Initial commit

output/run_3scores.csv

+name,F,A,I,R,average_score
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+prigsa2,0.54,0.0,0.0,0.0,0.135
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+imtrdb,0.54,0.15,0.0,0.5,0.2975
+hhrep,0.54,0.0,0.0,0.0,0.135
+cbs das protein viewer,0.54,0.0,0.0,0.2,0.185
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+repex,0.54,0.42,0.0,0.5,0.365
+hipstr,0.54,0.48999999999999994,0.6,0.3,0.4825
+scdney,0.54,0.0,0.0,0.2,0.185
+expansionhunter denovo,0.54,0.0,0.0,0.0,0.135
+deepspcas9_autogenerated,0.54,0.0,0.0,0.2,0.185
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+trdistiller,0.54,0.15,0.0,0.3,0.2475
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+lrrsearch,0.54,0.0,0.0,0.5,0.26
+detectir,0.54,0.6399999999999999,0.0,0.5,0.42
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+sewer,0.54,0.0,0.0,0.2,0.185
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+comsin,0.54,0.0,0.0,0.5,0.26
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+sem,0.54,0.0,0.0,0.5,0.26
+ipda,0.54,0.0,0.0,0.2,0.185
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+power,0.54,0.0,0.0,0.5,0.26
+molprobity,0.54,0.0,0.0,0.5,0.26
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+ndb tools,0.54,0.0,0.0,0.5,0.26
+disulfind,0.54,0.0,0.0,0.5,0.26
+pcfamily,0.54,0.0,0.0,0.5,0.26
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+lowcomplexity,0.54,0.0,0.0,0.5,0.26
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+web 3dna,0.54,0.0,0.0,0.5,0.26
+logobar,0.54,0.0,0.0,0.5,0.26
+elastodb,0.54,0.0,0.0,0.5,0.26
+chop,0.54,0.0,0.0,0.5,0.26
+popscomp,0.54,0.0,0.0,0.5,0.26
+ltr_finder,0.54,0.0,0.0,0.2,0.185
+pbil,0.54,0.0,0.0,0.5,0.26
+uniqueprot,0.54,0.0,0.0,0.5,0.26
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+tmsoc,0.54,0.0,0.0,0.5,0.26
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+newcpgreport (ebi),0.54,0.42,0.0,0.8,0.44
+cpgplot (ebi),0.54,0.42,0.0,0.8,0.44
+polyq,0.54,0.0,0.0,0.5,0.26
+tral,0.54,0.15,0.1,0.5,0.3225
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+reupred,0.54,0.15,0.1,0.3,0.2725
+trap,0.54,0.15,0.0,0.3,0.2475
+vntrfinder,0.54,0.15,0.0,0.3,0.2475
+metacluster,0.54,0.075,0.0,0.3,0.22875
+repeatrunner,0.54,0.075,0.0,0.3,0.22875
+seqcalc,0.54,0.0,0.0,0.3,0.21000000000000002
+appex,0.54,0.42,0.0,0.3,0.315
+kindock,0.54,0.0,0.0,0.0,0.135
+pdbselect,0.54,0.0,0.0,0.0,0.135
+repro,0.54,0.42,0.0,0.3,0.315
+atrhunter,0.54,0.42,0.0,0.3,0.315
+atrhunter,0.54,0.15,0.0,0.3,0.2475
+plotrep,0.54,0.0,0.0,0.0,0.135
+tmb-hunt,0.54,0.0,0.0,0.0,0.135
+crisprcompar,0.54,0.0,0.0,0.0,0.135
+mam,0.54,0.0,0.0,0.0,0.135
+repper,0.54,0.0,0.0,0.0,0.135
+genes by epitopes presence,0.48,0.0,0.1,0.5,0.27
+genes by molecular weight,0.48,0.0,0.1,0.5,0.27
+genes by predicted signal peptide,0.48,0.0,0.1,0.5,0.27

readme.md

+## Usage
+
+```
+python3 biotools_quality_assessment.py config.yaml
+```
+
+### Config file
+yaml file that specifies the input and output files paths
+```
+input_file: /home/eva/FAIRplus/tooling/tools_discovery/output/run_3.json
+output_path: /home/eva/FAIRplus/tooling/tool_quality_assessment/output
+output_name: run_3
+```
+
+## Requirements
+The packages:
+- `pyYAML` 
+- `pandas` 
+are needed to run this program. 
+A virtual environment can be used. To do so, run:
+
+```
+pipenv install
+```
+Then, do not forget to run the program in that environment either from `pipenv shell` or using `pipenv run` before each command.
+
+Alternaively to using a virtual environment, you can install the packages in your system:
+```
+python3 -m pip install pyYAML
+```
+```
+python3 -m pip install pandas
+```
\ No newline at end of file

src/Pipfile

+[[source]]
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+url = "https://pypi.org/simple"
+verify_ssl = true
+
+[dev-packages]
+
+[packages]
+pyyaml = "*"
+pandas = "*"
+
+[requires]
+python_version = "3.6"

src/Pipfile.lock

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+                "sha256:4f4b913ca1a7319b33cfb1369e91e50354d6f07a135f3b901aca02aa95940bd2",
+                "sha256:6034f55dab5fea9e53f436aa68fa3ace2634918e8b5994d82f3621c04ff5ed2e",
+                "sha256:69f00dca373f240f842b2931fb2c7e14ddbacd1397d57157a9b005a6a9942648",
+                "sha256:73f099454b799e05e5ab51423c7bcf361c58d3206fa7b0d555426b1f4d9a3eaf",
+                "sha256:74809a57b329d6cc0fdccee6318f44b9b8649961fa73144a98735b0aaf029f1f",
+                "sha256:7739fc0fa8205b3ee8808aea45e968bc90082c10aef6ea95e855e10abf4a37b2",
+                "sha256:95f71d2af0ff4227885f7a6605c37fd53d3a106fcab511b8860ecca9fcf400ee",
+                "sha256:ad9c67312c84def58f3c04504727ca879cb0013b2517c85a9a253f0cb6380c0a",
+                "sha256:b8eac752c5e14d3eca0e6dd9199cd627518cb5ec06add0de9d32baeee6fe645d",
+                "sha256:cc8955cfbfc7a115fa81d85284ee61147059a753344bc51098f3ccd69b0d7e0c",
+                "sha256:d13155f591e6fcc1ec3b30685d50bf0711574e2c0dfffd7644babf8b5102ca1a"
+            ],
+            "index": "pypi",
+            "version": "==5.3.1"
+        },
+        "six": {
+            "hashes": [
+                "sha256:30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259",
+                "sha256:8b74bedcbbbaca38ff6d7491d76f2b06b3592611af620f8426e82dddb04a5ced"
+            ],
+            "version": "==1.15.0"
+        }
+    },
+    "develop": {}
+}

src/config.yaml

+input_file: /home/eva/FAIRplus/tooling/tools_discovery/output/run_3.json
+output_path: /home/eva/FAIRplus/tooling/tool_quality_assessment/output
+output_name: run_3