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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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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
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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 sort_fasta( fasta_filename, sort_method, params ):
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96 if sort_method is None:
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97 return
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98 assert sort_method in SORTING_METHODS, ValueError( "%s is not a valid sorting option." % sort_method )
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99 return SORTING_METHODS[ sort_method ]( fasta_filename, params )
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100
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101
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102 def _move_and_index_fasta_for_sorting( fasta_filename ):
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103 unsorted_filename = tempfile.NamedTemporaryFile().name
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104 shutil.move( fasta_filename, unsorted_filename )
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105 fasta_offsets = {}
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106 unsorted_fh = open( unsorted_filename )
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107 while True:
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108 offset = unsorted_fh.tell()
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109 line = unsorted_fh.readline()
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110 if not line:
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111 break
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112 if line.startswith( ">" ):
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113 line = line.split( None, 1 )[0][1:]
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114 fasta_offsets[ line ] = offset
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115 unsorted_fh.close()
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116 current_order = map( lambda x: x[1], sorted( map( lambda x: ( x[1], x[0] ), fasta_offsets.items() ) ) )
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117 return ( unsorted_filename, fasta_offsets, current_order )
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118
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119
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120 def _write_sorted_fasta( sorted_names, fasta_offsets, sorted_fasta_filename, unsorted_fasta_filename ):
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121 unsorted_fh = open( unsorted_fasta_filename )
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122 sorted_fh = open( sorted_fasta_filename, 'wb+' )
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123
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124 for name in sorted_names:
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125 offset = fasta_offsets[ name ]
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126 unsorted_fh.seek( offset )
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127 sorted_fh.write( unsorted_fh.readline() )
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128 while True:
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129 line = unsorted_fh.readline()
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130 if not line or line.startswith( ">" ):
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131 break
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132 sorted_fh.write( line )
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133 unsorted_fh.close()
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134 sorted_fh.close()
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135
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136
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137 def _sort_fasta_as_is( fasta_filename, params ):
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138 return
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139
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140 def _sort_fasta_lexicographical( fasta_filename, params ):
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141 ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename )
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142 sorted_names = sorted( fasta_offsets.keys() )
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143 if sorted_names == current_order:
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144 shutil.move( unsorted_filename, fasta_filename )
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145 else:
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146 _write_sorted_fasta( sorted_names, fasta_offsets, fasta_filename, unsorted_filename )
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147
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148
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149 def _sort_fasta_gatk( fasta_filename, params ):
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150 #This method was added by reviewer request.
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151 ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename )
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152 sorted_names = map( str, range( 1, 23 ) ) + [ 'X', 'Y' ]
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153 #detect if we have chrN, or just N
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154 has_chr = False
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155 for chrom in sorted_names:
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156 if "chr%s" % chrom in current_order:
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157 has_chr = True
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158 break
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159
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160 if has_chr:
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161 sorted_names = map( lambda x: "chr%s" % x, sorted_names)
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162 sorted_names.insert( 0, "chrM" )
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163 else:
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164 sorted_names.insert( 0, "MT" )
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165 sorted_names.extend( map( lambda x: "%s_random" % x, sorted_names ) )
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166
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167 existing_sorted_names = []
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168 for name in sorted_names:
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169 if name in current_order:
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170 existing_sorted_names.append( name )
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171 for name in current_order:
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172 #TODO: confirm that non-canonical names do not need to be sorted specially
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173 if name not in existing_sorted_names:
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174 existing_sorted_names.append( name )
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175
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176 if existing_sorted_names == current_order:
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177 shutil.move( unsorted_filename, fasta_filename )
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178 else:
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179 _write_sorted_fasta( existing_sorted_names, fasta_offsets, fasta_filename, unsorted_filename )
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180
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181
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182 def _sort_fasta_custom( fasta_filename, params ):
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183 ( unsorted_filename, fasta_offsets, current_order ) = _move_and_index_fasta_for_sorting( fasta_filename )
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184 sorted_names = []
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185 for id_repeat in params['param_dict']['sorting']['sequence_identifiers']:
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186 sorted_names.append( id_repeat[ 'identifier' ] )
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187 handle_not_listed = params['param_dict']['sorting']['handle_not_listed_selector']
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188 if handle_not_listed.startswith( 'keep' ):
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189 add_list = []
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190 for name in current_order:
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191 if name not in sorted_names:
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192 add_list.append( name )
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193 if add_list:
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194 if handle_not_listed == 'keep_append':
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195 sorted_names.extend( add_list )
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196 else:
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197 add_list.extend( sorted_names )
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198 sorted_names = add_list
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199 if sorted_names == current_order:
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200 shutil.move( unsorted_filename, fasta_filename )
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201 else:
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202 _write_sorted_fasta( sorted_names, fasta_offsets, fasta_filename, unsorted_filename )
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203
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204
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205 def _download_file(start, fh):
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206 tmp = tempfile.NamedTemporaryFile()
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207 tmp.write(start)
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208 tmp.write(fh.read())
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209 tmp.flush()
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210 tmp.seek(0)
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211 return tmp
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212
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213
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214 def get_stream_reader(fh, tmp_dir):
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215 """
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216 Check if file is compressed and return correct stream reader.
