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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 import urllib2
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10 #import uuid
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11 from ftplib import FTP
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12 import tarfile
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13 import zipfile
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14 import gzip
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15 import bz2
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16
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17 from galaxy.util.json import from_json_string, to_json_string
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18
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19
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20 CHUNK_SIZE = 2**20 #1mb
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21
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22 def cleanup_before_exit( tmp_dir ):
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23 if tmp_dir and os.path.exists( tmp_dir ):
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24 shutil.rmtree( tmp_dir )
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25
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26 def stop_err(msg):
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27 sys.stderr.write(msg)
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28 sys.exit(1)
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29
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30 def get_dbkey_id_name( params, dbkey_description=None ):
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31 dbkey = params['param_dict']['dbkey']
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32 #TODO: ensure sequence_id is unique and does not already appear in location file
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33 sequence_id = params['param_dict']['sequence_id']
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34 if not sequence_id:
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35 sequence_id = dbkey #uuid.uuid4() generate and use an uuid instead?
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36
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37 sequence_name = params['param_dict']['sequence_name']
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38 if not sequence_name:
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39 sequence_name = dbkey_description
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40 if not sequence_name:
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41 sequence_name = dbkey
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42 return dbkey, sequence_id, sequence_name
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43
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44 def _get_files_in_ftp_path( ftp, path ):
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45 path_contents = []
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46 ftp.retrlines( 'MLSD %s' % ( path ), path_contents.append )
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47 return [ line.split( ';' )[ -1 ].lstrip() for line in path_contents ]
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48
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49 def _get_stream_readers_for_tar( file_obj, tmp_dir ):
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50 fasta_tar = tarfile.open( fileobj=file_obj, mode='r:*' )
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51 return [ fasta_tar.extractfile( member ) for member in fasta_tar.getmembers() ]
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52
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53 def _get_stream_readers_for_zip( file_obj, tmp_dir ):
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54 fasta_zip = zipfile.ZipFile( file_obj, 'r' )
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55 rval = []
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56 for member in fasta_zip.namelist():
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57 fasta_zip.extract( member, tmp_dir )
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58 rval.append( open( os.path.join( tmp_dir, member ), 'rb' ) )
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59 return rval
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60
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61 def _get_stream_readers_for_gzip( file_obj, tmp_dir ):
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62 return [ gzip.GzipFile( fileobj=file_obj, mode='rb' ) ]
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63
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64 def _get_stream_readers_for_bz2( file_obj, tmp_dir ):
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65 return [ bz2.BZ2File( file_obj.name, 'rb' ) ]
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66
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67 def sort_fasta( fasta_filename, sort_method, params ):
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68 if sort_method is None:
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69 return
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70 assert sort_method in SORTING_METHODS, ValueError( "%s is not a valid sorting option." % sort_method )
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71 return SORTING_METHODS[ sort_method ]( fasta_filename, params )
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72
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73 def _move_and_index_fasta_for_sorting( fasta_filename ):
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74 unsorted_filename = tempfile.NamedTemporaryFile().name
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75 shutil.move( fasta_filename, unsorted_filename )
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76 fasta_offsets = {}
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77 unsorted_fh = open( unsorted_filename )
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78 while True:
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79 offset = unsorted_fh.tell()
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80 line = unsorted_fh.readline()
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81 if not line:
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82 break
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83 if line.startswith( ">" ):
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84 line = line.split( None, 1 )[0][1:]
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85 fasta_offsets[ line ] = offset
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86 unsorted_fh.close()
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87 current_order = map( lambda x: x[1], sorted( map( lambda x: ( x[1], x[0] ), fasta_offsets.items() ) ) )
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88 return ( unsorted_filename, fasta_offsets, current_order )
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89
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90 def _write_sorted_fasta( sorted_names, fasta_offsets, sorted_fasta_filename, unsorted_fasta_filename ):
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91 unsorted_fh = open( unsorted_fasta_filename )
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92 sorted_fh = open( sorted_fasta_filename, 'wb+' )
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93
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94 for name in sorted_names:
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95 offset = fasta_offsets[ name ]
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96 unsorted_fh.seek( offset )
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97 sorted_fh.write( unsorted_fh.readline() )
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98 while True:
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99 line = unsorted_fh.readline()
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100 if not line or line.startswith( ">" ):
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101 break
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102 sorted_fh.write( line )
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103 unsorted_fh.close()
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104 sorted_fh.close()
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105
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106 def _sort_fasta_as_is( fasta_filename, params ):
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107 return
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108
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109 def _sort_fasta_lexicographical( fasta_filename, params ):
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110 ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename )
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111 sorted_names = sorted( fasta_offsets.keys() )
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112 if sorted_names == current_order:
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113 shutil.move( unsorted_filename, fasta_filename )
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114 else:
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115 _write_sorted_fasta( sorted_names, fasta_offsets, fasta_filename, unsorted_filename )
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116
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117 def _sort_fasta_gatk( fasta_filename, params ):
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118 #This method was added by reviewer request.
