/tests/kcount_test.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import unittest
import os
import filecmp
diff --git a/iva/tests/kmers_test.py b/iva/tests/kmers_test.py
index c7c6912..762f013 100644
--- a/iva/tests/kmers_test.py
+++ b/iva/tests/kmers_test.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import unittest
import os
from iva import kmers
diff --git a/iva/tests/kraken_test.py b/iva/tests/kraken_test.py
index 88b9c80..01ed131 100644
--- a/iva/tests/kraken_test.py
+++ b/iva/tests/kraken_test.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import unittest
import os
import shutil
diff --git a/iva/tests/mapping_test.py b/iva/tests/mapping_test.py
index 3b20e62..9d4033b 100644
--- a/iva/tests/mapping_test.py
+++ b/iva/tests/mapping_test.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import unittest
import pickle
import shutil
diff --git a/iva/tests/mummer_test.py b/iva/tests/mummer_test.py
index 2ed0a35..b037e9a 100644
--- a/iva/tests/mummer_test.py
+++ b/iva/tests/mummer_test.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import unittest
import os
import filecmp
diff --git a/iva/tests/qc_external_test.py b/iva/tests/qc_external_test.py
index bf620df..3507ab8 100644
--- a/iva/tests/qc_external_test.py
+++ b/iva/tests/qc_external_test.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import unittest
import os
import shutil
diff --git a/iva/tests/qc_test.py b/iva/tests/qc_test.py
index 48c47cc..62c0b78 100644
--- a/iva/tests/qc_test.py
+++ b/iva/tests/qc_test.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import unittest
import os
import filecmp
diff --git a/iva/tests/read_trim_test.py b/iva/tests/read_trim_test.py
index 6deebcc..0f7915f 100644
--- a/iva/tests/read_trim_test.py
+++ b/iva/tests/read_trim_test.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import os
import unittest
from iva import read_trim
diff --git a/iva/tests/seed_processor_test.py b/iva/tests/seed_processor_test.py
index 4f14d3e..386518d 100644
--- a/iva/tests/seed_processor_test.py
+++ b/iva/tests/seed_processor_test.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import unittest
import os
import filecmp
diff --git a/iva/tests/seed_test.py b/iva/tests/seed_test.py
index c099725..eb8ef2c 100644
--- a/iva/tests/seed_test.py
+++ b/iva/tests/seed_test.py
@@ -1,3 +1,17 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import unittest
import os
import filecmp
diff --git a/scripts/iva b/scripts/iva
old mode 100755
new mode 100644
index 1484839..55dd7e2
--- a/scripts/iva
+++ b/scripts/iva
@@ -1,4 +1,18 @@
#!/usr/bin/env python3
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import argparse
import os
@@ -15,10 +29,10 @@ parser.add_argument('outdir', help='Name of output directory (must not already e
io_group = parser.add_argument_group('Input and output')
-io_group.add_argument('-f', '--reads_fwd', action=iva.common.abspathAction, help='Name of forward reads fasta/q file. Must be used in conjuction with --reads_rev', metavar='filename[.gz]')
-io_group.add_argument('-r', '--reads_rev', action=iva.common.abspathAction, help='Name of reverse reads fasta/q file. Must be used in conjuction with --reads_fwd', metavar='filename[.gz]')
+io_group.add_argument('-f', '--reads_fwd', action=iva.common.abspathAction, help='Name of forward reads fasta/q file. Must be used in conjunction with --reads_rev', metavar='filename[.gz]')
+io_group.add_argument('-r', '--reads_rev', action=iva.common.abspathAction, help='Name of reverse reads fasta/q file. Must be used in conjunction with --reads_fwd', metavar='filename[.gz]')
io_group.add_argument('--fr', action=iva.common.abspathAction, dest='reads', help='Name of interleaved fasta/q file', metavar='filename[.gz]')
-io_group.add_argument('--keep_files', action='store_true', help='Keep intermediate files (could be many!). Default is to delete all unecessary files')
+io_group.add_argument('--keep_files', action='store_true', help='Keep intermediate files (could be many!). Default is to delete all unnecessary files')
io_group.add_argument('--contigs', action=iva.common.abspathAction, help='Fasta file of contigs to be extended. Incompatible with --reference', metavar='filename[.gz]')
io_group.add_argument('--reference', action=iva.common.abspathAction, help='Fasta file of reference genome, or parts thereof. IVA will try to assemble one contig per sequence in this file. Incompatible with --contigs', metavar='filename[.gz]')
io_group.add_argument('-v', '--verbose', action='count', help='Be verbose by printing messages to stdout. Use up to three times for increasing verbosity.', default=0)
diff --git a/scripts/iva_qc b/scripts/iva_qc
old mode 100755
new mode 100644
index 4849a02..ec4f154
--- a/scripts/iva_qc
+++ b/scripts/iva_qc
@@ -1,4 +1,18 @@
#!/usr/bin/env python3
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import argparse
import os
diff --git a/scripts/iva_qc_make_db b/scripts/iva_qc_make_db
old mode 100755
new mode 100644
index 5798e7c..96d5669
--- a/scripts/iva_qc_make_db
+++ b/scripts/iva_qc_make_db
@@ -1,4 +1,18 @@
#!/usr/bin/env python3
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
import sys
import argparse
diff --git a/setup.py b/setup.py
index dec5c89..f6b1f93 100644
--- a/setup.py
+++ b/setup.py
@@ -1,3 +1,18 @@
+# Copyright (c) 2014-2016 Genome Research Ltd.
+#
+# This file is part of IVA.
+#
+# IVA 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.
+# This program 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
+# this program. If not, see <http://www.gnu.org/licenses/>.
+
import os
import glob
import sys
@@ -32,7 +47,7 @@ if not found_all_progs:
setup(
name='iva',
- version='1.0.4',
+ version='1.0.5',
description='Iterative Virus Assembler',
packages = find_packages(),
package_data={'iva': ['gage/*', 'ratt/*', 'read_trim/*', 'test_run_data/*']},
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/iva.git
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