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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 = 'tx2gene'
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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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42 # dbkey = params['param_dict']['dbkey_source']['dbkey']
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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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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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53 # dbkey_name = None
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54 dbkey = params['param_dict']['dbkey']
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55 dbkey_name = dbkey_description
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56 sequence_name = params['param_dict']['sequence_name']
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57 if not sequence_name:
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58 sequence_name = dbkey_description
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59 if not sequence_name:
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60 sequence_name = dbkey
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61 return dbkey, dbkey_name, sequence_id, sequence_name
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62
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63
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64 def _get_files_in_ftp_path( ftp, path ):
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65 path_contents = []
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66 ftp.retrlines( 'MLSD %s' % ( path ), path_contents.append )
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67 return [ line.split( ';' )[ -1 ].lstrip() for line in path_contents ]
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68
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69
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70 def _get_stream_readers_for_tar( fh, tmp_dir ):
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71 fasta_tar = tarfile.open( fileobj=fh, mode='r:*' )
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72 return [x for x in [fasta_tar.extractfile(member) for member in fasta_tar.getmembers()] if x]
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73
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74
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75 def _get_stream_readers_for_zip( fh, tmp_dir ):
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76 """
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77 Unpacks all archived files in a zip file.
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78 Individual files will be concatenated (in _stream_fasta_to_file)
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79 """
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80 fasta_zip = zipfile.ZipFile( fh, 'r' )
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81 rval = []
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82 for member in fasta_zip.namelist():
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83 fasta_zip.extract( member, tmp_dir )
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84 rval.append( open( os.path.join( tmp_dir, member ), 'rb' ) )
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85 return rval
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86
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87
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88 def _get_stream_readers_for_gzip( fh, tmp_dir ):
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89 return [ gzip.GzipFile( fileobj=fh, mode='rb') ]
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90
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91
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92 def _get_stream_readers_for_bz2( fh, tmp_dir ):
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93 return [ bz2.BZ2File( fh.name, 'rb') ]
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94
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95
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96 def convert_tx2gene( fasta_filename, file_type, params ):
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97 if file_type is 'tx2gene':
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98 return #no need to extract tx2gene table
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99 #If the file is actually a GFF/GTF file then extract the tx2gene
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100 gff_temp_filename = tempfile.NamedTemporaryFile().name
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101 shutil.move(fasta_filename, gff_temp_filename)
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102 args= ['Rscript']
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103 args.append(RSCRIPT_GFF_TO_TX2GENE)
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104 args.append(gff_temp_filename)
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105 args.append(fasta_filename)
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106
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107 #assert sort_method in SORTING_METHODS, ValueError( "%s is not a valid sorting option." % sort_method )
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108 #return SORTING_METHODS[ sort_method ]( fasta_filename, params )
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109
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110 def _download_file(start, fh):
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111 tmp = tempfile.NamedTemporaryFile()
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112 tmp.write(start)
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113 tmp.write(fh.read())
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114 tmp.flush()
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115 tmp.seek(0)
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116 return tmp
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117
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118
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119 def get_stream_reader(fh, tmp_dir):
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120 """
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121 Check if file is compressed and return correct stream reader.
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122 If file has to be downloaded, do it now.
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123 """
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124 magic_dict = {
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125 b"\x1f\x8b\x08": _get_stream_readers_for_gzip,
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126 b"\x42\x5a\x68": _get_stream_readers_for_bz2,
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127 b"\x50\x4b\x03\x04": _get_stream_readers_for_zip,
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128 }
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129 start_of_file = fh.read(CHUNK_SIZE)
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130 try:
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131 fh.seek(0)
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132 except UnsupportedOperation: # This is if fh has been created by urlopen
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133 fh = _download_file(start_of_file, fh)
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134 for k,v in magic_dict.items():
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135 if start_of_file.startswith(k):
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136 return v(fh, tmp_dir)
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137 try: # Check if file is tar file
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138 if tarfile.open(fileobj=StringIO(start_of_file)):
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139 return _get_stream_readers_for_tar(fh, tmp_dir)
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140 except tarfile.ReadError:
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141 pass
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142 return fh
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143
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144
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145
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146 def add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params):
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147 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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148 if data_table_entry:
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149 _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name )
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150
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151
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152 def download_from_url( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
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153 urls = filter( bool, map( lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split( '\n' ) ) )
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154 fasta_readers = [ get_stream_reader(urlopen( url ), tmp_dir) for url in urls ]
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155 add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id,sequence_name, params)
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156
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157
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158 def download_from_history( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
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159 #TODO: allow multiple FASTA input files
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160 input_filename = params['param_dict']['reference_source']['input_fasta']
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161 if isinstance( input_filename, list ):
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162 fasta_readers = [ get_stream_reader(open(filename, 'rb'), tmp_dir) for filename in input_filename ]
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163 else:
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164 fasta_readers = get_stream_reader(open(input_filename), tmp_dir)
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165 add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params)
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166
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167
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168 def copy_from_directory( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
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169 input_filename = params['param_dict']['reference_source']['fasta_filename']
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170 create_symlink = params['param_dict']['reference_source']['create_symlink'] == 'create_symlink'
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171 if create_symlink:
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172 data_table_entries = _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name )
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173 else:
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174 if isinstance( input_filename, list ):
