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1 #!/usr/bin/env python
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2 # pair_fetch_DNA_ff.py
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3 # Function: filter microsat and flanking region by quality score;
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4 # remove read with any base that has lower quality score than "quality_require" within "flanking_base" and convert from snoope to fastq
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5 # Note that require flanking length need to be screen by Bob snoope script first
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6
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7 # Author: Arkarachai Fungtammasan
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8 # Version 1.0.0 (15 July 2012)
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9 # Input format: length_of_repeat[0] left_flank_length[1] right_flank_length[2] repeat_motif[3] hamming_distance[4] read_name[5] read_sequence[6] read_quality[7]
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10 # Output format: two fastq file. First file contain left flank. Second file contain right flank.
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11 # Command: python pair_fetch_DNA_ff.py input.txt
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12
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13 import sys
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14 from galaxy import eggs
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15
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16 def stop_err(msg):
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17 sys.stderr.write(msg)
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18 sys.exit()
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19
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20 # read file name
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21
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22
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23
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24 filename=sys.argv[1]
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25 L_filename=sys.argv[2]
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26 R_filename=sys.argv[3]
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27 quality_require=sys.argv[4]
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28 flanking_base=sys.argv[5]
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29 try:
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30 quality_require=int(quality_require)
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31 flanking_base=int(flanking_base)
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32 except Exception, eee:
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33 print eee
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34 stop_err("Quality score cutoff and Length of flanking regions that require quality screening must be integer")
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35
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36 fd=open(filename)
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37 fdd1=open(L_filename,'w')
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38 fdd2=open(R_filename,'w')
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39 lines=fd.xreadlines()
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40 for line in lines:
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41 temp=line.strip().split('\t')
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42 temp=filter(None,temp)
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43 #get index
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44 left_flank=(0,int(temp[1]))
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45 microsat=(int(temp[1]),int(temp[1])+int(temp[0]))
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46 right_flank=(int(temp[1])+int(temp[0]),int(temp[1])+int(temp[0])+int(temp[2]))
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47 flag=0
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48 #filter length of left and right flank
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49 if (right_flank[1]-right_flank[0])<flanking_base:
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50 continue
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51 if (left_flank[1]-left_flank[0])<flanking_base:
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52 continue
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53 #filter quality score
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54 for i in temp[7][microsat[0]-flanking_base:microsat[1]+flanking_base]:
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55 if ord(i)<(quality_require+33):
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56 flag=1
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57 else:
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58 flag=flag
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59 #print out to seperated files
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60 if flag ==0:
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61 newname= temp[5]##+'_'+temp[3]+'_'+temp[0]
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62 fdd1.writelines('@'+newname+'\n')
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63 fdd2.writelines('@'+newname+'\n')
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64 fdd1.writelines(temp[6][left_flank[0]:left_flank[1]]+'\n')
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65 fdd2.writelines(temp[6][right_flank[0]:right_flank[1]]+'\n')
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66 fdd1.writelines('+'+newname+'\n')
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67 fdd2.writelines('+'+newname+'\n')
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68 fdd1.writelines(temp[7][left_flank[0]:left_flank[1]]+'\n')
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69 fdd2.writelines(temp[7][right_flank[0]:right_flank[1]]+'\n')
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70
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71 fd.close()
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72 fdd1.close()
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73 fdd2.close()
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74
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75
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