v1.3.0 : updated command line argument --mode to --phylum ; added columns...
v1.3.0 : updated command line argument --mode to --phylum ; added columns Start_of_most_upstream_SP and Stop_of_most_downstream_SP ; fixed visualization files (.gb, .embl, .gff) generated by ICEscreen for genome accession that generates no significant alignment match ; New ICEscreen command line option: --print_version_dependencies ; fixed [Issue #13](https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/issues/13), [Issue #14](https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/issues/14), [Issue #15](https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/issues/15), and [Issue #16](https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/issues/16) ; only the overall best alignment match for a query locus tag is considered ; more consistent selection of best scoring HMM profile ; module to detect the structure of the mobile element is now generic for the type of signature proteins from the conjugation module
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- .gitignore 2 additions, 1 deletion.gitignore
- .gitlab-ci.yml 3 additions, 4 deletions.gitlab-ci.yml
- LOG_public_releases.md 24 additions, 1 deletionLOG_public_releases.md
- README.md 1 addition, 1 deletionREADME.md
- icescreen 201 additions, 56 deletionsicescreen
- icescreen_detection_ME/README 1 addition, 1 deletionicescreen_detection_ME/README
- icescreen_detection_ME/icescreen.conf 2 additions, 1 deletionicescreen_detection_ME/icescreen.conf
- icescreen_detection_ME/runTests.sh 92 additions, 476 deletionsicescreen_detection_ME/runTests.sh
- icescreen_detection_ME/src/EMStructure.py 210 additions, 467 deletionsicescreen_detection_ME/src/EMStructure.py
- icescreen_detection_ME/src/EMTypeStructure.py 141 additions, 144 deletionsicescreen_detection_ME/src/EMTypeStructure.py
- icescreen_detection_ME/src/commonMethods.py 79 additions, 3 deletionsicescreen_detection_ME/src/commonMethods.py
- icescreen_detection_ME/src/hit.py 51 additions, 187 deletionsicescreen_detection_ME/src/hit.py
- icescreen_detection_ME/src/icescreen_OO.py 156 additions, 336 deletionsicescreen_detection_ME/src/icescreen_OO.py
- icescreen_detection_ME/src/rulesAddIntegrases.py 130 additions, 183 deletionsicescreen_detection_ME/src/rulesAddIntegrases.py
- icescreen_detection_ME/src/rulesMergeICEIMEStructures.py 105 additions, 245 deletionsicescreen_detection_ME/src/rulesMergeICEIMEStructures.py
- icescreen_detection_ME/src/rulesSeedSPExtension.py 21 additions, 58 deletionsicescreen_detection_ME/src/rulesSeedSPExtension.py
- icescreen_detection_ME/tests/test_files/mode/bacillota.yml 1 addition, 1 deletionicescreen_detection_ME/tests/test_files/mode/bacillota.yml
- icescreen_detection_ME/tests/test_files/mode/pseudomonadota.yml 214 additions, 0 deletions...een_detection_ME/tests/test_files/mode/pseudomonadota.yml
- icescreen_detection_ME/tests/test_files/test10_fragmented_SPs.gb 224 additions, 0 deletions...en_detection_ME/tests/test_files/test10_fragmented_SPs.gb
- icescreen_detection_ME/tests/test_files/test1_NC_004668.1.gb 28 additions, 0 deletionsicescreen_detection_ME/tests/test_files/test1_NC_004668.1.gb
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