Mercurial > repos > bgruening > data_manager_diamond_database_builder

annotate data_manager/data_manager_diamond_database_builder.py @ 1:5a0d0bee4f8d draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/data_managers/data_manager_diamond_database_builder commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
author bgruening
date Tue, 03 Dec 2019 17:39:48 -0500
parents ce62d0912b10
children 5558f74bd296
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1 #!/usr/bin/env python
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2 import json
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3 import sys
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4 import os
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5 import tempfile
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6 import shutil
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7 import optparse
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8 import urllib2
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9 import subprocess
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10 from ftplib import FTP
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11 import tarfile
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12 import zipfile
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13 import gzip
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14 import bz2
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15
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16 CHUNK_SIZE = 2**20 # 1mb
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19 def cleanup_before_exit(tmp_dir):
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20 if tmp_dir and os.path.exists(tmp_dir):
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21 shutil.rmtree(tmp_dir)
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24 def stop_err(msg):
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25 sys.stderr.write(msg)
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26 sys.exit(1)
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29 def _get_files_in_ftp_path(ftp, path):
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30 path_contents = []
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31 ftp.retrlines('MLSD %s' % (path), path_contents.append)
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32 return [line.split(';')[-1].lstrip() for line in path_contents]
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35 def _get_stream_readers_for_tar(file_obj, tmp_dir):
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36 fasta_tar = tarfile.open(fileobj=file_obj, mode='r:*')
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37 return [fasta_tar.extractfile(member) for member in fasta_tar.getmembers()]
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40 def _get_stream_readers_for_zip(file_obj, tmp_dir):
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41 fasta_zip = zipfile.ZipFile(file_obj, 'r')
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42 rval = []
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43 for member in fasta_zip.namelist():
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44 fasta_zip.extract(member, tmp_dir)
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45 rval.append(open(os.path.join(tmp_dir, member), 'rb'))
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46 return rval
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49 def _get_stream_readers_for_gzip(file_obj, tmp_dir):
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50 return [gzip.GzipFile(fileobj=file_obj, mode='rb')]
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53 def _get_stream_readers_for_bz2(file_obj, tmp_dir):
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54 return [bz2.BZ2File(file_obj.name, 'rb')]
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57 def download_from_ncbi(data_manager_dict, params, target_directory, database_id, database_name):
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58 NCBI_FTP_SERVER = 'ftp.ncbi.nlm.nih.gov'
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59 NCBI_DOWNLOAD_PATH = '/blast/db/FASTA/'
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60 COMPRESSED_EXTENSIONS = [('.tar.gz', _get_stream_readers_for_tar), ('.tar.bz2', _get_stream_readers_for_tar), ('.zip', _get_stream_readers_for_zip), ('.gz', _get_stream_readers_for_gzip), ('.bz2', _get_stream_readers_for_bz2)]
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62 ncbi_identifier = params['param_dict']['reference_source']['requested_identifier']
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63 ftp = FTP(NCBI_FTP_SERVER)
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64 ftp.login()
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65
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66 path_contents = _get_files_in_ftp_path(ftp, NCBI_DOWNLOAD_PATH)
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68 ncbi_file_name = None
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69 get_stream_reader = None
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70 ext = None
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71 for ext, get_stream_reader in COMPRESSED_EXTENSIONS:
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72 if "%s%s" % (ncbi_identifier, ext) in path_contents:
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73 ncbi_file_name = "%s%s%s" % (NCBI_DOWNLOAD_PATH, ncbi_identifier, ext)
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74 break
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75
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76 if not ncbi_file_name:
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77 raise Exception('Unable to determine filename for NCBI database for %s: %s' % (ncbi_identifier, path_contents))
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79 tmp_dir = tempfile.mkdtemp(prefix='tmp-data-manager-ncbi-')
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80 ncbi_fasta_filename = os.path.join(tmp_dir, "%s%s" % (ncbi_identifier, ext))
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81
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82 fasta_base_filename = "%s.fa" % database_id
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83 fasta_filename = os.path.join(target_directory, fasta_base_filename)
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84 fasta_writer = open(fasta_filename, 'wb+')
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86 tmp_extract_dir = os.path.join(tmp_dir, 'extracted_fasta')
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87 os.mkdir(tmp_extract_dir)
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89 tmp_fasta = open(ncbi_fasta_filename, 'wb+')
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91 ftp.retrbinary('RETR %s' % ncbi_file_name, tmp_fasta.write)
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93 tmp_fasta.flush()
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94 tmp_fasta.seek(0)
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96 fasta_readers = get_stream_reader(tmp_fasta, tmp_extract_dir)
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98 data_table_entry = _stream_fasta_to_file(fasta_readers, target_directory, database_id, database_name, params)
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99 _add_data_table_entry(data_manager_dict, data_table_entry)
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100
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101 for fasta_reader in fasta_readers:
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102 fasta_reader.close()
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103 tmp_fasta.close()
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104 cleanup_before_exit(tmp_dir)
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107 def download_from_url(data_manager_dict, params, target_directory, database_id, database_name):
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108 # TODO: we should automatically do decompression here
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109 urls = filter(bool, map(lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split('\n')))
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110 fasta_reader = [urllib2.urlopen(url) for url in urls]
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111
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112 data_table_entry = _stream_fasta_to_file(fasta_reader, target_directory, database_id, database_name, params)
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113 _add_data_table_entry(data_manager_dict, data_table_entry)
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114
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115
1
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116 def download_from_history(data_manager_dict, params, target_directory, database_id, database_name):
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117 # TODO: allow multiple FASTA input files
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118 input_filename = params['param_dict']['reference_source']['input_fasta']
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119 if isinstance(input_filename, list):
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120 fasta_reader = [open(filename, 'rb') for filename in input_filename]
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121 else:
1
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122 fasta_reader = open(input_filename)
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123
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124 data_table_entry = _stream_fasta_to_file(fasta_reader, target_directory, database_id, database_name, params)
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125 _add_data_table_entry(data_manager_dict, data_table_entry)
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126
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127
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128 def copy_from_directory(data_manager_dict, params, target_directory, database_id, database_name):