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119 ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename )
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120 sorted_names = map( str, range( 1, 23 ) ) + [ 'X', 'Y' ]
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121 #detect if we have chrN, or just N
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122 has_chr = False
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123 for chrom in sorted_names:
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124 if "chr%s" % chrom in current_order:
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125 has_chr = True
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126 break
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127
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128 if has_chr:
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129 sorted_names = map( lambda x: "chr%s" % x, sorted_names)
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130 sorted_names.insert( 0, "chrM" )
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131 else:
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132 sorted_names.insert( 0, "MT" )
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133 sorted_names.extend( map( lambda x: "%s_random" % x, sorted_names ) )
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134
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135 existing_sorted_names = []
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136 for name in sorted_names:
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137 if name in current_order:
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138 existing_sorted_names.append( name )
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139 for name in current_order:
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140 #TODO: confirm that non-canonical names do not need to be sorted specially
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141 if name not in existing_sorted_names:
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142 existing_sorted_names.append( name )
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143
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144 if existing_sorted_names == current_order:
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145 shutil.move( unsorted_filename, fasta_filename )
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146 else:
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147 _write_sorted_fasta( existing_sorted_names, fasta_offsets, fasta_filename, unsorted_filename )
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148
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149 def _sort_fasta_custom( fasta_filename, params ):
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150 ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename )
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151 sorted_names = []
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152 for id_repeat in params['param_dict']['sorting']['sequence_identifiers']:
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153 sorted_names.append( id_repeat[ 'identifier' ] )
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154 handle_not_listed = params['param_dict']['sorting']['handle_not_listed']['handle_not_listed_selector']
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155 if handle_not_listed.startswith( 'keep' ):
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156 add_list = []
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157 for name in current_order:
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158 if name not in sorted_names:
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159 add_list.append( name )
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160 if add_list:
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161 if handle_not_listed == 'keep_append':
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162 sorted_names.extend( add_list )
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163 else:
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164 add_list.extend( sorted_names )
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165 sorted_names = add_list
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166 if sorted_names == current_order:
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167 shutil.move( unsorted_filename, fasta_filename )
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168 else:
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169 _write_sorted_fasta( sorted_names, fasta_offsets, fasta_filename, unsorted_filename )
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170
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171 def download_from_ucsc( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name ):
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172 UCSC_FTP_SERVER = 'hgdownload.cse.ucsc.edu'
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173 UCSC_CHROM_FA_FILENAME = 'chromFa'
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174 UCSC_DOWNLOAD_PATH = '/goldenPath/%s/bigZips/'
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175 COMPRESSED_EXTENSIONS = [ ( '.tar.gz', _get_stream_readers_for_tar ), ( '.tar.bz2', _get_stream_readers_for_tar ), ( '.zip', _get_stream_readers_for_zip ), ( '.fa.gz', _get_stream_readers_for_gzip ), ( '.fa.bz2', _get_stream_readers_for_bz2 ) ]
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176
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177 email = params['param_dict']['__user_email__']
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178 if not email:
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179 email = 'anonymous@example.com'
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180
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181 ucsc_dbkey = params['param_dict']['reference_source']['requested_dbkey'] or dbkey
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182 ftp = FTP( UCSC_FTP_SERVER )
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183 ftp.login( 'anonymous', email )
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184
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185 ucsc_path = UCSC_DOWNLOAD_PATH % ucsc_dbkey
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186 path_contents = _get_files_in_ftp_path( ftp, ucsc_path )
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187
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188 ucsc_file_name = None
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189 get_stream_reader = None
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190 ext = None
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191 for ext, get_stream_reader in COMPRESSED_EXTENSIONS:
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192 if "%s%s" % ( UCSC_CHROM_FA_FILENAME, ext ) in path_contents:
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193 ucsc_file_name = "%s%s%s" % ( ucsc_path, UCSC_CHROM_FA_FILENAME, ext )
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194 break
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195
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196 if not ucsc_file_name:
