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1 import subprocess, os, sys, shutil, tempfile, os.path
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2 from os.path import basename, splitext
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3
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4 ## inputs
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5 kmer_value = sys.argv[7]
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6 smallc_value = sys.argv[8]
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7 bigc_value = sys.argv[9]
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8 output_contex_value = sys.argv[10]
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9 counts_value = sys.argv[11]
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10 input_dat = sys.argv[12:len(sys.argv):2] # contains filename1... filenameq
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11 input_ext = sys.argv[13:len(sys.argv):2] # contains extension1... extensionq
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12
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13 ## tmp directory
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14 tmp_dir = tempfile.mkdtemp(prefix='kissplice-galaxy.')
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15
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16 ## command line (init)
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17 command_line = []
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18 command_line.append("kissplice")
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19
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20 ## symlink for .fasta/q (extension required)
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21 ## command line built with -r option
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22 identifier = ""
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23 for i in range(0,len(input_dat)):
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24 tmp_input_fasta = os.path.join(tmp_dir, 'input'+str(i)+'.'+input_ext[i])
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25 identifier += 'input'+str(i)+'_'
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26 os.symlink(input_dat[i], tmp_input_fasta)
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27 command_line.append("-r")
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28 command_line.append(tmp_input_fasta)
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29
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30 ## command line (end)
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31 opath=tmp_dir+"/results"
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32 nocontext = ""
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33 nosnp = ""
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34 if output_contex_value == "yes":
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35 command_line.extend(["-k", kmer_value,
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36 "-c", smallc_value, "-C", bigc_value,
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37 "--counts", counts_value, "--output-context",
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38 "-o", opath, "-s"])
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39 else:
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40 command_line.extend(["-k", kmer_value,
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41 "-c", smallc_value, "-C", bigc_value,
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42 "--counts", counts_value,
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43 "-o", opath, "-s"])
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44
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45 ## running kissplice
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46 p=subprocess.Popen(command_line,
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47 stdout=subprocess.PIPE,stderr=subprocess.PIPE)
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48 stdoutput = p.communicate()
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49
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50 ## outputs
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51 output_f1=sys.argv[1]
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52 out1=open(output_f1, 'w' )
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53 out1.write(stdoutput[0])
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54 out1.close()
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55
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56 output_type0=sys.argv[2]
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57 output_type1=sys.argv[3]
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58 output_type2=sys.argv[4]
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59 output_type3=sys.argv[5]
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60 output_type4=sys.argv[6]
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61
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62 result_type0 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_0.fa"
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63 result_type1 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_1.fa"
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64 result_type2 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_2.fa"
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65 result_type3 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_3.fa"
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66 result_type4 = opath+"/"+"results_"+identifier+"k"+kmer_value+"_coherents_type_4.fa"
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67
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68 shutil.move(result_type0, output_type0)
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69 shutil.move(result_type1, output_type1)
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70 shutil.move(result_type2, output_type2)
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71 shutil.move(result_type3, output_type3)
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72 shutil.move(result_type4, output_type4)
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73
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74 ## cleaning
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75 shutil.rmtree(tmp_dir)
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