diff --git a/VERSION b/VERSION index 7d2ed7c..399088b 100644 --- a/VERSION +++ b/VERSION @@ -1 +1 @@ -2.1.4 +2.1.6 diff --git a/scripts/socru b/scripts/socru index c883024..366200f 100755 --- a/scripts/socru +++ b/scripts/socru @@ -16,8 +16,10 @@ except pkg_resources.DistributionNotFound: version = 'x.y.z' parser = argparse.ArgumentParser( - description = 'calculate the order and orientation of complete bacterial genomes', - usage = 'socru [options] species assembly.fasta', + description = '''Please cite our paper, "Socru: Typing of genome level order and orientation in bacteria", + Andrew J Page, Gemma Langridge, + bioRxiv 543702; (2019) doi: https://doi.org/10.1101/543702''', + usage = 'socru [options] species assembly.fasta', formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('species', help='Species name, use socru_species to see all available', type=str) diff --git a/scripts/socru_create b/scripts/socru_create index da6a007..a46512f 100755 --- a/scripts/socru_create +++ b/scripts/socru_create @@ -14,9 +14,12 @@ except pkg_resources.DistributionNotFound: version = 'x.y.z' parser = argparse.ArgumentParser( - description = 'create genome arrangement type scheme', - usage = 'socru_create [options] output_directory assembly.fasta' - , formatter_class=argparse.ArgumentDefaultsHelpFormatter) + description = ''' + Create genome arrangement type scheme. Please cite our paper, "Socru: Typing of genome level order and orientation in bacteria", + Andrew J Page, Gemma Langridge, + bioRxiv 543702; (2019) doi: https://doi.org/10.1101/543702''', + usage = 'socru_create [options] output_directory assembly.fasta', + formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('output_directory', help='Output directory', type=str) parser.add_argument('input_file', help='Input FASTA file (optionally gzipped)', type=str) diff --git a/scripts/socru_lookup b/scripts/socru_lookup index f4849fc..b69aea1 100755 --- a/scripts/socru_lookup +++ b/scripts/socru_lookup @@ -16,9 +16,12 @@ except pkg_resources.DistributionNotFound: version = 'x.y.z' parser = argparse.ArgumentParser( - description = 'Given a set of fragments, output the type', - usage = 'socru_lookup[options] /path/to/database 1-2-3-4-5-6-7' - , formatter_class=argparse.ArgumentDefaultsHelpFormatter) + description = ''' + "Given a set of fragments, output the type. Please cite our paper, Socru: Typing of genome level order and orientation in bacteria", + Andrew J Page, Gemma Langridge, + bioRxiv 543702; (2019) doi: https://doi.org/10.1101/543702''', + usage = 'socru_lookup[options] /path/to/database 1-2-3-4-5-6-7', + formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('db_dir', help='Database directory', type=str ) parser.add_argument('fragments', help="Fragments such as 1-2-3-4-5-6-7 or 1'-3-4'-5'-6'-7-2", type=str) diff --git a/scripts/socru_rebuild_profile b/scripts/socru_rebuild_profile