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197 raise Exception( 'Unable to determine filename for UCSC Genome for %s: %s' % ( ucsc_dbkey, path_contents ) )
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198
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199
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200 tmp_dir = tempfile.mkdtemp( prefix='tmp-data-manager-ucsc-' )
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201 ucsc_fasta_filename = os.path.join( tmp_dir, "%s%s" % ( UCSC_CHROM_FA_FILENAME, ext ) )
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202
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203 fasta_base_filename = "%s.fa" % sequence_id
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204 fasta_filename = os.path.join( target_directory, fasta_base_filename )
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205 fasta_writer = open( fasta_filename, 'wb+' )
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206
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207 tmp_extract_dir = os.path.join ( tmp_dir, 'extracted_fasta' )
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208 os.mkdir( tmp_extract_dir )
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209
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210 tmp_fasta = open( ucsc_fasta_filename, 'wb+' )
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211
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212 ftp.retrbinary( 'RETR %s' % ucsc_file_name, tmp_fasta.write )
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213
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214 tmp_fasta.flush()
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215 tmp_fasta.seek( 0 )
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216
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217 fasta_readers = get_stream_reader( tmp_fasta, tmp_extract_dir )
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218
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219 data_table_entry = _stream_fasta_to_file( fasta_readers, target_directory, dbkey, sequence_id, sequence_name, params )
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220 _add_data_table_entry( data_manager_dict, data_table_entry )
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221
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222 for fasta_reader in fasta_readers:
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223 fasta_reader.close()
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224 tmp_fasta.close()
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225 cleanup_before_exit( tmp_dir )
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226
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227 def download_from_ncbi( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name ):
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228 NCBI_DOWNLOAD_URL = 'http://togows.dbcls.jp/entry/ncbi-nucleotide/%s.fasta' #FIXME: taken from dave's genome manager...why some japan site?
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229
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230 requested_identifier = params['param_dict']['reference_source']['requested_identifier']
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231 url = NCBI_DOWNLOAD_URL % requested_identifier
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232 fasta_reader = urllib2.urlopen( url )
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233
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234 data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, dbkey, sequence_id, sequence_name, params )
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235 _add_data_table_entry( data_manager_dict, data_table_entry )
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236
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237 def download_from_url( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name ):
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238 #TODO: we should automatically do decompression here
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239 urls = filter( bool, map( lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split( '\n' ) ) )
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240 fasta_reader = [ urllib2.urlopen( url ) for url in urls ]
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241
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242 data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, dbkey, sequence_id, sequence_name, params )
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243 _add_data_table_entry( data_manager_dict, data_table_entry )
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244
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245 def download_from_history( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name ):
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246 #TODO: allow multiple FASTA input files
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247 input_filename = params['param_dict']['reference_source']['input_fasta']
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248 if isinstance( input_filename, list ):
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249 fasta_reader = [ open( filename, 'rb' ) for filename in input_filename ]
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250 else:
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251 fasta_reader = open( input_filename )
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252
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253 data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, dbkey, sequence_id, sequence_name, params )
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254 _add_data_table_entry( data_manager_dict, data_table_entry )
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255
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256 def copy_from_directory( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name ):
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257 input_filename = params['param_dict']['reference_source']['fasta_filename']
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258 create_symlink = params['param_dict']['reference_source']['create_symlink'] == 'create_symlink'
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259 if create_symlink:
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260 data_table_entry = _create_symlink( input_filename, target_directory, dbkey, sequence_id, sequence_name )
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261 else:
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262 if isinstance( input_filename, list ):
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263 fasta_reader = [ open( filename, 'rb' ) for filename in input_filename ]
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264 else:
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265 fasta_reader = open( input_filename )
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266 data_table_entry = _stream_fasta_to_file( fasta_reader, target_directory, dbkey, sequence_id, sequence_name, params )
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267 _add_data_table_entry( data_manager_dict, data_table_entry )
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268
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269 def _add_data_table_entry( data_manager_dict, data_table_entry ):