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217 If file has to be downloaded, do it now.
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218 """
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219 magic_dict = {
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220 b"\x1f\x8b\x08": _get_stream_readers_for_gzip,
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221 b"\x42\x5a\x68": _get_stream_readers_for_bz2,
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222 b"\x50\x4b\x03\x04": _get_stream_readers_for_zip,
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223 }
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224 start_of_file = fh.read(CHUNK_SIZE)
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225 try:
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226 fh.seek(0)
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227 except UnsupportedOperation: # This is if fh has been created by urlopen
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228 fh = _download_file(start_of_file, fh)
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229 for k,v in magic_dict.items():
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230 if start_of_file.startswith(k):
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231 return v(fh, tmp_dir)
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232 try: # Check if file is tar file
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233 if tarfile.open(fileobj=StringIO(start_of_file)):
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234 return _get_stream_readers_for_tar(fh, tmp_dir)
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235 except tarfile.ReadError:
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236 pass
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237 return fh
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238
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239
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240 def _get_ucsc_download_address(params, dbkey):
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241 """
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242 Check if we can find the correct file for the supplied dbkey on UCSC's FTP server
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243 """
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244 UCSC_FTP_SERVER = 'hgdownload.cse.ucsc.edu'
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245 UCSC_DOWNLOAD_PATH = '/goldenPath/%s/bigZips/'
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246 COMPRESSED_EXTENSIONS = ['.tar.gz', '.tgz', '.tar.bz2', '.zip', '.fa.gz', '.fa.bz2']
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247
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248 email = params['param_dict']['__user_email__']
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249 if not email:
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250 email = 'anonymous@example.com'
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251
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252 ucsc_dbkey = params['param_dict']['reference_source']['requested_dbkey'] or dbkey
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253 UCSC_CHROM_FA_FILENAMES = ['%s.chromFa' % ucsc_dbkey, 'chromFa', ucsc_dbkey]
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254
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255 ftp = FTP(UCSC_FTP_SERVER)
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256 ftp.login('anonymous', email)
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257
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258 ucsc_path = UCSC_DOWNLOAD_PATH % ucsc_dbkey
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259 path_contents = _get_files_in_ftp_path(ftp, ucsc_path)
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260 ftp.quit()
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261
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262 for ucsc_chrom_fa_filename in UCSC_CHROM_FA_FILENAMES:
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263 for ext in COMPRESSED_EXTENSIONS:
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264 if "%s%s" % (ucsc_chrom_fa_filename, ext) in path_contents:
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265 ucsc_file_name = "%s%s%s" % (ucsc_path, ucsc_chrom_fa_filename, ext)
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266 return "ftp://%s%s" % (UCSC_FTP_SERVER, ucsc_file_name)
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267
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268 raise Exception('Unable to determine filename for UCSC Genome for %s: %s' % (ucsc_dbkey, path_contents))
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269
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270 def add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params):
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271 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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272 if data_table_entry:
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273 _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name )
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274
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275
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276 def download_from_ucsc( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
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277 url = _get_ucsc_download_address(params, dbkey)
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278 fasta_readers = get_stream_reader(urlopen(url), tmp_dir)
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279 add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params)
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280
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281
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282 def download_from_ncbi( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
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283 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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284 requested_identifier = params['param_dict']['reference_source']['requested_identifier']
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285 url = NCBI_DOWNLOAD_URL % requested_identifier
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286 fasta_readers = get_stream_reader(urlopen(url), tmp_dir)
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287 add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params)
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288
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289
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290 def download_from_url( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
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291 urls = filter( bool, map( lambda x: x.strip(), params['param_dict']['reference_source']['user_url'].split( '\n' ) ) )
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292 fasta_readers = [ get_stream_reader(urlopen( url ), tmp_dir) for url in urls ]
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293 add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id,sequence_name, params)
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294
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295
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296 def download_from_history( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
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297 #TODO: allow multiple FASTA input files
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298 input_filename = params['param_dict']['reference_source']['input_fasta']
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299 if isinstance( input_filename, list ):
