diff sequencingdepthconversion_G.py @ 0:07588b899c13 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sequencingdepthconversion_G.py	Wed Apr 01 17:05:51 2015 -0400
@@ -0,0 +1,54 @@
+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
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