old mode 100644 new mode 100755 index e219155..7e747d6 --- a/scripts/socru_rebuild_profile +++ b/scripts/socru_rebuild_profile @@ -14,8 +14,11 @@ except pkg_resources.DistributionNotFound: version = 'x.y.z' parser = argparse.ArgumentParser( - description = 'Admin utility which will take in an existing profile and rebuild it', - usage = 'socru_rebuild_profile [options]', + description = ''' + "Admin utility which will take in an existing profile and rebuild it. Please cite our paper, Socru: Typing of genome level order and orientation in bacteria", + Andrew J Page, Gemma Langridge, + bioRxiv 543702; (2019) doi: https://doi.org/10.1101/543702''', + usage = 'socru_rebuild_profile [options]', formatter_class=argparse.ArgumentDefaultsHelpFormatter) parser.add_argument('profile_filename', help="profile.txt from database", type=str) @@ -30,5 +33,3 @@ options = parser.parse_args() g = SocruRebuildProfile(options) g.run() - - diff --git a/setup.py b/setup.py index f8c4404..08ea238 100644 --- a/setup.py +++ b/setup.py @@ -18,7 +18,7 @@ def read(fname): long_description=read('README.md'), packages = find_packages(), author='Andrew J. Page', - author_email='path-help@sanger.ac.uk', + author_email='andrew.page@quadram.ac.uk', url='https://github.com/quadram-institute-bioscience/socru', scripts=glob.glob('scripts/*'), test_suite='nose.collector', diff --git a/socru/data/Acinetobacter_baumannii/profile.txt b/socru/data/Acinetobacter_baumannii/profile.txt index 8dddab2..c8f9459 100644 --- a/socru/data/Acinetobacter_baumannii/profile.txt +++ b/socru/data/Acinetobacter_baumannii/profile.txt @@ -1,6 +1,7 @@ GS Frag_1 Frag_2 Frag_3 Frag_4 Frag_5 Frag_6 1.0 1 2 3 4 5 6 1.1 1' 2 3 4 5 6 +1.8 1 2 3 4' 5 6 1.9 1' 2 3 4' 5 6 2.24 1 2 3 5' 4' 6 2.25 1' 2 3 5' 4' 6 diff --git a/socru/data/Enterobacter_asburiae/1.fa.gz b/socru/data/Enterobacter_asburiae/1.fa.gz index ef91c04..de708e9 100644 Binary files a/socru/data/Enterobacter_asburiae/1.fa.gz and b/socru/data/Enterobacter_asburiae/1.fa.gz differ diff --git a/socru/data/Enterobacter_asburiae/2.fa.gz b/socru/data/Enterobacter_asburiae/2.fa.gz index ce0a07b..a3fee22 100644 Binary files a/socru/data/Enterobacter_asburiae/2.fa.gz and b/socru/data/Enterobacter_asburiae/2.fa.gz differ diff --git a/socru/data/Enterobacter_asburiae/3.fa.gz b/socru/data/Enterobacter_asburiae/3.fa.gz index 90456fe..638880b 100644 Binary files a/socru/data/Enterobacter_asburiae/3.fa.gz and b/socru/data/Enterobacter_asburiae/3.fa.gz differ diff --git a/socru/data/Enterobacter_asburiae/4.fa.gz b/socru/data/Enterobacter_asburiae/4.fa.gz index 916f0f9..9e8b3d2 100644 Binary files a/socru/data/Enterobacter_asburiae/4.fa.gz and b/socru/data/Enterobacter_asburiae/4.fa.gz differ diff --git a/socru/data/Enterobacter_asburiae/5.fa.gz b/socru/data/Enterobacter_asburiae/5.fa.gz index 69f4ac5..3e73cbd 100644 Binary files