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129 input_filename = params['param_dict']['reference_source']['fasta_filename']
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130 create_symlink = params['param_dict']['reference_source']['create_symlink'] == 'create_symlink'
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131 if create_symlink:
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132 data_table_entry = _create_symlink(input_filename, target_directory, database_id, database_name)
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133 else:
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134 if isinstance(input_filename, list):
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135 fasta_reader = [open(filename, 'rb') for filename in input_filename]
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136 else:
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137 fasta_reader = open(input_filename)
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138 data_table_entry = _stream_fasta_to_file(fasta_reader, target_directory, database_id, database_name, params)
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139 _add_data_table_entry(data_manager_dict, data_table_entry)
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140
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141
1
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142 def _add_data_table_entry(data_manager_dict, data_table_entry):
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143 data_manager_dict['data_tables'] = data_manager_dict.get('data_tables', {})
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144 data_manager_dict['data_tables']['diamond_database'] = data_manager_dict['data_tables'].get('diamond_database', [])
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145 data_manager_dict['data_tables']['diamond_database'].append(data_table_entry)
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146 return data_manager_dict
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147
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148
1
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149 def _stream_fasta_to_file(fasta_stream, target_directory, database_id, database_name, params, close_stream=True):
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150 fasta_base_filename = "%s.fa" % database_id
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151 fasta_filename = os.path.join(target_directory, fasta_base_filename)
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152
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153 temp_fasta = tempfile.NamedTemporaryFile(delete=False, suffix=".fasta")
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154 temp_fasta.close()
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155 fasta_writer = open(temp_fasta.name, 'wb+')
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156
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157 if isinstance(fasta_stream, list) and len(fasta_stream) == 1:
0
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158 fasta_stream = fasta_stream[0]
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159
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160 if isinstance(fasta_stream, list):
0
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161 last_char = None
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162 for fh in fasta_stream:
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163 if last_char not in [None, '\n', '\r']:
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164 fasta_writer.write('\n')
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165 while True:
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166 data = fh.read(CHUNK_SIZE)
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167 if data:
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168 fasta_writer.write(data)
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169 last_char = data[-1]
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170 else:
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171 break
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172 if close_stream:
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173 fh.close()
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174 else:
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175 while True:
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176 data = fasta_stream.read(CHUNK_SIZE)
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177 if data:
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178 fasta_writer.write(data)
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179 else:
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180 break
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181 if close_stream:
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182 fasta_stream.close()
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183
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184 fasta_writer.close()
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185
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186 args = ['diamond', 'makedb', '--in', temp_fasta.name, '--db', fasta_filename]
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187
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188 tmp_stderr = tempfile.NamedTemporaryFile(prefix="tmp-data-manager-diamond-database-builder-stderr")
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189 proc = subprocess.Popen(args=args, shell=False, cwd=target_directory, stderr=tmp_stderr.fileno())
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190 return_code = proc.wait()
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191 if return_code:
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192 tmp_stderr.flush()
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193 tmp_stderr.seek(0)
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194 print >> sys.stderr, "Error building diamond database:"
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195 while True:
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196 chunk = tmp_stderr.read(CHUNK_SIZE)
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197 if not chunk:
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198 break
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199 sys.stderr.write(chunk)
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200 sys.exit(return_code)
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201 tmp_stderr.close()
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202 os.remove(temp_fasta.name)
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203 return dict(value=database_id, name=database_name, db_path="%s.dmnd" % fasta_base_filename)
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204
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205
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206 def _create_symlink(input_filename, target_directory, database_id, database_name):
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207 fasta_base_filename = "%s.fa" % database_id
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208 fasta_filename = os.path.join(target_directory, fasta_base_filename)
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209 os.symlink(input_filename, fasta_filename)
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210 return dict(value=database_id, name=database_name, db_path=fasta_base_filename)
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211
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212
1
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213 REFERENCE_SOURCE_TO_DOWNLOAD = dict(ncbi=download_from_ncbi, url=download_from_url, history=download_from_history, directory=copy_from_directory)
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214
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215
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216 def main():
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217 # Parse Command Line
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218 parser = optparse.OptionParser()
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219 parser.add_option('-d', '--dbkey_description', dest='dbkey_description', action='store', type="string", default=None, help='dbkey_description')
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220 (options, args) = parser.parse_args()
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221
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222 filename = args[0]
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223
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224 params = json.loads(open(filename).read())
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225 target_directory = params['output_data'][0]['extra_files_path']
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226 os.mkdir(target_directory)
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227 data_manager_dict = {}
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228
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229 database_id = params['param_dict']['database_id']
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230 database_name = params['param_dict']['database_name']
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231
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232 # Fetch the FASTA
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233 REFERENCE_SOURCE_TO_DOWNLOAD[params['param_dict']['reference_source']['reference_source_selector']](data_manager_dict, params, target_directory, database_id, database_name)
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234
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235 # save info to json file
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236 open(filename, 'w').write(json.dumps(data_manager_dict, sort_keys=True))
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237
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238
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239 if __name__ == "__main__":
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240 main()