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1 import pandas as pd
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2 import re
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3 import argparse
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4 import os
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5
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1
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6 def stop_err( msg, ret=1 ):
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7 sys.stderr.write( msg )
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8 sys.exit( ret )
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0
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9
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10 #docs.python.org/dev/library/argparse.html
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11 parser = argparse.ArgumentParser()
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12 parser.add_argument("--input", help="Input folder with files")
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13 parser.add_argument("--output", help="Output file")
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14
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15 args = parser.parse_args()
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16
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17 old_summary_columns = [u'Sequence ID', u'JUNCTION frame', u'V-GENE and allele', u'D-GENE and allele', u'J-GENE and allele', u'CDR1-IMGT length', u'CDR2-IMGT length', u'CDR3-IMGT length', u'Orientation']
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18 old_sequence_columns = [u'CDR1-IMGT', u'CDR2-IMGT', u'CDR3-IMGT']
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19 old_junction_columns = [u'JUNCTION']
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20
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21 added_summary_columns = [u'V-REGION identity %', u'V-REGION identity nt', u'D-REGION reading frame', u'AA JUNCTION', u'Functionality comment', u'Sequence']
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22 added_sequence_columns = [u'FR1-IMGT', u'FR2-IMGT', u'FR3-IMGT', u'CDR3-IMGT', u'JUNCTION', u'J-REGION', u'FR4-IMGT']
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23 added_junction_columns = [u"P3'V-nt nb", u'N1-REGION-nt nb', u"P5'D-nt nb", u"P3'D-nt nb", u'N2-REGION-nt nb', u"P5'J-nt nb", u"3'V-REGION trimmed-nt nb", u"5'D-REGION trimmed-nt nb", u"3'D-REGION trimmed-nt nb", u"5'J-REGION trimmed-nt nb"]
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24
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25 inputFolder = args.input
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0
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26
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27 dirContents = os.listdir(inputFolder)
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28 if len(dirContents) == 1:
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29 inputFolder = os.path.join(inputFolder, dirContents[0])
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30 if os.path.isdir(inputFolder):
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31 print "is dir"
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32 dirContents = os.listdir(inputFolder)
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33 files = sorted([os.path.join(inputFolder, f) for f in dirContents])
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34
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35 if len(files) % 3 is not 0:
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1
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36 stop_err("Files in zip not a multiple of 3, it should contain the all the 1_, 5_ and 6_ files for a sample")
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37 import sys
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38 sys.exit()
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39
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40 triplets = []
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41 step = len(files) / 3
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42 for i in range(0, step):
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43 triplets.append((files[i], files[i + step], files[i + step + step]))
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44
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45 outFile = args.output
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46
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47 fSummary = pd.read_csv(triplets[0][0], sep="\t")
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48 fSequence = pd.read_csv(triplets[0][1], sep="\t")
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49 fJunction = pd.read_csv(triplets[0][2], sep="\t")
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50 tmp = fSummary[["Sequence ID", "JUNCTION frame", "V-GENE and allele", "D-GENE and allele", "J-GENE and allele"]]
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51
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52 tmp["CDR1 Seq"] = fSequence["CDR1-IMGT"]
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53 tmp["CDR1 Length"] = fSummary["CDR1-IMGT length"]
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54
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55 tmp["CDR2 Seq"] = fSequence["CDR2-IMGT"]
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56 tmp["CDR2 Length"] = fSummary["CDR2-IMGT length"]
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57
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58 tmp["CDR3 Seq"] = fSequence["CDR3-IMGT"]
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59 tmp["CDR3 Length"] = fSummary["CDR3-IMGT length"]
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60
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61 tmp["CDR3 Seq DNA"] = fJunction["JUNCTION"]
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62 tmp["CDR3 Length DNA"] = '1'
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63 tmp["Strand"] = fSummary["Orientation"]
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64 tmp["CDR3 Found How"] = 'a'
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65
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66 for col in added_summary_columns:
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67 tmp[col] = fSummary[col]
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68
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69 for col in added_sequence_columns:
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70 tmp[col] = fSequence[col]
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71
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72 for col in added_junction_columns:
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73 tmp[col] = fJunction[col]
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74
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75 outFrame = tmp
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76
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77 for triple in triplets[1:]:
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78 fSummary = pd.read_csv(triple[0], sep="\t")
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79 fSequence = pd.read_csv(triple[1], sep="\t")
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80 fJunction = pd.read_csv(triple[2], sep="\t")
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81
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82 tmp = fSummary[["Sequence ID", "JUNCTION frame", "V-GENE and allele", "D-GENE and allele", "J-GENE and allele"]]
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83
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84 tmp["CDR1 Seq"] = fSequence["CDR1-IMGT"]
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85 tmp["CDR1 Length"] = fSummary["CDR1-IMGT length"]
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86
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87 tmp["CDR2 Seq"] = fSequence["CDR2-IMGT"]
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88 tmp["CDR2 Length"] = fSummary["CDR2-IMGT length"]
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89
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90 tmp["CDR3 Seq"] = fSequence["CDR3-IMGT"]
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91 tmp["CDR3 Length"] = fSummary["CDR3-IMGT length"]
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92
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93 tmp["CDR3 Seq DNA"] = fJunction["JUNCTION"]
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94 tmp["CDR3 Length DNA"] = '1'
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95 tmp["Strand"] = fSummary["Orientation"]
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96 tmp["CDR3 Found How"] = 'a'
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97
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98 for col in added_summary_columns:
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99 tmp[col] = fSummary[col]
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100
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101 for col in added_sequence_columns:
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102 tmp[col] = fSequence[col]
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103
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104 for col in added_junction_columns:
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105 tmp[col] = fJunction[col]
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106
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107 outFrame.append(tmp)
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108
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109 outFrame.columns = [u'ID', u'VDJ Frame', u'Top V Gene', u'Top D Gene', u'Top J Gene', u'CDR1 Seq', u'CDR1 Length', u'CDR2 Seq', u'CDR2 Length', u'CDR3 Seq', u'CDR3 Length', u'CDR3 Seq DNA', u'CDR3 Length DNA', u'Strand', u'CDR3 Found How', 'V-REGION identity %', 'V-REGION identity nt', 'D-REGION reading frame', 'AA JUNCTION', 'Functionality comment', 'Sequence', 'FR1-IMGT', 'FR2-IMGT', 'FR3-IMGT', 'CDR3-IMGT', 'JUNCTION', 'J-REGION', 'FR4-IMGT', 'P3V-nt nb', 'N1-REGION-nt nb', 'P5D-nt nb', 'P3D-nt nb', 'N2-REGION-nt nb', 'P5J-nt nb', '3V-REGION trimmed-nt nb', '5D-REGION trimmed-nt nb', '3D-REGION trimmed-nt nb', '5J-REGION trimmed-nt nb']
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110
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111 vPattern = re.compile(r"IGHV[1-9]-[0-9ab]+-?[1-9]?")
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112 dPattern = re.compile(r"IGHD[1-9]-[0-9ab]+")
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113 jPattern = re.compile(r"IGHJ[1-9]")
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114
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115 def filterGenes(s, pattern):
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116 if type(s) is not str:
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117 return "NA"
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118 res = pattern.search(s)
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119 if res:
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120 return res.group(0)
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121 return "NA"
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122
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123
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124 outFrame["Top V Gene"] = outFrame["Top V Gene"].apply(lambda x: filterGenes(x, vPattern))
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125 outFrame["Top D Gene"] = outFrame["Top D Gene"].apply(lambda x: filterGenes(x, dPattern))
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126 outFrame["Top J Gene"] = outFrame["Top J Gene"].apply(lambda x: filterGenes(x, jPattern))
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127
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128
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129
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130 tmp = outFrame["VDJ Frame"]
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131 tmp = tmp.replace("in-frame", "In-frame")
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132 tmp = tmp.replace("null", "Out-of-frame")
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133 tmp = tmp.replace("out-of-frame", "Out-of-frame")
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134 outFrame["VDJ Frame"] = tmp
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135 outFrame["CDR3 Length"] = outFrame["CDR3 Seq DNA"].map(str).map(len)
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136 safeLength = lambda x: len(x) if type(x) == str else 0
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137 outFrame = outFrame[(outFrame["CDR3 Seq DNA"].map(safeLength) > 0) & (outFrame["Top V Gene"] != "NA") & (outFrame["Top D Gene"] != "NA") & (outFrame["Top J Gene"] != "NA")] #filter out weird rows?
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138 outFrame.to_csv(outFile, sep="\t", index=False) |