a/socru/data/Enterobacter_asburiae/5.fa.gz and b/socru/data/Enterobacter_asburiae/5.fa.gz differ diff --git a/socru/data/Enterobacter_asburiae/6.fa.gz b/socru/data/Enterobacter_asburiae/6.fa.gz index 20d08d7..063b19d 100644 Binary files a/socru/data/Enterobacter_asburiae/6.fa.gz and b/socru/data/Enterobacter_asburiae/6.fa.gz differ diff --git a/socru/data/Enterobacter_asburiae/7.fa.gz b/socru/data/Enterobacter_asburiae/7.fa.gz index db94958..1bd6de8 100644 Binary files a/socru/data/Enterobacter_asburiae/7.fa.gz and b/socru/data/Enterobacter_asburiae/7.fa.gz differ diff --git a/socru/data/Enterobacter_asburiae/8.fa.gz b/socru/data/Enterobacter_asburiae/8.fa.gz new file mode 100644 index 0000000..99fa5ed Binary files /dev/null and b/socru/data/Enterobacter_asburiae/8.fa.gz differ diff --git a/socru/data/Enterobacter_asburiae/profile.txt b/socru/data/Enterobacter_asburiae/profile.txt index d298cca..64ae40e 100644 --- a/socru/data/Enterobacter_asburiae/profile.txt +++ b/socru/data/Enterobacter_asburiae/profile.txt @@ -1,2 +1,4 @@ -GS Frag_1 Frag_2 Frag_3 Frag_4 Frag_5 Frag_6 Frag_7 -1.0 1 2 3 4 5 6 7 +GS Frag_1 Frag_2 Frag_3 Frag_4 Frag_5 Frag_6 Frag_7 Frag_8 +1.0 1 2 3 4 5 6 7 8 +1.1 1' 2 3 4 5 6 7 8 + diff --git a/socru/data/Enterobacter_asburiae/profile.txt.yml b/socru/data/Enterobacter_asburiae/profile.txt.yml index 14d1fc1..00bd450 100644 --- a/socru/data/Enterobacter_asburiae/profile.txt.yml +++ b/socru/data/Enterobacter_asburiae/profile.txt.yml @@ -1,3 +1,3 @@ -dnaa_forward_orientation: true -dnaa_fragment: 6 -reference_genome: Enterobacter/asburiae/LF7a/GCF_000224675.1_ASM22467v1_genomic.fna.gz +dnaa_forward_orientation: false +dnaa_fragment: 4 +reference_genome: Enterobacter/asburiae/asburiae_L1/GCF_000632395.1_ASM63239v1_genomic.fna.gz diff --git a/socru/data/Enterobacter_cloacae/1.fa.gz b/socru/data/Enterobacter_cloacae/1.fa.gz index a597c88..7502e7b 100644 Binary files a/socru/data/Enterobacter_cloacae/1.fa.gz and b/socru/data/Enterobacter_cloacae/1.fa.gz differ diff --git a/socru/data/Enterobacter_cloacae/2.fa.gz b/socru/data/Enterobacter_cloacae/2.fa.gz index 5ab4688..092edcc 100644 Binary files a/socru/data/Enterobacter_cloacae/2.fa.gz and b/socru/data/Enterobacter_cloacae/2.fa.gz differ diff --git a/socru/data/Enterobacter_cloacae/3.fa.gz b/socru/data/Enterobacter_cloacae/3.fa.gz index 66b7ca5..c229403 100644 Binary files a/socru/data/Enterobacter_cloacae/3.fa.gz and b/socru/data/Enterobacter_cloacae/3.fa.gz differ diff --git a/socru/data/Enterobacter_cloacae/4.fa.gz b/socru/data/Enterobacter_cloacae/4.fa.gz index 99544ed..0a41fa2 100644 Binary files a/socru/data/Enterobacter_cloacae/4.fa.gz and b/socru/data/Enterobacter_cloacae/4.fa.gz differ diff --git a/socru/data/Enterobacter_cloacae/5.fa.gz b/socru/data/Enterobacter_cloacae/5.fa.gz index 92602d2..94d56a7 100644 Binary files a/socru/data/Enterobacter_cloacae/5.fa.gz and