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1 from __future__ import print_function
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2 import os
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3 import pickle
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4 from reportlab.platypus import SimpleDocTemplate, Paragraph, Spacer, Image, Table, TableStyle, PageBreak
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5 from reportlab.lib.pagesizes import letter, landscape
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6 from _modules.functions_PhageTerm import SummaryReport,WorkflowReport,ExportCohesiveSeq,ExportPhageSequence,CreateReport
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7
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8
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9 def loadDR(DR_path,DR):
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10 for d in os.listdir(DR_path): # iterate over P_class subdirectories.
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11 if not os.path.isdir(os.path.join(DR_path,d)):
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12 err_str=DR_path+" should contain only directories."
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13 raise RuntimeError(err_str)
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14 for fic_name in os.listdir(os.path.join(DR_path,d)): # iterate over all files for a given P_class
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15 p=os.path.join(DR_path,d)
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16 fname=os.path.join(p,fic_name)
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17 with open(fname, 'rb') as f:
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18 loaded_items=pickle.load(f)
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19 # d is P_class name, fic_name is phagename.
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20 dict_tmp=dict()
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21 dict_tmp["phagename"]=loaded_items[0]
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22 dict_tmp["seed"]=loaded_items[1]
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23 dict_tmp["added_whole_coverage"]=loaded_items[2]
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24 dict_tmp["Redundant"]=loaded_items[3]
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25 dict_tmp["P_left"]=loaded_items[4]
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26 print("P_left=",dict_tmp["P_left"],type(dict_tmp["P_left"]))
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27 dict_tmp["P_right"] = loaded_items[5]
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28 print("P_right=",dict_tmp["P_right"],type(dict_tmp["P_right"]))
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29 dict_tmp["Permuted"]=loaded_items[6]
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30 dict_tmp["P_orient"] =loaded_items[7]
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31 dict_tmp["termini_coverage_norm_close"] =loaded_items[8]
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32 dict_tmp["picMaxPlus_norm_close"] =loaded_items[9]
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33 dict_tmp["picMaxMinus_norm_close"] =loaded_items[10]
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34 dict_tmp["gen_len"] =loaded_items[11]
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35 dict_tmp["tot_reads"] =loaded_items[12]
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36 dict_tmp["P_seqcoh"] =loaded_items[13]
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37 dict_tmp["phage_plus_norm"] =loaded_items[14]
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38 dict_tmp["phage_minus_norm"] =loaded_items[15]
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39 dict_tmp["ArtPackmode"] = loaded_items[16]
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40 dict_tmp["termini"] = loaded_items[17]
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41 dict_tmp["forward"] = loaded_items[18]
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42 dict_tmp["reverse"] = loaded_items[19]
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43 dict_tmp["ArtOrient"] = loaded_items[20]
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44 dict_tmp["ArtcohesiveSeq"] = loaded_items[21]
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45 dict_tmp["termini_coverage_close"] = loaded_items[22]
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46 dict_tmp["picMaxPlus_close"] = loaded_items[23]
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47 dict_tmp["picMaxMinus_close"] = loaded_items[24]
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48 dict_tmp["picOUT_norm_forw"] = loaded_items[25]
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49 dict_tmp["picOUT_norm_rev"] = loaded_items[26]
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50 dict_tmp["picOUT_forw"] = loaded_items[27]
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51 dict_tmp["picOUT_rev"] = loaded_items[28]
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52 dict_tmp["lost_perc"] = loaded_items[29]
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53 dict_tmp["ave_whole_cov"] = loaded_items[30]
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54 dict_tmp["R1"] = loaded_items[31]
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55 dict_tmp["R2"] = loaded_items[32]
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56 dict_tmp["R3"] = loaded_items[33]
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57 dict_tmp["host"] = loaded_items[34]
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58 dict_tmp["host_len"] = loaded_items[35]
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59 dict_tmp["host_whole_coverage"] = loaded_items[36]
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60 dict_tmp["picMaxPlus_host"] = loaded_items[37]
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61 dict_tmp["picMaxMinus_host"] = loaded_items[38]
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62 dict_tmp["surrounding"] = loaded_items[39]
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63 dict_tmp["drop_cov"] = loaded_items[40]
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64 dict_tmp["paired"] = loaded_items[41]
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65 dict_tmp["insert"] = loaded_items[42]
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66 dict_tmp["phage_hybrid_coverage"] = loaded_items[43]
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67 dict_tmp["host_hybrid_coverage"] = loaded_items[44]
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68 dict_tmp["added_paired_whole_coverage"] = loaded_items[45]
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69 dict_tmp["Mu_like"] = loaded_items[46]
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70 dict_tmp["test_run"] = loaded_items[47]
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71 dict_tmp["P_class"] = loaded_items[48]
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72 dict_tmp["P_type"] = loaded_items[49]
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73 dict_tmp["P_concat"] = loaded_items[50]
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74 dict_tmp["idx_refseq_in_list"] = loaded_items[51]
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75 DR [d][fic_name]=dict_tmp
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76 f.close()
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77
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78
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79
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80
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81 def genReport(fParms,inDArgs,inRawDArgs,no_match,DR):
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82 # Test No Match
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83 if len(no_match) == inDArgs.nbr_virome:
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84 print("\n\nERROR: No reads match, please check your reference file.")
