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11
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1 import sys
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2
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3 compldna = {'A':'T',
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4 'C':'G',
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5 'G':'C',
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6 'T':'A',
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7 'U':'A',
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8 'M':'K',
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9 'K':'M',
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10 'W':'W',
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11 'S':'S',
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12 'R':'Y',
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13 'Y':'R',
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14 'N':'N'}
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15 complrna = {'A':'U',
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16 'C':'G',
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17 'G':'C',
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18 'T':'A',
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19 'U':'A',
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20 'M':'K',
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21 'K':'M',
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22 'W':'W',
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23 'S':'S',
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24 'R':'Y',
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25 'Y':'R',
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26 'N':'N'}
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27 def complement(seq,compl):
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28 complseq = [compl[base] for base in seq]
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29 return complseq
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30
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31 def reverse_complement(seq,compl):
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32 seq = list(seq)
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33 seq.reverse()
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34 return ''.join(complement(seq,compl))
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35
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36 def readFastaFile(infile,outfile,compl):
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37
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38 fin = open(infile)
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39 out = open(outfile,'w')
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40
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41 currSeq=''
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42 currSeqname=None
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43 for line in fin:
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44 if '>' in line:
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45 if currSeqname !=None:
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46 out.write(currSeqname+reverse_complement(currSeq,compl)+'\n')
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47 currSeqname=None
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48 currSeq=''
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49 currSeqname=line
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50 else:
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51 currSeq=currSeq+line.strip().upper()
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52
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53 if currSeqname!=None:
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54 out.write(currSeqname+reverse_complement(currSeq,compl)+'\n')
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55
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56 fin.close()
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57 out.close()
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58
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59 def readrawseq(infile,outfile,compl):
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60 '''
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61 each line is a sequence
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62 '''
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63 fin = open(infile)
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64 out = open(outfile,'w')
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65 for line in fin:
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66 out.write(reverse_complement(line.strip().upper(),compl)+'\n')
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67 fin.close()
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68 out.close()
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69
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70 def main():
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71 seqfile = sys.argv[1]
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72 outfile = sys.argv[2]
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73 fasta = sys.argv[3]
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74 rna = sys.argv[4]
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75 if rna == 'rna':
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76 compl = complrna
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77 else:
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78 compl = compldna
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79 if fasta == 'fasta':
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80 readFastaFile(seqfile,outfile,compl)
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81 else:
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82 readrawseq(seqfile,outfile,compl)
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83
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84 main()
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