Mercurial > repos > megan-shortridge > degenerateprimerremoval_fastq

annotate cut_degen.py @ 0:716cdcccc919 draft default tip

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planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
author megan-shortridge
date Tue, 15 Sep 2015 14:14:41 -0400
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716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
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1 #This is a version that is meant to work with Fastq files
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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2 import Bio
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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3 from Bio import SeqUtils
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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4 from Bio import SeqIO
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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5 import sys
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
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7
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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8 #for records and adapter, should be sys.argv[1 and 2]
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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9 fastqfile = sys.argv[1] #This is the input fasta file
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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10 adapter = sys.argv[2] #This is the input adapter as a string
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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11 keepreads = sys.argv[3] #True or false, this will determine whether or not reads are kept. If true, it will keep reads that do not have the adapter in it. If false, it will get rid of those reads.
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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12 removeadapters = sys.argv[4] #True or false, if this is True, the adapters will be removed. If true, removes the adapters from the sequences. If false, it keeps them.
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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13 end_defn = sys.argv[5] #If 5, the primer is removed from the 5' end of the sequence. If 3, then it is removed from the 3' end of the sequence.
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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14 adapter_name = sys.argv[6] #This is the name of the adapter that you can put into the output text file.
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
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716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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17 # Here is the command for the test: python cut_degen.py 'test.fastq' 'GAACWAYWYCT' 'True' 'True' '5' 'test'
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
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716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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19 keepreads = str(keepreads)
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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20 removeadapters = str(removeadapters)
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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21 fastqfile=str(fastqfile)
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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22 end_defn = str(end_defn)
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
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megan-shortridge
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24 fh = open(fastqfile, mode='r+')
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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25 len_adapter = len(adapter)
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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26 count_adapter_found = 0
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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27 count_adapter_not_found = 0
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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28 total_seq_count = 0
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
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megan-shortridge
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30 parsed = SeqIO.parse(fh, format="fastq")
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32 output_fh_name = "output.fastq"
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
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33
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34 if fastqfile=="test3prime.fastq":
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35 output_fh_name="output2.fastq"
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
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36
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37 output_fh = open(output_fh_name, mode='w+')
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
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38
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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39 output_text_name = "output.txt"
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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40 if fastqfile=="test3prime.fastq":
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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41 output_text_name="output2.txt"
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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42 output_text_fh = open(output_text_name, mode='w+')
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
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43
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44
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
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45 for record in parsed:
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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46 try:
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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47 sequence = str(record.seq)
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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48 search = SeqUtils.nt_search(sequence, adapter) #This will search the
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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49 index = int(search[1]) #If it finds the adapter, is the starting index from which it was found.
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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50 adapter_start = index
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
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51 adapter_end = index+len_adapter
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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52 count_adapter_found +=1
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megan-shortridge
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53 total_seq_count+=1
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
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54 if removeadapters == "True": #if the value is true, it removes the adapters from the sequences.
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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55 if end_defn=="5":
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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56 record = record[adapter_end:] #If a 5' adapter, you remove adapter from beginning
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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57 elif end_defn=="3":
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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58 record = record[:adapter_start] #If it is a 3' adapter, you remove the adapter at the end
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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59 elif removeadapters == "False": #if the value is false, it does not remove the adapters from the sequences.
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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60 record = record
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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61 SeqIO.write(record, output_fh, format="fastq") #No matter what, write the reads.
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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62 except IndexError:
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63 count_adapter_not_found+=1
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megan-shortridge
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64 total_seq_count+=1
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
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65 record = record
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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66 if keepreads=="True":
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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67 SeqIO.write(record, output_fh, format="fastq")
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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68 elif keepreads=="False":
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69 pass
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megan-shortridge
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70 else:
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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71 pass
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72
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73 output_fh.close()
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74
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75 percent_cut = 100*(float(count_adapter_found)/float(total_seq_count))
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76
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77
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78 output_text_fh.write("The total number of sequences that were analyzed was %i.\n\n"%total_seq_count)
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
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79 output_text_fh.write("Adapter was found and removed for %i sequences (%i%% of total).\n\n"%(count_adapter_found, percent_cut))
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
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80
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megan-shortridge
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81 if keepreads =="True":
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
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82 output_text_fh.write("Sequences that did not contain the adapter were kept.\n\n")
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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83 elif keepreads=="False":
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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84 output_text_fh.write("Sequences that did not contain the adapter were removed from the dataset.\n\n")
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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85 if removeadapters=="True":
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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86 output_text_fh.write("The adapters were removed from the dataset.\n\n")
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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87 elif removeadapters=="False":
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
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diff changeset
88 output_text_fh.write("The adapters were not removed from the dataset.\n\n")
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
89 if end_defn=="5":
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
90 output_text_fh.write("Adapters were removed from the 5\' end.\n\n")
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
91 elif end_defn=="3":
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
92 output_text_fh.write("Adapters were removed from the 3\'end.\n\n")
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
93
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
94 output_text_fh.write("The name of the adapter that was removed was named %s, and had the sequence %s.\n\n"%(adapter_name,adapter))
716cdcccc919 planemo upload for repository https://github.com/mshortr/degenerateprimerremoval_fastq commit 7d51a7e3ccb0164b530bf1664068d86241f2f2f5-dirty
megan-shortridge
parents:
diff changeset
95 output_text_fh.close()