b/socru/data/Enterobacter_cloacae/5.fa.gz differ diff --git a/socru/data/Enterobacter_cloacae/6.fa.gz b/socru/data/Enterobacter_cloacae/6.fa.gz index a9e0ba3..75da6ef 100644 Binary files a/socru/data/Enterobacter_cloacae/6.fa.gz and b/socru/data/Enterobacter_cloacae/6.fa.gz differ diff --git a/socru/data/Enterobacter_cloacae/7.fa.gz b/socru/data/Enterobacter_cloacae/7.fa.gz index d2bb858..984233e 100644 Binary files a/socru/data/Enterobacter_cloacae/7.fa.gz and b/socru/data/Enterobacter_cloacae/7.fa.gz differ diff --git a/socru/data/Enterobacter_cloacae/8.fa.gz b/socru/data/Enterobacter_cloacae/8.fa.gz index 89c97bc..470ac8e 100644 Binary files a/socru/data/Enterobacter_cloacae/8.fa.gz and b/socru/data/Enterobacter_cloacae/8.fa.gz differ diff --git a/socru/data/Enterobacter_cloacae/profile.txt b/socru/data/Enterobacter_cloacae/profile.txt index e98dee6..db79a53 100644 --- a/socru/data/Enterobacter_cloacae/profile.txt +++ b/socru/data/Enterobacter_cloacae/profile.txt @@ -1,3 +1,4 @@ -GS Frag_1 Frag_2 Frag_3 Frag_4 Frag_5 Frag_6 Frag_7 Frag_8 -1.0 1 2 3 4 5 6 7 8 -2.57 1' 2 3 6' 5' 4' 7 8 +GS Frag_1 Frag_2 Frag_3 Frag_4 Frag_5 Frag_6 Frag_7 Frag_8 +1.0 1 2 3 4 5 6 7 8 +1.1 1' 2 3 4 5 6 7 8 +2.57 1' 2 3 6' 5' 4' 7 8 diff --git a/socru/data/Enterobacter_cloacae/profile.txt.yml b/socru/data/Enterobacter_cloacae/profile.txt.yml index d5454e3..157c3b4 100644 --- a/socru/data/Enterobacter_cloacae/profile.txt.yml +++ b/socru/data/Enterobacter_cloacae/profile.txt.yml @@ -1,3 +1,3 @@ dnaa_forward_orientation: true dnaa_fragment: 6 -reference_genome: Enterobacter/cloacae/ATCC_13047/GCF_000025565.1_ASM2556v1_genomic.fna.gz +reference_genome: Enterobacter/cloacae/cloacae_ATCC_13047/GCF_000025565.1_ASM2556v1_genomic.fna.gz diff --git a/socru/data/Enterobacter_hormaechei/profile.txt b/socru/data/Enterobacter_hormaechei/profile.txt index 8d6db2e..2f85587 100644 --- a/socru/data/Enterobacter_hormaechei/profile.txt +++ b/socru/data/Enterobacter_hormaechei/profile.txt @@ -1,3 +1,4 @@ GS Frag_1 Frag_2 Frag_3 Frag_4 Frag_5 Frag_6 Frag_7 Frag_8 1.0 1 2 3 4 5 6 7 8 -2.131 1' 8' 3 4 5 6 7 2' +2.0 1 2 5 3 4 6 7 8 +3.131 1' 8' 3 4 5 6 7 2' diff --git a/socru/data/Enterobacter_sp./profile.txt b/socru/data/Enterobacter_sp./profile.txt index d298cca..00df186 100644 --- a/socru/data/Enterobacter_sp./profile.txt +++ b/socru/data/Enterobacter_sp./profile.txt @@ -1,2 +1,3 @@ GS Frag_1 Frag_2 Frag_3 Frag_4 Frag_5 Frag_6 Frag_7 1.0 1 2 3 4 5 6 7 +2.24 1 2 3 5' 4' 6 7 diff --git a/socru/data/Enterococcus_faecium/profile.txt b/socru/data/Enterococcus_faecium/profile.txt index b2c9280..aad3f20 100644 --- a/socru/data/Enterococcus_faecium/profile.txt +++ b/socru/data/Enterococcus_faecium/profile.txt @@ -5,4 +5,5 @@ GS Frag_1 Frag_2 Frag_3 Frag_4 Frag_5 Frag_6 2.0 6 1 2 3 4 5 3.24 1 5' 4' 2 3 6 4.32 1 6' 2 3 4 5 +4.33 1' 6' 2 3 4 5 5.35 1' 6' 3 4 5 2' diff --git a/socru/data/Escherichia_coli/profile.txt