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1 import pandas as pd
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2 try:
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3 pd.options.mode.chained_assignment = None # default='warn'
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4 except:
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5 pass
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6 import re
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7 import argparse
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8 import os
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9
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10 def stop_err( msg, ret=1 ):
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11 sys.stderr.write( msg )
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12 sys.exit( ret )
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13
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14 #docs.python.org/dev/library/argparse.html
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15 parser = argparse.ArgumentParser()
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16 parser.add_argument("--summ", help="The 1_Summary file from the imgt output")
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17 parser.add_argument("--aa", help="The 5_AA-Sequence file from the imgt output")
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18 parser.add_argument("--junction", help="The 6_Junction file from the imgt output")
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19 parser.add_argument("--output", help="Output file")
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20
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21 args = parser.parse_args()
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22
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23 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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24 old_sequence_columns = [u'CDR1-IMGT', u'CDR2-IMGT', u'CDR3-IMGT']
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25 old_junction_columns = [u'JUNCTION']
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26
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27 added_summary_columns = [u'Functionality', 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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28 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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29 added_junction_columns = [u"P3'V-nt nb", u'N-REGION-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",
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30 u"5'D-REGION trimmed-nt nb", u"3'D-REGION trimmed-nt nb", u"5'J-REGION trimmed-nt nb", u"N-REGION", u"N1-REGION", u"N2-REGION"]
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31
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32 outFile = args.output
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33
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34 #fSummary = pd.read_csv(triplets[0][0], sep="\t", low_memory=False)
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35 fSummary = pd.read_csv(args.summ, sep="\t", dtype=object)
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36 #fSequence = pd.read_csv(triplets[0][1], sep="\t", low_memory=False)
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37 fSequence = pd.read_csv(args.aa, sep="\t", dtype=object)
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38 #fJunction = pd.read_csv(triplets[0][2], sep="\t", low_memory=False)
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39 fJunction = pd.read_csv(args.junction, sep="\t", dtype=object)
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40 tmp = fSummary[["Sequence ID", "JUNCTION frame", "V-GENE and allele", "D-GENE and allele", "J-GENE and allele"]]
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41
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42 tmp["CDR1 Seq"] = fSequence["CDR1-IMGT"]
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43 tmp["CDR1 Length"] = fSummary["CDR1-IMGT length"]
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44
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45 tmp["CDR2 Seq"] = fSequence["CDR2-IMGT"]
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46 tmp["CDR2 Length"] = fSummary["CDR2-IMGT length"]
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47
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48 tmp["CDR3 Seq"] = fSequence["CDR3-IMGT"]
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49 tmp["CDR3 Length"] = fSummary["CDR3-IMGT length"]
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50
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51 tmp["CDR3 Seq DNA"] = fJunction["JUNCTION"]
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52 tmp["CDR3 Length DNA"] = '1'
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53 tmp["Strand"] = fSummary["Orientation"]
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54 tmp["CDR3 Found How"] = 'a'
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55
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56 for col in added_summary_columns:
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57 tmp[col] = fSummary[col]
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58
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59 for col in added_sequence_columns:
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60 tmp[col] = fSequence[col]
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61
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62 for col in added_junction_columns:
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63 tmp[col] = fJunction[col]
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64
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65 outFrame = tmp
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66
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67 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',
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68 u'CDR3 Seq DNA', u'CDR3 Length DNA', u'Strand', u'CDR3 Found How', u'Functionality', 'V-REGION identity %', 'V-REGION identity nt', 'D-REGION reading frame',
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69 'AA JUNCTION', 'Functionality comment', 'Sequence', 'FR1-IMGT', 'FR2-IMGT', 'FR3-IMGT', 'CDR3-IMGT', 'JUNCTION', 'J-REGION', 'FR4-IMGT', 'P3V-nt nb',
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70 'N-REGION-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',
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71 '5J-REGION trimmed-nt nb', "N-REGION", "N1-REGION", "N2-REGION"]
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72
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73 """
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74 IGHV[0-9]-[0-9ab]+-?[0-9]?D?
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75 TRBV[0-9]{1,2}-?[0-9]?-?[123]?
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76 IGKV[0-3]D?-[0-9]{1,2}
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77 IGLV[0-9]-[0-9]{1,2}
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78 TRAV[0-9]{1,2}(-[1-46])?(/DV[45678])?
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79 TRGV[234589]
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80 TRDV[1-3]
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81
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82 IGHD[0-9]-[0-9ab]+
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83 TRBD[12]
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84 TRDD[1-3]
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85
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86 IGHJ[1-6]
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87 TRBJ[12]-[1-7]
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88 IGKJ[1-5]
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89 IGLJ[12367]
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90 TRAJ[0-9]{1,2}
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91 TRGJP?[12]
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92 TRDJ[1-4]
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93 """
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94
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95 vPattern = [r"(IGHV[0-9]-[0-9ab]+-?[0-9]?D?)",
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96 r"(TRBV[0-9]{1,2}-?[0-9]?-?[123]?)",
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97 r"(IGKV[0-3]D?-[0-9]{1,2})",
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98 r"(IGLV[0-9]-[0-9]{1,2})",
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99 r"(TRAV[0-9]{1,2}(-[1-46])?(/DV[45678])?)",
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100 r"(TRGV[234589])",
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101 r"(TRDV[1-3])",
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102 r"(IGHV[0-9]S[0-9]+)"]
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103
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104 dPattern = [r"(IGHD[0-9]-[0-9ab]+)",
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105 r"(TRBD[12])",
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106 r"(TRDD[1-3])"]
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107
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108 jPattern = [r"(IGHJ[1-6])",
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109 r"(TRBJ[12]-[1-7])",
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110 r"(IGKJ[1-5])",
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111 r"(IGLJ[12367])",
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112 r"(TRAJ[0-9]{1,2})",
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113 r"(TRGJP?[12])",
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114 r"(TRDJ[1-4])"]
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115
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116 vPattern = re.compile(r"|".join(vPattern))
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117
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118 dPattern = re.compile(r"|".join(dPattern))
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119
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120 jPattern = re.compile(r"|".join(jPattern))
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121
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122
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123 def filterGenes(s, pattern):
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124 if type(s) is not str:
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125 return "NA"
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126 res = pattern.search(s)
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127 if res:
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128 return res.group(0)
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129 return "NA"
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130
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131
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132
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133 outFrame["Top V Gene"] = outFrame["Top V Gene"].apply(lambda x: filterGenes(x, vPattern))
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134 outFrame["Top D Gene"] = outFrame["Top D Gene"].apply(lambda x: filterGenes(x, dPattern))
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135 outFrame["Top J Gene"] = outFrame["Top J Gene"].apply(lambda x: filterGenes(x, jPattern))
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136
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137
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138 tmp = outFrame["VDJ Frame"]
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139 tmp = tmp.replace("in-frame", "In-frame")
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140 tmp = tmp.replace("null", "Out-of-frame")
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141 tmp = tmp.replace("out-of-frame", "Out-of-frame")
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142 outFrame["VDJ Frame"] = tmp
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143 outFrame["CDR3 Length DNA"] = outFrame["CDR3 Seq DNA"].map(str).map(len)
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144 safeLength = lambda x: len(x) if type(x) == str else 0
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145 #outFrame = outFrame[(outFrame["CDR3 Seq DNA"].map(safeLength) > 0) & (outFrame["Top V Gene"] != "NA") & (outFrame["Top J Gene"] != "NA")] #filter out weird rows?
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146 #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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147 outFrame.to_csv(outFile, sep="\t", index=False, index_label="index")
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