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def sequence(f):
  4     seq=""
  5     f=open(f)
  6     for line in f:
  7         if ">" in line:
  8             continue
  9         print 'in sequence'
 10         seq+=line.replace("\n","")
 11     return seq
 12     
 13 def domains(fname,seq):
 14     output=open(fname+".fa",'w')
 15     f=open(fname)   
 16     print output
 17     for line in f:
 18         if ">" in line:
 19             continue
 20         print 'in domains'
 21         start=int(line.split()[0])
 22         end=int(line.split()[1])
 23         name=line.split()[2]
 24         test=seq[(start)-1:end]
 25         output.write(">"+name+"\n"+test+"\n")
 26     return test
 27     
 28 #main
 29 
 30 x=os.listdir('.')
 31 
 32 for f in x:
 33     if f.endswith("fasta"):
 34         seq=sequence(f)
 35         fname=f.split('.')[0]
 36         print"erstes",fname
 37     for fname in x:
 38         print "fname",fname
 39         if fname.endswith(".xdom"):
 40             print fname,"xdom"
 41             test=domains(fname,seq)

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  x=os.listdir('.')
 60     for fname in x:
 61         if fname.endswith("fasta"):

aber es gibt einen Fehler in Zeile 17 bei def get_sequence

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from __future__ import with_statement 

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 x=os.listdir('.')
 61     for fasta in x:
 62         if fasta.endswith("fasta"):
 63             print fasta

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def get_domains(fname, xdom_fname):
    with open(fname, "r") as data:
        metas = data.read()
    # Nun den Namen nehmen, der übergeben wird
    seq = get_sequences(fname=xdom_fname)
    # Sequenzen finden
    seq_parts = []
    for lines in re.findall(PARAMS, metas):
        start, end, seq_name = lines.split()
        seq_parts.append(seq[int(start): int(end)])
    return seq_name, seq_parts