Commit 31180b32 authored by emarti2's avatar emarti2
Browse files

Initial commit

parents
This diff is collapsed.
This diff is collapsed.
name,F,A,I,R,average_score
repeatmodeler,0.54,0.0,0.0,0.0,0.135
prigsa2,0.54,0.0,0.0,0.0,0.135
popstr2,0.54,0.0,0.0,0.0,0.135
nanosatellite,0.54,0.0,0.0,0.2,0.185
tricolor,0.9400000000000002,0.565,0.6,0.7,0.7012499999999999
repet,1.0,0.6399999999999999,0.6,0.5,0.6849999999999999
kmasker,1.0,0.0,0.6,0.7,0.575
kmasker,1.0,0.5,0.6,0.7,0.7
ostrfpd,0.54,0.15,0.0,0.5,0.2975
ultra,0.54,0.15,0.0,0.5,0.2975
pipealign2,0.54,0.0,0.0,0.0,0.135
imtrdb,0.54,0.0,0.0,0.5,0.26
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
3d-partner,0.54,0.0,0.0,0.5,0.26
crisprfinder,0.54,0.0,0.0,0.2,0.185
neuropp,0.54,0.0,0.0,0.2,0.185
iterm-pseknc,0.54,0.42,0.0,0.5,0.365
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
mlcs,0.54,0.0,0.0,0.0,0.135
idef-pseraac,0.54,0.0,0.0,0.2,0.185
ltr_finder_parallel,0.54,0.0,0.0,0.0,0.135
mitopred,0.54,0.0,0.0,0.0,0.135
trf,0.54,0.0,0.0,0.3,0.21000000000000002
trf,0.54,0.15,0.0,0.3,0.2475
repeatmasker,0.48,0.075,0.0,0.3,0.21375
repeatmodeler,0.48,0.075,0.0,0.3,0.21375
moods,0.6000000000000001,0.075,0.0,0.5,0.29375
gendecoder,0.54,0.0,0.0,0.0,0.135
remus,0.54,0.0,0.0,0.2,0.185
protparam,0.54,0.0,0.0,0.5,0.26
prorepeat,0.54,0.0,0.0,0.5,0.26
modpropep,0.54,0.0,0.0,0.0,0.135
hslpred,0.54,0.42,0.0,0.5,0.365
fasta,0.54,0.0,0.0,0.5,0.26
snpmasker,0.54,0.0,0.0,0.5,0.26
crisprs database,0.54,0.0,0.0,0.2,0.185
interpro,0.54,0.0,0.0,0.5,0.26
pfam,0.54,0.42,0.1,0.5,0.39
repeatsdb,0.9400000000000002,0.0,0.1,0.5,0.38500000000000006
reputer,0.6000000000000001,0.42,0.7,0.5,0.5549999999999999
reputer,0.6000000000000001,0.6399999999999999,0.7,0.5,0.61
radar,0.54,0.42,0.0,0.8,0.44
trdistiller,0.54,0.15,0.0,0.3,0.2475
gcat,0.9400000000000002,0.15,0.0,0.3,0.34750000000000003
kmer-ssr,0.54,0.075,0.0,0.5,0.27875
repeataround,0.54,0.0,0.0,0.3,0.21000000000000002
uniprobe,0.54,0.0,0.0,0.2,0.185
vivaxgen,0.54,0.0,0.0,0.5,0.26
lrrsearch,0.54,0.0,0.0,0.5,0.26
detectir,0.54,0.6399999999999999,0.0,0.5,0.42
esap plus,0.54,0.0,0.0,0.2,0.185
spotyping,0.9400000000000002,0.15,0.0,0.5,0.3975
sewer,0.54,0.0,0.0,0.2,0.185
gream,0.54,0.0,0.0,0.5,0.26
mreps,0.54,0.0,0.0,0.5,0.26
comsin,0.54,0.0,0.0,0.5,0.26
semgen,0.54,0.15,0.0,0.3,0.2475
sem,0.54,0.0,0.0,0.5,0.26
ipda,0.54,0.0,0.0,0.2,0.185
pvs,0.54,0.0,0.0,0.5,0.26
webmam,0.54,0.0,0.0,0.2,0.185
3d-footprint,0.54,0.0,0.0,0.5,0.26
power,0.54,0.0,0.0,0.5,0.26
molprobity,0.54,0.0,0.0,0.5,0.26
nucleic acid database (ndb),0.54,0.0,0.0,0.5,0.26
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
curves+,0.54,0.0,0.0,0.5,0.26
qgrs mapper,0.54,0.0,0.0,0.5,0.26
gpcrsclass,0.54,0.0,0.0,0.5,0.26
corgen,0.54,0.0,0.0,0.5,0.26
sequence harmony,0.54,0.0,0.0,0.5,0.26
lowcomplexity,0.54,0.0,0.0,0.5,0.26
pubcrawler,0.54,0.0,0.0,0.5,0.26
acg,0.54,0.15,0.0,0.5,0.2975
doutfinder,0.54,0.0,0.0,0.5,0.26
proteus,0.54,0.0,0.0,0.5,0.26
