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1 #!/usr/bin/env python3
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2 import os
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3 ''' configuration file to set up the paths and constants '''
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4
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5 ######## PROFREP #######################################################
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6 ## Constansts
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7 N_segment = 50
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8 MAX_FILES_SUBPROFILES = 1000
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9 MAX_PIC_NUM = 50
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10 IMAGE_RES = 300
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11 FASTA_LINE = 60
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12 SEQ_LEN_VIZ = 200000
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13 FORBIDDEN_CHARS = "\\/"
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14 HTML_STR = '''
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15 <!DOCTYPE html>
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16 <html>
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17 <body>
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18 <h2>PROFREP OUTPUT</h2>
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19 <h4> Sequences processed: </h4>
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20 {}
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21 <h4> Total length: </h4>
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22 <pre> {} bp </pre>
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23 <h4> Database: </h4>
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24 <pre> {} </pre>
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25 <hr>
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26 <h3> Repetitive profile(s)</h3> </br>
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27 {} <br/>
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28 <h4>References: </h4>
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29 {}
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30 </h6>
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31 </body>
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32 </html>
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33 '''
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34
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35 ## IO
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36 DOMAINS_GFF = "output_domains.gff"
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37 N_GFF = "N_regions.gff"
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38 REPEATS_GFF = "output_repeats.gff"
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39 HTML = "output.html"
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40 LOG_FILE = "log.txt"
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41 PROFREP_DATA = "tool_data/profrep"
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42 PROFREP_TBL = "prepared_datasets.txt"
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43 PROFREP_OUTPUT_DIR = "profrep_output_dir"
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44 ## JBrowse and Tracks Conf
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45 jbrowse_data_dir = "data"
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46 JSON_CONF_R = """{"hooks" : {"modify": "function( track, f, fdiv ) {fdiv.style.backgroundColor = '#278ECF'}"}}"""
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47 JSON_CONF_N = """{"hooks" : {"modify": "function( track, f, fdiv ) {fdiv.style.background = '#474747'}"}}"""
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48 COLORS_HEX = ["#7F7F7F", "#00FF00", "#0000FF", "#FF0000", "#01FFFE", "#FFA6FE",
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49 "#FFDB66", "#006401", "#010067", "#95003A", "#007DB5", "#FF00F6",
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50 "#774D00", "#90FB92", "#0076FF", "#D5FF00", "#FF937E", "#6A826C",
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51 "#FF029D", "#FE8900", "#7A4782", "#7E2DD2", "#85A900", "#FF0056",
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52 "#A42400", "#00AE7E", "#683D3B", "#BDC6FF", "#263400", "#BDD393",
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53 "#00B917", "#9E008E", "#001544", "#C28C9F", "#FF74A3", "#01D0FF",
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54 "#004754", "#E56FFE", "#788231", "#0E4CA1", "#91D0CB", "#BE9970",
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55 "#968AE8", "#BB8800", "#43002C", "#DEFF74", "#00FFC6", "#FFE502",
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56 "#620E00", "#008F9C", "#98FF52", "#7544B1", "#B500FF", "#00FF78",
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57 "#FF6E41", "#005F39", "#6B6882", "#5FAD4E", "#A75740", "#A5FFD2",
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58 "#FFB167", "#009BFF", "#E85EBE"]
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59 COLORS_RGB = ["127,127,127", "0,255,0", "0,0,255", "255,0,0", "1,255,254",
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60 "255,166,254", "255,219,102", "0,100,1", "1,0,103", "149,0,58",
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61 "0,125,181", "255,0,246", "119,77,0", "144,251,146", "0,118,255",
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62 "213,255,0", "255,147,126", "106,130,108", "255,2,157",
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63 "254,137,0", "122,71,130", "126,45,210", "133,169,0", "255,0,86",
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64 "164,36,0", "0,174,126", "104,61,59", "189,198,255", "38,52,0",
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65 "189,211,147", "0,185,23", "158,0,142", "0,21,68", "194,140,159",
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66 "255,116,163", "1,208,255", "0,71,84", "229,111,254",
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67 "120,130,49", "14,76,161", "145,208,203", "190,153,112",
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68 "150,138,232", "187,136,0", "67,0,44", "222,255,116",
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69 "0,255,198", "255,229,2", "98,14,0", "0,143,156", "152,255,82",
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70 "117,68,177", "181,0,255", "0,255,120", "255,110,65", "0,95,57",
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71 "107,104,130", "95,173,78", "167,87,64", "165,255,210",
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72 "255,177,103", "0,155,255", "232,94,190"]
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73 TRACK_LIST = '''
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74 \t,{}\n
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75 \t"storeClass" : "JBrowse/Store/SeqFeature/BigWig",
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76 \t"urlTemplate" : "{}",
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77 \t"type" : "JBrowse/View/Track/Wiggle/XYPlot",
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78 \t"label" : "{}",
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79 \t"key" : "{}",
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80 \t"style": {}
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81 \t\t"pos_color": "{}"
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82 \t {},
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83 \t"scale" : "log"
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84 \t{}\n
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85 '''
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86
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87 ## GFF tracks
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88 HEADER_GFF = "##gff-version 3"
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89 SOURCE_PROFREP = "profrep"
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90 SOURCE_DANTE = "dante"
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91 PHASE = "."
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92 DOMAINS_FEATURE = "protein_domain"
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93 REPEATS_FEATURE = "repeat"
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94 N_NAME = "N"
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95 N_FEATURE = "N_region"
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96 HEADER_WIG = "variableStep\tchrom="
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97 GFF_EMPTY = "."
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98
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99 ######### BIG WIG ######################################################
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100 CHROM_SIZES_FILE = "chrom_sizes.txt"
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101
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102 ######### EXTRACT_DATA_DOR_PROFREP #####################################
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103 HITSORT_CLS = "seqclust/clustering/hitsort.cls"
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104 READS_ALL = "seqclust/sequences/sequences.fasta"
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105 ANNOTATION = "PROFREP_CLASSIFICATION_TEMPLATE.csv"
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106
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107 ######### PROFREP_DB_REDUCING ##########################################
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108 MEM_LIM = 1500 # MB
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109 CLS_REDUCED = "hitsort_reduced.cls"
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110 READS_ALL_REDUCED = "reads_all_reduced"
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111
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112 ######### PROFREP_REFINING #############################################
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113 WITH_DOMAINS = "mobile_element"
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114 QUALITY_DIFF_TO_REMOVE = 0.05 # 5% tolerance of PID
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115
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116 ######### DANTE ##############################################
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117 MAIN_GIT_DIR = os.path.dirname(os.path.realpath(__file__))
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118 DOMAINS_DATA = os.path.join(MAIN_GIT_DIR, "domains_data")
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119 TMP = "tmp"
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120 SC_MATRIX = os.path.join(DOMAINS_DATA, "blosum80.txt")
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121 AMBIGUOUS_TAG = "Ambiguous_domain"
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122 ## IO
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123 CLASS_FILE = "ALL.classification-new"
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124 LAST_DB_FILE = "ALL_protein-domains_05.fasta"
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125 DOM_PROT_SEQ = "dom_prot_seq.fa"
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126 FILT_DOM_GFF = "domains_filtered.gff"
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127 EXTRACT_DOM_STAT = "domains_counts.txt"
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128 EXTRACT_OUT_DIR = "extracted_domains"
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