Python Bioseq.traduit示例

示例#1

文件： fastaDB.py 项目： chungtseng/HCPU_midterm

def dbTraduit(inFileName,phase=0,complement='T',pep_filename=""):
	"""
	deprecated
	"""
	file_db=open(inFileName)
	if pep_filename=="":
		pep_filename=inFileName+'.pep'
	file_pep=open(pep_filename,'w')
	seq=Bioseq()
	seq_out=Bioseq()
	numseq=0
	while 1:
		seq.read(file_db)
		if seq.sequence==None:
			break
		numseq=numseq+1
		print 'sequence #',numseq,'=',seq.getLength(),\
		      '[',seq.header[0:40],'...]'
		
		if phase>=0 :
			if phase==1 or phase==0 :
				seq_out.sequence=seq.traduit(1)
				seq_out.header=seq.header+" (phase 1)"
				seq_out.write(file_pep)

			if phase==2 or phase==0 :
				seq_out.sequence=seq.traduit(2)
				seq_out.header=seq.header+" (phase 2)"
				seq_out.write(file_pep)

			if phase==3 or phase==0 :
				seq_out.sequence=seq.traduit(3)
				seq_out.header=seq.header+" (phase 3)"
				seq_out.write(file_pep)

		if complement=='T' or phase<0 :
			seq.sequence=seq.complement()

			if phase==-1 or phase==0 :
				seq_out.sequence=seq.traduit(1)
				seq_out.header=seq.header+" (phase -1)"
				seq_out.write(file_pep)

			if phase==-2 or phase==0 :
				seq_out.sequence=seq.traduit(2)
				seq_out.header=seq.header+" (phase -2)"
				seq_out.write(file_pep)

			if phase==-3 or phase==0 :
				seq_out.sequence=seq.traduit(3)
				seq_out.header=seq.header+" (phase -3)"
				seq_out.write(file_pep)

	file_db.close()
	file_pep.close()