LeeHuangChen/2018_1_4_MyAlgorithm
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############################# # INSTALLATION INSTRUCTIONS # ############################# To run this program, first you need to run an all-to-all blast from NCBI BLASTp, which you can download at the following link: https://www.biostars.org/p/6541/ Then you should be able to run the all-to-all blast by typing the following in the terminal $ ncbi-blast-2.2.24+/bin/blastp -db my_prot_blast_db -query good_proteins.fasta -outfmt 6 -out all-vs-all.tsv -num_threads 4 (you can change the option -num_threads to the number of cores you have in your computer) now make sure you have an result file that is tab delimited, the format of this file should be: 0 , 1 , 2 , 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 query, subject, %id, alignlen, mismatch, gapopen, qst, qend, sst, send, Evalue, bitscore Now you can put the all-to-all data file(s) to the following folder: InputFiles/BLASTp_AllToAll_Data (a.k.a "blastdir" in configuration.py) Edit the configuration.py file with the parameters you are interested in testing. The parameters are: cutoffRatio: This parameter is used to determine if two hits on the same protein overlapped enough to be consider the same area of the protein. evalueCutoff: This parameter is used to filter out the blast hits that has EValue larger then this number The parameter file is a python file. So make sure you follow python syntax when you are changing its contents! Now open the folder in a terminal (FYI, I use Ubuntu) and type $ python run.py And the program should run! The results should be located in Results/ (a.k.a. "borderResultdir" in configuration.py) ################# # OUTPUT FORMAT # ################# This program also dumps it's information through gpickle so you can load it up and do analysis using python. The ouput format for the python gpickle dump is (moduleNumInfo,familyInfoWrap) , where moduleNumInfo=("Number of modules detected",NumberOfModulesDetected) familyInfoWrap=("ModuleFamilyInfo, Format: Dict\{proteinName, list[borders[moduleId,start,end]] \}", ModuleFamilyInfo) , where ModuleFamilyInfo= Dict{proteinName, list[borders] }" ,where borders=[moduleId,start,end] i.e. if you want to access the dictionary information that contains the protein names as keys and the border information as the values you will have to get it through: loadedinfo[1][1] This output should be located in GeneratedFiles/borderInformation (a.k.a "borderInfodir" in configuration.py)
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