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85 exit()
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86
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87 # Report Resume
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88 multiReport = SummaryReport(inRawDArgs.phagename, DR, no_match)
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89 multiCohSeq = ""
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90 multiPhageSeq = ""
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91 multiWorkflow = "#phagename\tClass\tLeft\tRight\tType\tOrient\tCoverage\tComments\n"
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92
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93 # No Match in workflow
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94 if fParms.workflow:
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95 for no_match_contig in no_match:
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96 multiWorkflow += WorkflowReport(no_match_contig, "-", "-", "-", "-", "-", 0, 1)
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97
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98 for DPC in DR:
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99 for DC in DR[DPC]:
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100 # Text report
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101 if fParms.workflow: # phagename, P_class, P_left, P_right, P_type, P_orient, ave_whole_cov, multi = 0
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102 multiWorkflow += WorkflowReport(DC, DR[DPC][DC]["P_class"], DR[DPC][DC]["P_left"],
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103 DR[DPC][DC]["P_right"],
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104 DR[DPC][DC]["P_type"], DR[DPC][DC]["P_orient"],
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105 DR[DPC][DC]["ave_whole_cov"], 1)
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106
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107 # Sequence
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108 idx_refseq = DR[DPC][DC]["idx_refseq_in_list"]
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109 refseq = inDArgs.refseq_liste[idx_refseq]
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110 multiCohSeq += ExportCohesiveSeq(DC, DR[DPC][DC]["ArtcohesiveSeq"], DR[DPC][DC]["P_seqcoh"], fParms.test_run, 1)
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111 multiPhageSeq += ExportPhageSequence(DC, DR[DPC][DC]["P_left"], DR[DPC][DC]["P_right"], refseq,
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112 DR[DPC][DC]["P_orient"], DR[DPC][DC]["Redundant"], DR[DPC][DC]["Mu_like"],
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113 DR[DPC][DC]["P_class"], DR[DPC][DC]["P_seqcoh"], fParms.test_run, 1)
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114
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115 # Report
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116 draw=0 # TODO VL: ask what is the use of this parameter that is alwayes 0...
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117 multiReport = CreateReport(DC, DR[DPC][DC]["seed"], DR[DPC][DC]["added_whole_coverage"], draw,
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118 DR[DPC][DC]["Redundant"], DR[DPC][DC]["P_left"], DR[DPC][DC]["P_right"],
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119 DR[DPC][DC]["Permuted"], DR[DPC][DC]["P_orient"],
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120 DR[DPC][DC]["termini_coverage_norm_close"], DR[DPC][DC]["picMaxPlus_norm_close"],
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121 DR[DPC][DC]["picMaxMinus_norm_close"], DR[DPC][DC]["gen_len"],
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122 DR[DPC][DC]["tot_reads"], DR[DPC][DC]["P_seqcoh"], DR[DPC][DC]["phage_plus_norm"],
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123 DR[DPC][DC]["phage_minus_norm"], DR[DPC][DC]["ArtPackmode"], DR[DPC][DC]["termini"],
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124 DR[DPC][DC]["forward"], DR[DPC][DC]["reverse"], DR[DPC][DC]["ArtOrient"],
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125 DR[DPC][DC]["ArtcohesiveSeq"], DR[DPC][DC]["termini_coverage_close"],
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126 DR[DPC][DC]["picMaxPlus_close"], DR[DPC][DC]["picMaxMinus_close"],
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127 DR[DPC][DC]["picOUT_norm_forw"], DR[DPC][DC]["picOUT_norm_rev"],
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128 DR[DPC][DC]["picOUT_forw"], DR[DPC][DC]["picOUT_rev"], DR[DPC][DC]["lost_perc"],
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129 DR[DPC][DC]["ave_whole_cov"], DR[DPC][DC]["R1"], DR[DPC][DC]["R2"],
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130 DR[DPC][DC]["R3"], DR[DPC][DC]["host"], DR[DPC][DC]["host_len"],
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131 DR[DPC][DC]["host_whole_coverage"], DR[DPC][DC]["picMaxPlus_host"],
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132 DR[DPC][DC]["picMaxMinus_host"], DR[DPC][DC]["surrounding"], DR[DPC][DC]["drop_cov"],
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133 DR[DPC][DC]["paired"], DR[DPC][DC]["insert"], DR[DPC][DC]["phage_hybrid_coverage"],
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134 DR[DPC][DC]["host_hybrid_coverage"], DR[DPC][DC]["added_paired_whole_coverage"],
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135 DR[DPC][DC]["Mu_like"], fParms.test_run, DR[DPC][DC]["P_class"],
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136 DR[DPC][DC]["P_type"], DR[DPC][DC]["P_concat"], 1, multiReport)
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137
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138 # Workflow
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139 if not fParms.test:
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140 if fParms.workflow:
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141 filoutWorkflow = open(inRawDArgs.phagename + "_workflow.txt", "w")
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142 filoutWorkflow.write(multiWorkflow)
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143 filoutWorkflow.close()
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144
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145 # Concatene Sequences
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146 filoutCohSeq = open(inRawDArgs.phagename + "_cohesive-sequence.fasta", "w")
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147 filoutCohSeq.write(multiCohSeq)
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148 filoutCohSeq.close()
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149
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150 filoutPhageSeq = open(inRawDArgs.phagename + "_sequence.fasta", "w")
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151 filoutPhageSeq.write(multiPhageSeq)
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152 filoutPhageSeq.close()
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153
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154 # Concatene Report
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155 doc = SimpleDocTemplate("%s_PhageTerm_report.pdf" % inRawDArgs.phagename, pagesize=letter, rightMargin=10,
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156 leftMargin=10, topMargin=5, bottomMargin=10)
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157 doc.build(multiReport)
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