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1 #!/usr/bin/env python
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2 #Dan Blankenberg
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3
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4 import sys
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5 import os
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6 import tempfile
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7 import shutil
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8 import optparse
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9 from ftplib import FTP
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10 import tarfile
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11 import zipfile
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12 import gzip
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13 import bz2
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14 try:
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15 # For Python 3.0 and later
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16 from urllib.request import urlopen
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17 from io import BytesIO as StringIO
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18 from io import UnsupportedOperation
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19 except ImportError:
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20 # Fall back to Python 2's urllib2
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21 from urllib2 import urlopen
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22 from StringIO import StringIO
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23 UnsupportedOperation = AttributeError
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24 from json import loads, dumps
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25
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26
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27 CHUNK_SIZE = 2**20 # 1mb
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28
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29 DATA_TABLE_NAME = 'all_gff'
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30
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31 def cleanup_before_exit( tmp_dir ):
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32 if tmp_dir and os.path.exists( tmp_dir ):
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33 shutil.rmtree( tmp_dir )
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34
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35
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36 def stop_err(msg):
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37 sys.stderr.write(msg)
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38 sys.exit(1)
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39
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40
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41 def get_dbkey_dbname_id_name( params, dbkey_description=None ):
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5
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42 dbkey = params['param_dict']['dbkey']
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0
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43 #TODO: ensure sequence_id is unique and does not already appear in location file
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44 sequence_id = params['param_dict']['sequence_id']
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45 if not sequence_id:
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46 sequence_id = dbkey #uuid.uuid4() generate and use an uuid instead?
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47
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2
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48 # if params['param_dict']['dbkey_source']['dbkey_source_selector'] == 'new':
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49 # dbkey_name = params['param_dict']['dbkey_source']['dbkey_name']
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50 # if not dbkey_name:
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51 # dbkey_name = dbkey
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52 # else:
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5
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53 # dbkey_name = None
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2
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54 dbkey_name = dbkey_description
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0
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55 sequence_name = params['param_dict']['sequence_name']
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56 if not sequence_name:
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57 sequence_name = dbkey_description
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58 if not sequence_name:
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59 sequence_name = dbkey
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60 return dbkey, dbkey_name, sequence_id, sequence_name
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61
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62
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63 def _get_files_in_ftp_path( ftp, path ):
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64 path_contents = []
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65 ftp.retrlines( 'MLSD %s' % ( path ), path_contents.append )
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66 return [ line.split( ';' )[ -1 ].lstrip() for line in path_contents ]
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67
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68
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69 def _get_stream_readers_for_tar( fh, tmp_dir ):
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70 fasta_tar = tarfile.open( fileobj=fh, mode='r:*' )
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71 return [x for x in [fasta_tar.extractfile(member) for member in fasta_tar.getmembers()] if x]
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72
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73
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74 def _get_stream_readers_for_zip( fh, tmp_dir ):
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75 """
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76 Unpacks all archived files in a zip file.
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77 Individual files will be concatenated (in _stream_fasta_to_file)
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78 """
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79 fasta_zip = zipfile.ZipFile( fh, 'r' )
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80 rval = []
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81 for member in fasta_zip.namelist():
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82 fasta_zip.extract( member, tmp_dir )
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83 rval.append( open( os.path.join( tmp_dir, member ), 'rb' ) )
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84 return rval
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85
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86
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87 def _get_stream_readers_for_gzip( fh, tmp_dir ):
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88 return [ gzip.GzipFile( fileobj=fh, mode='rb') ]
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89
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90
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91 def _get_stream_readers_for_bz2( fh, tmp_dir ):
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92 return [ bz2.BZ2File( fh.name, 'rb') ]
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93
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94
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95 def _download_file(start, fh):
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96 tmp = tempfile.NamedTemporaryFile()
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97 tmp.write(start)
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98 tmp.write(fh.read())
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99 tmp.flush()
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100 tmp.seek(0)
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101 return tmp
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102
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103
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104 def get_stream_reader(fh, tmp_dir):
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105 """
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106 Check if file is compressed and return correct stream reader.
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107 If file has to be downloaded, do it now.