b/socru/data/Escherichia_coli/profile.txt index 3118557..2e815d3 100644 --- a/socru/data/Escherichia_coli/profile.txt +++ b/socru/data/Escherichia_coli/profile.txt @@ -1,8 +1,14 @@ GS Frag_1 Frag_2 Frag_3 Frag_4 Frag_5 Frag_6 Frag_7 1.0 1 2 3 4 5 6 7 +1.1 1' 2 3 4 5 6 7 1.2 1 2' 3 4 5 6 7 +1.24 1 2 3 4' 5' 6 7 +1.25 1' 2 3 4' 5' 6 7 +1.64 1 2 3 4 5 6 7' +1.9 1' 2 3 4' 5 6 7 1.123 1' 7' 6' 5' 4' 3 2' 2.67 1' 7' 3 4 5 6 2' +2.90 1 7' 3 4' 5' 6 2' 3.25 1' 4' 5' 2 3 6 7 4.96 1 7' 6' 2 3 4 5 4.97 1' 7' 6' 2 3 4 5 @@ -14,3 +20,5 @@ GS Frag_1 Frag_2 Frag_3 Frag_4 Frag_5 Frag_6 Frag_7 10.65 1' 7' 2 3 4 5 6 11.59 1' 4' 6' 5' 3 7 2' 12.56 1 2 3 6' 5' 4' 7 +13.113 1' 7' 6' 5' 2 3 4 +14.64 1 2 7' 3 4 5 6 diff --git a/socru/data/Klebsiella_pneumoniae/profile.txt b/socru/data/Klebsiella_pneumoniae/profile.txt index 09ea341..cce3685 100644 --- a/socru/data/Klebsiella_pneumoniae/profile.txt +++ b/socru/data/Klebsiella_pneumoniae/profile.txt @@ -6,3 +6,6 @@ GS Frag_1 Frag_2 Frag_3 Frag_4 Frag_5 Frag_6 Frag_7 Frag_8 3.24 1 2 5' 4' 3 6 7 8 4.131 1' 8' 3 4 5 6 7 2' 5.0 1 2 3 5 4 6 7 8 +6.3 1' 3 4 5 6 7 8 2' +7.32 1 2 3 4 5 7 8 6' +8.35 1' 6' 3 4 5 6 7 2' diff --git a/socru/data/Listeria_monocytogenes/profile.txt b/socru/data/Listeria_monocytogenes/profile.txt index d9ded42..becf4e2 100644 --- a/socru/data/Listeria_monocytogenes/profile.txt +++ b/socru/data/Listeria_monocytogenes/profile.txt @@ -1,5 +1,7 @@ GS Frag_1 Frag_2 Frag_3 Frag_4 Frag_5 Frag_6 1.0 1 2 3 4 5 6 +1.16 1 2 3 4 5' 6 2.56 1 2 3 6' 5' 4' 3.33 1' 6' 2 3 4 5 4.48 1 2 3 4 6' 5' +5.35 1' 6' 3 4 5 2' diff --git a/socru/data/Pseudomonas_aeruginosa/profile.txt b/socru/data/Pseudomonas_aeruginosa/profile.txt index d5f2987..861c14f 100644 --- a/socru/data/Pseudomonas_aeruginosa/profile.txt +++ b/socru/data/Pseudomonas_aeruginosa/profile.txt @@ -1,7 +1,7 @@ GS Frag_1 Frag_2 Frag_3 Frag_4 1.0 1 2 3 4 +1.1 1' 2 3 4 1.9 1' 2 3 4' -2.1 2 3 4 1' -3.2 1 3 4 2' -3.3 1' 3 4 2' -3.11 1' 3 4' 2' +2.2 1 3 4 2' +2.3 1' 3 4 2' +2.11 1' 3 4' 2' diff --git a/socru/data/Salmonella_enterica/profile.txt b/socru/data/Salmonella_enterica/profile.txt index 07cc9c5..31f4c26 100644 --- a/socru/data/Salmonella_enterica/profile.txt +++ b/socru/data/Salmonella_enterica/profile.txt @@ -14,6 +14,7 @@ GS Frag_1 Frag_2 Frag_3 Frag_4 Frag_5 Frag_6 Frag_7 8.66 1 7' 3 4 5 6 2' 8.67 1' 7' 3 4 5 6 2' 9.2 1 3 4 5 6 7 2' +9.3 1' 3 4 5 6 7 2' 10.74 1 7' 4' 3 5 6 2' 11.0 1 2 3 5 6 4 7 11.1 1' 2 3 5 6 4 7 diff --git a/socru/data/Staphylococcus_aureus/profile.txt b/socru/data/Staphylococcus_aureus/profile.txt index 17f6a64..ac78f8b 100644 --- a/socru/data/Staphylococcus_aureus/profile.txt +++ b/socru/data/Staphylococcus_aureus/profile.txt @@ -1,3 +1,8 @@ GS Frag_1 Frag_2 Frag_3 Frag_4 Frag_5 Frag_6 1.0 1 2 3 4 5 2.0 1 2 3 4 5 6 +2.1 1' 2 3 4 5 6 +3.16 1 2 5' 3 4 +4.17 1' 5' 2 3 4 +5.3 1' 3 4 5 2' +6.3 1' 3 4 5 6 2'