def Read_sequencing( path ):
seq_files=[]
if os.path.isdir(path):
seq_files = glob(path+'*.zip')
else: seq_files.append( path )
DNAseq_objs={}
for File in seq_files:
try:
fixBadZipfile( File )
zf = zipfile.ZipFile(File, 'r')
for f in zf.namelist():
if '.seq' not in f: continue
name,seq = read_assembly(zf.open(f,'r').readlines())
name = name.split('.')[0]
if 'Term' in f: seq = libDNA.reverse_complement(seq.lower())
DNAseq_objs[name]= seq.lower().replace(' ','')
except:
print "Can not open "+File
continue
return DNAseq_objs
return (name,seq.lower())
fixBadZipfile(opt.file_path)
zf = zipfile.ZipFile(opt.file_path, 'r')
files= zf.namelist()
out_name=opt.file_path.split("/")[-1].split('.')[0]
dna=open("./"+out_name+'_dna.fasta','w')
out=open("./"+out_name+'_aa.fasta','w')
print "./"+out_name+'_aa.fasta'
for f in files:
if ".seq" not in f: continue
name,seq=read_assembly(zf.open(f,'r').readlines())
if 'Term' in f: seq= libDNA.reverse_complement(seq)
if len(seq) < 20: continue
DnaSeqObj = libDNA.DNASeq(seq)
rf, found = DnaSeqObj.auto_phase(opt.sub)
if found:
aaobj = libAA.AASeq( DnaSeqObj.translate().replace(' ','') )
out.write(">"+name+ aaobj.seq +"\n\n")
else:
out.write(">"+name+ DnaSeqObj.translate().replace(' ','') +"\n\n")
dna.write(">"+name+DnaSeqObj.seq+"\n\n")
continue
i,count = 0,0
while i < len(nativeS):
if nativeS[i] != s1[i]: count+=1
i+=1
return count
dna=libDNA.DNASeq( opt.seq, int(opt.phase) )
start_pos = dna.fetch_position( int(opt.cutsite) - 3 )
end_pos = dna.fetch_position( int(opt.cutsite) + 3 )
sub=dna.seq[start_pos:end_pos+3]
h=libDNA.DNASeq(sub)
nativeAA=libDNA.translate( h.trips )
print nativeAA
slots=[]
for a in nativeAA.replace(' ',''): slots.append([])
for enzyme in ref.restriction.keys():
cut_seq = ref.restriction[ enzyme ][0]
for ph in range(0,3):
tmp=libDNA.DNASeq(dna.seq, int(opt.phase) )
tmp.insert_restrict( enzyme, int(opt.cutsite), int(ph) )
sub=tmp.seq[start_pos:end_pos+3]
h=libDNA.DNASeq(sub)
