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annotate infernal.py @ 20:b10f7688d14c draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/infernal commit 09c1d4ab75f5cd057ed57bf694217f0e355f785e
author bgruening
date Mon, 11 Nov 2024 10:26:56 +0000
parents 94cc7ef25867
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 # -*- coding: utf-8 -*-
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2
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3 import logging
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4 import os
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5 import subprocess
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6
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7 from galaxy.datatypes.data import get_file_peek, Text
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8 from galaxy.datatypes.metadata import MetadataElement
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9
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11 def count_special_lines(word, filename, invert=False):
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12 """
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13 searching for special 'words' using the grep tool
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14 grep is used to speed up the searching and counting
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15 The number of hits is returned.
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16 """
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17 try:
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18 cmd = ["grep", "-c"]
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19 if invert:
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20 cmd.append("-v")
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21 cmd.extend([word, filename])
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22 out = subprocess.Popen(cmd, stdout=subprocess.PIPE)
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23 return int(out.communicate()[0].split()[0])
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24 except Exception:
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25 pass
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26 return 0
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29 def count_lines(filename, non_empty=False):
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30 """
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31 counting the number of lines from the 'filename' file
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32 """
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33 try:
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34 if non_empty:
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35 out = subprocess.Popen(
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36 ["grep", "-cve", "^\s*$", filename], stdout=subprocess.PIPE # noqa W605
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37 )
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38 else:
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39 out = subprocess.Popen(["wc", "-l", filename], stdout=subprocess.PIPE)
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40 return int(out.communicate()[0].split()[0])
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41 except Exception:
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42 pass
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43 return 0
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46 class Infernal_CM_1_1(Text):
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47 file_ext = "cm"
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48
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49 MetadataElement(
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50 name="number_of_models",
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51 default=0,
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52 desc="Number of covariance models",
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53 readonly=True,
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54 visible=True,
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55 optional=True,
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56 no_value=0,
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57 )
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59 def set_peek(self, dataset, is_multi_byte=False):
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60 if not dataset.dataset.purged:
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61 dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
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62 if dataset.metadata.number_of_models == 1:
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63 dataset.blurb = "1 model"
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64 else:
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65 dataset.blurb = "%s models" % dataset.metadata.number_of_models
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66 dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte)
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67 else:
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68 dataset.peek = "file does not exist"
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69 dataset.blurb = "file purged from disc"
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71 def sniff(self, filename):
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72 if count_special_lines("^INFERNAL1/a", filename) > 0:
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73 return True
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74 else:
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75 return False
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77 def set_meta(self, dataset, **kwd):
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78 """
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79 Set the number of models in dataset.
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80 """
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81 dataset.metadata.number_of_models = count_special_lines(
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82 "^INFERNAL1/a", dataset.file_name
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83 )
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84
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85 def split(cls, input_datasets, subdir_generator_function, split_params):
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86 """
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87 Split the input files by model records.
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88 """
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89 if split_params is None:
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90 return None
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91
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92 if len(input_datasets) > 1:
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93 raise Exception("CM-file splitting does not support multiple files")
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94 input_files = [ds.file_name for ds in input_datasets]
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95
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96 chunk_size = None
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97 if split_params["split_mode"] == "number_of_parts":
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98 raise Exception(
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99 'Split mode "%s" is currently not implemented for CM-files.'
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100 % split_params["split_mode"]
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101 )
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102 elif split_params["split_mode"] == "to_size":
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103 chunk_size = int(split_params["split_size"])
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104 else:
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105 raise Exception("Unsupported split mode %s" % split_params["split_mode"])
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106
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107 def _read_cm_records(filename):
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108 lines = []
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109 with open(filename) as handle:
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110 for line in handle:
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111 if line.startswith("INFERNAL1/a") and lines:
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112 yield lines
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113 lines = [line]
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114 else:
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115 lines.append(line)
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116 yield lines
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117
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118 def _write_part_cm_file(accumulated_lines):
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119 part_dir = subdir_generator_function()
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120 part_path = os.path.join(part_dir, os.path.basename(input_files[0]))
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121 part_file = open(part_path, "w")
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122 part_file.writelines(accumulated_lines)
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123 part_file.close()
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124
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125 try:
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126 cm_records = _read_cm_records(input_files[0])
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127 cm_lines_accumulated = []
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128 for counter, cm_record in enumerate(cm_records, start=1):
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129 cm_lines_accumulated.extend(cm_record)
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130 if counter % chunk_size == 0:
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131 _write_part_cm_file(cm_lines_accumulated)
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132 cm_lines_accumulated = []
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133 if cm_lines_accumulated:
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134 _write_part_cm_file(cm_lines_accumulated)
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135 except Exception as e:
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136 logging.error("Unable to split files: %s" % str(e))
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137 raise
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138
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139 split = classmethod(split)
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140
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141
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142 if __name__ == "__main__":
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143 Infernal_CM_1_1()
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144 # Stockholm_1_0() # ???