SuperProteinTree computes a super protein tree given a set of protein clusters. ####Reconstructing protein and gene phylogenies using reconciliation and soft-clustering Read More: https://www.worldscientific.com/doi/abs/10.1142/S0219720017400078 ####Esaie Kuitche, Manuel Lafond and Aïda Ouangraoua #####Contact Esaie.Kuitche.Kamela@USherbrooke.ca
##Requirements The program requires the following to be available
- python (2.7 and +)
- argparse (https://pypi.python.org/pypi/argparse)
- ete3 (https://pypi.python.org/pypi/ete3/)
##Usage
usage: main.py [-h] [-g GUIDETREE] [-c CLUSTERS] [-o OUTFILE]
SuperProteinTree program parameters
optional arguments:
-h, --help show this help message and exit
-g GUIDETREE, --guideTree GUIDETREE
-c CLUSTERS, --clusters CLUSTERS
-o OUTFILE, --outfile OUTFILE
##Input files ###guideTree Example
((((((ENST00000378295,(ENST00000346387,ENST00000604479)),(ENST00000354437,(ENST00000604074,(ENST00000603362,ENST00000357733)))),((ENST00000378290,ENST00000378288),(ENST00000378285,ENST00000378280))),ENSBTAT00000007643),(ENSMUST00000105644,(ENSMUST00000105643,(ENSMUST00000097762,ENSMUST00000133533)))),((ENSGALT00000011850,ENSGALT00000033346),((ENSMUST00000065523,((ENSMUST00000115310,(ENSMUST00000115305,(ENSMUST00000115307,ENSMUST00000115308))),(ENSMUST00000115304,(ENSMUST00000040231,ENSMUST00000115306)))),(ENSBTAT00000020544,(ENST00000264731,((ENST00000354600,(ENST00000449992,(ENST00000456148,ENST00000392463))),(ENST00000440651,(ENST00000392460,((ENST00000418709,ENST00000437221),(ENST00000392461,ENST00000320472))))))))));
##CLUSTERS Example
/home/user/datas/cluster.cls/
##example of cluter file
ENST00000320472
ENST00000392460
ENSMUST00000065523
ENSBTAT00000007643
ENST00000604074
ENST00000357733
ENST00000603362
ENSGALT00000033346
ENSMUST00000115306
ENSMUST00000115304
ENSMUST00000115307
(ENSBTAT00000020544-ENSMUST00000115310) 0.0
(ENST00000264731-ENSBTAT00000020544) 0.00258519388954
(ENST00000264731-ENSMUST00000115310) 0.00705052878966
(ENSBTAT00000020544-(ENST00000264731-ENSMUST00000115310)) 0.00258519388954
(ENSBTAT00000020544-ENST00000440651) 0.0129259694477
(ENSMUST00000115310-ENST00000440651) 0.0173913043478
(ENSBTAT00000020544-(ENSMUST00000115310-ENST00000440651)) 0.0129259694477
(ENSBTAT00000020544-ENSGALT00000011850) 0.0517038777908
(ENSMUST00000115310-ENSGALT00000011850) 0.0540540540541
(ENSBTAT00000020544-(ENSMUST00000115310-ENSGALT00000011850)) 0.0517038777908
(ENST00000264731-ENSGALT00000011850) 0.056169212691
(ENSBTAT00000020544-(ENST00000264731-ENSGALT00000011850)) 0.0517038777908
((ENSBTAT00000020544-ENSMUST00000115310)-(ENST00000264731-ENSGALT00000011850)) 0.0540540540541
(ENSGALT00000011850-ENST00000440651) 0.0665099882491
##NOTICE each line represents a cluster of proteins, and one protein can be found in more than one cluster
outfile name
superProteinTree.txt
##Running Protein2GeneTree on an example
python src/main.py --guideTree "/home/user/Document/gene/guideTree.nw" --clusters "/home/user/Document/tree/clusters.cls" --outfile "superProteinTree.txt"
or simply
python src/main.py