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270 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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271 data_manager_dict['data_tables']['all_fasta'] = data_manager_dict['data_tables'].get( 'all_fasta', [] )
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272 data_manager_dict['data_tables']['all_fasta'].append( data_table_entry )
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273 return data_manager_dict
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274
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275 def _stream_fasta_to_file( fasta_stream, target_directory, dbkey, sequence_id, sequence_name, params, close_stream=True ):
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276 fasta_base_filename = "%s.fa" % sequence_id
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277 fasta_filename = os.path.join( target_directory, fasta_base_filename )
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278 fasta_writer = open( fasta_filename, 'wb+' )
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279
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280 if isinstance( fasta_stream, list ) and len( fasta_stream ) == 1:
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281 fasta_stream = fasta_stream[0]
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282
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283 if isinstance( fasta_stream, list ):
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284 last_char = None
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285 for fh in fasta_stream:
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286 if last_char not in [ None, '\n', '\r' ]:
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287 fasta_writer.write( '\n' )
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288 while True:
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289 data = fh.read( CHUNK_SIZE )
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290 if data:
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291 fasta_writer.write( data )
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292 last_char = data[-1]
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293 else:
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294 break
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295 if close_stream:
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296 fh.close()
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297 else:
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298 while True:
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299 data = fasta_stream.read( CHUNK_SIZE )
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300 if data:
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301 fasta_writer.write( data )
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302 else:
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303 break
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304 if close_stream:
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305 fasta_stream.close()
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306
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307 fasta_writer.close()
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308
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309 sort_fasta( fasta_filename, params['param_dict']['sorting']['sort_selector'], params )
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310
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311 return dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename )
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312
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313 def _create_symlink( input_filename, target_directory, dbkey, sequence_id, sequence_name ):
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314 fasta_base_filename = "%s.fa" % sequence_id
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315 fasta_filename = os.path.join( target_directory, fasta_base_filename )
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316 os.symlink( input_filename, fasta_filename )
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317 return dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename )
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318
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319
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320
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321
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322 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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323
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324 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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325
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326 def main():
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327 #Parse Command Line
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328 parser = optparse.OptionParser()
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329 parser.add_option( '-d', '--dbkey_description', dest='dbkey_description', action='store', type="string", default=None, help='dbkey_description' )
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330 (options, args) = parser.parse_args()
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331
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332 filename = args[0]
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333
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334 params = from_json_string( open( filename ).read() )
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335 target_directory = params[ 'output_data' ][0]['extra_files_path']
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336 os.mkdir( target_directory )
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337 data_manager_dict = {}
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338
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339 dbkey, sequence_id, sequence_name = get_dbkey_id_name( params, dbkey_description=options.dbkey_description )
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340
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341 if dbkey in [ None, '', '?' ]:
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342 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
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343
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344 #Fetch the FASTA
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345 REFERENCE_SOURCE_TO_DOWNLOAD[ params['param_dict']['reference_source']['reference_source_selector'] ]( data_manager_dict, params, target_directory, dbkey, sequence_id, sequence_name )
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346
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347 #save info to json file
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348 open( filename, 'wb' ).write( to_json_string( data_manager_dict ) )
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349
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350 if __name__ == "__main__": main()
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