protinfo ppc,0.54,0.0,0.0,0.5,0.26
repeatoire,0.54,0.15,0.0,0.3,0.2475
eslpred,0.54,0.0,0.0,0.5,0.26
strap,0.54,0.0,0.0,0.5,0.26
genebreak,0.9400000000000002,0.6399999999999999,0.22,0.5,0.575
subseqer,0.54,0.0,0.0,0.5,0.26
adgo,0.54,0.0,0.0,0.5,0.26
barcode generator,0.48,0.15,0.0,0.5,0.2825
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
rjprimers,0.54,0.0,0.0,0.5,0.26
tmsoc,0.54,0.0,0.0,0.5,0.26
oddcomp,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
palindrome,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
cpgreport,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
newcpgreport,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
freak,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
density,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
geecee,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
compseq,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
chaos,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
seqentropy,0.54,0.15,0.0,0.3,0.2475
sbars,0.54,0.15,0.0,0.3,0.2475
equicktandem,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
genes by isoelectric point,0.48,0.0,0.1,0.5,0.27
mwcontam,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
wordcount,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
emowse,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
etandem,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
iva,0.54,0.075,0.0,0.0,0.15375
newcpgseek,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
trust,0.54,0.42,0.0,0.3,0.315
peptide match,0.54,0.0,0.1,0.5,0.28500000000000003
mwfilter,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
repdenovo,0.54,0.15,0.0,0.3,0.2475
cpgplot,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
isochore,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
einverted,0.6000000000000001,0.6399999999999999,0.0,0.5,0.435
pssrdb,0.54,0.0,0.0,0.2,0.185
lalign,0.54,0.42,0.0,0.8,0.44
censor,0.54,0.42,0.0,0.8,0.44
satellog,0.54,0.0,0.0,0.5,0.26
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
isochore (ebi),0.54,0.42,0.0,0.8,0.44
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
## 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
[[source]]
name = "pypi"
url = "https://pypi.org/simple"
verify_ssl = true
[dev-packages]
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pandas = "*"
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"sha256:cc8955cfbfc7a115fa81d85284ee61147059a753344bc51098f3ccd69b0d7e0c",
"sha256:d13155f591e6fcc1ec3b30685d50bf0711574e2c0dfffd7644babf8b5102ca1a"
],
"index": "pypi",
"version": "==5.3.1"
},
"six": {
"hashes": [
"sha256:30639c035cdb23534cd4aa2dd52c3bf48f06e5f4a941509c8bafd8ce11080259",
"sha256:8b74bedcbbbaca38ff6d7491d76f2b06b3592611af620f8426e82dddb04a5ced"
],
"version": "==1.15.0"
}
},
"develop": {}
}
This diff is collapsed.
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
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