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108 """
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109 magic_dict = {
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110 b"\x1f\x8b\x08": _get_stream_readers_for_gzip,
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111 b"\x42\x5a\x68": _get_stream_readers_for_bz2,
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112 b"\x50\x4b\x03\x04": _get_stream_readers_for_zip,
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113 }
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114 start_of_file = fh.read(CHUNK_SIZE)
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115 try:
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116 fh.seek(0)
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117 except UnsupportedOperation: # This is if fh has been created by urlopen
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118 fh = _download_file(start_of_file, fh)
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119 for k,v in magic_dict.items():
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120 if start_of_file.startswith(k):
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121 return v(fh, tmp_dir)
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122 try: # Check if file is tar file
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123 if tarfile.open(fileobj=StringIO(start_of_file)):
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124 return _get_stream_readers_for_tar(fh, tmp_dir)
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125 except tarfile.ReadError:
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126 pass
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127 return fh
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128
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129
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130
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131 def add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params):
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132 for data_table_name, data_table_entry in _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params ):
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133 if data_table_entry:
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134 _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name )
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135
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136
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137 def download_from_url( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
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138 urls = filter( bool, map( lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split( '\n' ) ) )
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139 fasta_readers = [ get_stream_reader(urlopen( url ), tmp_dir) for url in urls ]
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140 add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id,sequence_name, params)
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141
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142
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143 def download_from_history( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
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144 input_filename = params['param_dict']['reference_source']['input_fasta']
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145 if isinstance( input_filename, list ):
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146 fasta_readers = [ get_stream_reader(open(filename, 'rb'), tmp_dir) for filename in input_filename ]
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147 else:
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148 fasta_readers = get_stream_reader(open(input_filename), tmp_dir)
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149 add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params)
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150
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151
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152 def copy_from_directory( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
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153 input_filename = params['param_dict']['reference_source']['fasta_filename']
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154 create_symlink = params['param_dict']['reference_source']['create_symlink'] == 'create_symlink'
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155 if create_symlink:
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156 data_table_entries = _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name )
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157 else:
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158 if isinstance( input_filename, list ):
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159 fasta_readers = [ get_stream_reader(open(filename, 'rb'), tmp_dir) for filename in input_filename ]
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160 else:
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161 fasta_readers = get_stream_reader(open(input_filename), tmp_dir)
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162 data_table_entries = _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params )
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163 for data_table_name, data_table_entry in data_table_entries:
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164 if data_table_entry:
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165 _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name )
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166
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167
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168 def _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ):
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169 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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170 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get( DATA_TABLE_NAME, [] )
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171 data_manager_dict['data_tables'][data_table_name].append( data_table_entry )
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172 return data_manager_dict
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173
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174
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175 def _stream_fasta_to_file( fasta_stream, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params, close_stream=True ):
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176 fasta_base_filename = "%s.gff" % sequence_id
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177 fasta_filename = os.path.join( target_directory, fasta_base_filename )
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178 with open( fasta_filename, 'wb+' ) as fasta_writer:
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179
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180 if isinstance( fasta_stream, list ) and len( fasta_stream ) == 1:
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181 fasta_stream = fasta_stream[0]
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182
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183 if isinstance( fasta_stream, list ):
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184 last_char = None
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185 for fh in fasta_stream:
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186 if last_char not in [ None, '\n', '\r', b'\n', b'\r' ]:
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187 fasta_writer.write( b'\n' )
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188 while True:
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189 data = fh.read( CHUNK_SIZE )
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190 if data:
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191 fasta_writer.write( data )
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192 last_char = data[-1]
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193 else:
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194 break
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195 if close_stream:
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196 fh.close()
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197 else:
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198 while True:
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199 data = fasta_stream.read( CHUNK_SIZE )
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200 if data:
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201 fasta_writer.write( data )
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202 else:
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203 break
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204 if close_stream:
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205 fasta_stream.close()
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206
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207 #sort_fasta( fasta_filename, params['param_dict']['sorting']['sort_selector'], params )
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208
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209
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210 return [ ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]
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211
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212
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213 def compute_fasta_length( fasta_file, out_file, keep_first_word=False ):
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214
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215 infile = fasta_file
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216 out = open( out_file, 'w')
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217
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218 fasta_title = ''
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219 seq_len = 0
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220
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221 first_entry = True
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222
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223 for line in open( infile ):
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224 line = line.strip()
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225 if not line or line.startswith( '#' ):
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226 continue
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227 if line[0] == '>':
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228 if first_entry == False:
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229 if keep_first_word:
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230 fasta_title = fasta_title.split()[0]
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231 out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) )
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232 else:
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233 first_entry = False
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234 fasta_title = line
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235 seq_len = 0
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236 else:
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237 seq_len += len(line)
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238
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239 # last fasta-entry
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240 if keep_first_word:
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241 fasta_title = fasta_title.split()[0]
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242 out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) )
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243 out.close()
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244
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245
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246 def _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ):
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247 fasta_base_filename = "%s.fa" % sequence_id
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248 fasta_filename = os.path.join( target_directory, fasta_base_filename )
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249 os.symlink( input_filename, fasta_filename )
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250 return [ ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]
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0
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251
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252
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3
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253 #REFERENCE_SOURCE_TO_DOWNLOAD = dict( ucsc=download_from_ucsc, ncbi=download_from_ncbi, url=download_from_url, history=download_from_history, directory=copy_from_directory )
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254 REFERENCE_SOURCE_TO_DOWNLOAD = dict( url=download_from_url, history=download_from_history, directory=copy_from_directory )
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255 #SORTING_METHODS = dict( as_is=_sort_fasta_as_is, lexicographical=_sort_fasta_lexicographical, gatk=_sort_fasta_gatk, custom=_sort_fasta_custom )
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0
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256
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257
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258 def main():
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259 #Parse Command Line
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260 parser = optparse.OptionParser()
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261 parser.add_option( '-d', '--dbkey_description', dest='dbkey_description', action='store', type="string", default=None, help='dbkey_description' )
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262 (options, args) = parser.parse_args()
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263
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264 filename = args[0]
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3
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265 #global DATA_TABLE_NAME
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0
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266 params = loads( open( filename ).read() )
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267 target_directory = params[ 'output_data' ][0]['extra_files_path']
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268 os.mkdir( target_directory )
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269 data_manager_dict = {}
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270
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271 dbkey, dbkey_name, sequence_id, sequence_name = get_dbkey_dbname_id_name( params, dbkey_description=options.dbkey_description )
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272
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273 if dbkey in [ None, '', '?' ]:
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274 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
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275
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276 # Create a tmp_dir, in case a zip file needs to be uncompressed
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277 tmp_dir = tempfile.mkdtemp()
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278 #Fetch the FASTA
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279 try:
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280 REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir )
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281 finally:
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282 cleanup_before_exit(tmp_dir)
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283 #save info to json file
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284 open( filename, 'wb' ).write( dumps( data_manager_dict ).encode() )
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285
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286 if __name__ == "__main__":
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287 main()
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