Delete make_variable_fasta.py

scripts_phylogeny/make_variable_fasta.py

-
-from Bio import SeqIO
-from joblib import Parallel, delayed
-import argparse
-import re
-
-
-############################################################			define arg type float 0 < X > 1		###############################################################
-
-def restricted_float(x):
-    x = float(x)
-    if x < 0.0 or x > 1.0:
-        raise argparse.ArgumentTypeError("%r not in range [0.0, 1.0]"%(x,))
-    return x
-
-##########################################		find if a position is variable		#######################
-def find_variable(n):
-	out={}
-	#print "nnnnnnnnnnnnnn"
-	print n
-	pos=""
-	for name, seq in fasta.items():
-		pos += seq[n]
-	#print pos
-	seq_length=len(pos)
-	good_seq_length=len(re.findall('[ATCGatcg]', pos))
-	ratio= float(good_seq_length)/float(seq_length)
-	#print ratio
-	if (ratio >= arguments.missing):
-		A=len(re.findall('[Aa]', pos))		
-		T=len(re.findall('[Tt]', pos))
-		G=len(re.findall('[Gg]', pos))
-		C=len(re.findall('[Cc]', pos))
-		if (A > 0):
-			A=1
-		if (T > 0):
-			T=1
-		if (C > 0):
-			C=1
-		if (G > 0):
-			G=1
-		if ((A+C+G+T) > 1):
-			#print pos
-			for name_out, seq_out in fasta.items():
-				OUT[name_out] += seq_out[n]
-
-			#print OUT
-			
-
-	#print out
-	return OUT
-
-
-##########################################		parallel loop		#######################
-def parallel_loop(i):
-	n=i
-	print "iiiiii"
-	print i
-	while n < length:
-		print "n=" + str(n)
-		print "i=" + str(i)
-			
-		OUT=find_variable(n)
-		#print temp_out
-		n=n+arguments.cpu    			#n of  threads
-		#if temp_out:
-			#OUT.update(temp_out)
-			#for name_out, seq_out in temp_out.items():
-				#OUT[name_out] += temp_out[name_out]
-
-	#tot.update(OUT)		
-	#print OUT
-	return OUT
-
-
-
-
-
-parser = argparse.ArgumentParser()
-
-parser.add_argument('INFILE',type=str,help='path to the multi fasta alignment')
-parser.add_argument('-m','--missing', metavar='0-1', default='0.5', help='minimum percentage of NOT missing data', type =restricted_float,nargs='?')
-parser.add_argument('-c','--cpu', metavar='INT', default=1,help='number of cpu to use (default: 1)',type =int, nargs='?')
-
-
-
-
-
-arguments = parser.parse_args()
-tot={}
-fasta={}
-OUT={}
-
-for record in SeqIO.parse(arguments.INFILE, "fasta"):
-	length = len(record.seq)
-	fasta.update({str(record.id):str(record.seq)})
-	OUT.update({str(record.id):""})
-
-print "fasta reas" 
-OUT = Parallel(n_jobs=arguments.cpu)(delayed(find_variable)(i) for i in range(0,length))
-
-
-#print OUT
-
-
-result={}
-for d in OUT:								#when run
-	result.update(d)
-#print OUT
-
-
-#print result
-
-for name_out, seq_out in result.items():
-	print ">" + name_out
-	print seq_out
-	#scp print len(seq_out)
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