Mercurial > repos > arkarachai-fungtammasan > str_fm
view sequencingdepthconversion_G.py @ 7:90021d286a67 draft
Deleted selected files
author | arkarachai-fungtammasan |
---|---|
date | Mon, 24 Aug 2015 13:45:11 -0400 |
parents | 07588b899c13 |
children |
line wrap: on
line source
def stop_err(msg): sys.stderr.write(msg) sys.exit() def info2require(X,L,F,r): '''infodepth,readlength,flanksize,repeatlength ''' return int(math.ceil((X*L*1.0)/(L-(1*((2*F)+r-1))))) def poissondef(meancov,specificcov): nominator=1.0*(meancov**specificcov)*(math.e**(-1*meancov)) denominator=math.factorial(specificcov) return nominator/denominator def require2recommend(needprob,mindepth): i=mindepth reverseneedprob=1-needprob sumprob=1 while sumprob>reverseneedprob: #mean cov sumprob=0 for j in range(0,mindepth): #specific cov sumprob+=poissondef(i,j) i+=1 return i-1 import sys,math repeatlength=int(sys.argv[1]) flanksize=int(sys.argv[2])#20 readlength=int(sys.argv[3])#100 infodepth=int(sys.argv[4])#5 probdetection=float(sys.argv[5])#0.90 if probdetection >1: try: probvalue=int('probvalue') except Exception, eee: print eee stop_err("Proportion of genome to have certain locus specific must be between 0 and 1") print 'repeat_length'+'\t'+'read_length'+'\t'+'informative_read_depth''\t'+'=locus_specific_sequencing_depth'+'\t'+'=genome_wide_sequencing_depth' t_requiredepth=info2require(infodepth,readlength,flanksize,repeatlength) t_recomendseq=require2recommend(probdetection,t_requiredepth) preplotlist=[repeatlength,readlength,infodepth,t_requiredepth,t_recomendseq] plotlist=map(str,preplotlist) print '\t'.join(plotlist) #print info2require(infodepth,readlength,flanksize,repeatlength) #print poissondef(10,3) #print require2recommend(0.90,80) #informative_read_depth #required_seq_depth #recommend_seq_depth