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 <[email protected]> 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 [email protected] 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