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175 fasta_readers = [ get_stream_reader(open(filename, 'rb'), tmp_dir) for filename in input_filename ]
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176 else:
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177 fasta_readers = get_stream_reader(open(input_filename), tmp_dir)
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178 data_table_entries = _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params )
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179 for data_table_name, data_table_entry in data_table_entries:
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180 if data_table_entry:
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181 _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name )
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182
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183
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184 def _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ):
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185 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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186 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get( DATA_TABLE_NAME, [] )
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187 data_manager_dict['data_tables'][data_table_name].append( data_table_entry )
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188 return data_manager_dict
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189
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190
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191 def _stream_fasta_to_file( fasta_stream, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params, close_stream=True ):
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192 fasta_base_filename = "%s_tx2gene.tab" % sequence_id
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193 fasta_filename = os.path.join( target_directory, fasta_base_filename )
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194 with open( fasta_filename, 'wb+' ) as fasta_writer:
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195
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196 if isinstance( fasta_stream, list ) and len( fasta_stream ) == 1:
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197 fasta_stream = fasta_stream[0]
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198
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199 if isinstance( fasta_stream, list ):
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200 last_char = None
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201 for fh in fasta_stream:
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202 if last_char not in [ None, '\n', '\r', b'\n', b'\r' ]:
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203 fasta_writer.write( b'\n' )
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204 while True:
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205 data = fh.read( CHUNK_SIZE )
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206 if data:
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207 fasta_writer.write( data )
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208 last_char = data[-1]
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209 else:
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210 break
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211 if close_stream:
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212 fh.close()
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213 else:
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214 while True:
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215 data = fasta_stream.read( CHUNK_SIZE )
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216 if data:
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217 fasta_writer.write( data )
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218 else:
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219 break
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220 if close_stream:
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221 fasta_stream.close()
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222
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223 convert_to_tx2gene( fasta_filename, params['param_dict']['file_type'], params )
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224 return [ ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]
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225
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226
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227 def compute_fasta_length( fasta_file, out_file, keep_first_word=False ):
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228
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229 infile = fasta_file
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230 out = open( out_file, 'w')
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231
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232 fasta_title = ''
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233 seq_len = 0
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234
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235 first_entry = True
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236
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237 for line in open( infile ):
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238 line = line.strip()
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239 if not line or line.startswith( '#' ):
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240 continue
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241 if line[0] == '>':
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242 if first_entry == False:
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243 if keep_first_word:
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244 fasta_title = fasta_title.split()[0]
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245 out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) )
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246 else:
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247 first_entry = False
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248 fasta_title = line
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249 seq_len = 0
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250 else:
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251 seq_len += len(line)
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252
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253 # last fasta-entry
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254 if keep_first_word:
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255 fasta_title = fasta_title.split()[0]
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256 out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) )
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257 out.close()
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258
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259
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260 def _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ):
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261 fasta_base_filename = "%s.fa" % sequence_id
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262 fasta_filename = os.path.join( target_directory, fasta_base_filename )
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263 os.symlink( input_filename, fasta_filename )
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264 return [ ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]
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265
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266
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267 REFERENCE_SOURCE_TO_DOWNLOAD = dict( url=download_from_url, history=download_from_history, directory=copy_from_directory )
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268
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269
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270 def main():
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271 #Parse Command Line
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272 parser = optparse.OptionParser()
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273 parser.add_option( '-d', '--dbkey_description', dest='dbkey_description', action='store', type="string", default=None, help='dbkey_description' )
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274 parser.add_option( '-t', '--type', dest='file_type', action='store', type='string', default=None, help='file_type')
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275 (options, args) = parser.parse_args()
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276
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277 filename = args[0]
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278 #global DATA_TABLE_NAME
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279 global RSCRIPT_GFF_TO_TX2GENE= os.path.join( options.base_dir, 'tximport.r')
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280
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281
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282 if options.file_type == 'gff_gtf':
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283 #DATA_TABLE_NAME= 'representative_gff'
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284 else: #file_type='tx2gene'
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285
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286 params = loads( open( filename ).read() )
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287 target_directory = params[ 'output_data' ][0]['extra_files_path']
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288 os.mkdir( target_directory )
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289 data_manager_dict = {}
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290
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291 dbkey, dbkey_name, sequence_id, sequence_name = get_dbkey_dbname_id_name( params, dbkey_description=options.dbkey_description )
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292
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293 if dbkey in [ None, '', '?' ]:
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294 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
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295
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296 # Create a tmp_dir, in case a zip file needs to be uncompressed
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297 tmp_dir = tempfile.mkdtemp()
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298 #Fetch the input file
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299 try:
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300 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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301 finally:
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302 cleanup_before_exit(tmp_dir)
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303 #save info to json file
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304 open( filename, 'wb' ).write( dumps( data_manager_dict ).encode() )
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305
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306 if __name__ == "__main__":
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307 main()
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