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300 fasta_readers = [ get_stream_reader(open(filename, 'rb'), tmp_dir) for filename in input_filename ]
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301 else:
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302 fasta_readers = get_stream_reader(open(input_filename), tmp_dir)
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303 add_fasta_to_table(data_manager_dict, fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params)
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304
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305
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306 def copy_from_directory( data_manager_dict, params, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, tmp_dir ):
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307 input_filename = params['param_dict']['reference_source']['fasta_filename']
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308 create_symlink = params['param_dict']['reference_source']['create_symlink'] == 'create_symlink'
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309 if create_symlink:
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310 data_table_entries = _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name )
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311 else:
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312 if isinstance( input_filename, list ):
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313 fasta_readers = [ get_stream_reader(open(filename, 'rb'), tmp_dir) for filename in input_filename ]
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314 else:
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315 fasta_readers = get_stream_reader(open(input_filename), tmp_dir)
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316 data_table_entries = _stream_fasta_to_file( fasta_readers, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params )
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317 for data_table_name, data_table_entry in data_table_entries:
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318 if data_table_entry:
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319 _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name )
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320
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321
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322 def _add_data_table_entry( data_manager_dict, data_table_entry, data_table_name ):
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323 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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324 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get( DATA_TABLE_NAME, [] )
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325 data_manager_dict['data_tables'][data_table_name].append( data_table_entry )
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326 return data_manager_dict
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327
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328
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329 def _stream_fasta_to_file( fasta_stream, target_directory, dbkey, dbkey_name, sequence_id, sequence_name, params, close_stream=True ):
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330 fasta_base_filename = "%s.gff" % sequence_id
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331 fasta_filename = os.path.join( target_directory, fasta_base_filename )
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332 with open( fasta_filename, 'wb+' ) as fasta_writer:
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333
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334 if isinstance( fasta_stream, list ) and len( fasta_stream ) == 1:
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335 fasta_stream = fasta_stream[0]
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336
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337 if isinstance( fasta_stream, list ):
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338 last_char = None
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339 for fh in fasta_stream:
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340 if last_char not in [ None, '\n', '\r', b'\n', b'\r' ]:
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341 fasta_writer.write( b'\n' )
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342 while True:
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343 data = fh.read( CHUNK_SIZE )
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344 if data:
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345 fasta_writer.write( data )
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346 last_char = data[-1]
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347 else:
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348 break
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349 if close_stream:
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350 fh.close()
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351 else:
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352 while True:
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353 data = fasta_stream.read( CHUNK_SIZE )
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354 if data:
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355 fasta_writer.write( data )
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356 else:
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357 break
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358 if close_stream:
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359 fasta_stream.close()
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360
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361 #sort_fasta( fasta_filename, params['param_dict']['sorting']['sort_selector'], params )
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362
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363 dbkey_dict = None
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364 if dbkey_name:
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365 #do len calc here
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366 #len_base_name = "%s.len" % ( dbkey )
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367 #compute_fasta_length( fasta_filename, os.path.join( target_directory, len_base_name ), keep_first_word=True )
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368 dbkey_dict = dict( value=dbkey, name=dbkey_name, len_path='' )
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369
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370 return [ ( '__dbkeys__', dbkey_dict ), ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]
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371
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372
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373 def compute_fasta_length( fasta_file, out_file, keep_first_word=False ):
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374
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375 infile = fasta_file
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376 out = open( out_file, 'w')
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377
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378 fasta_title = ''
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379 seq_len = 0
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380
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381 first_entry = True
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382
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383 for line in open( infile ):
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384 line = line.strip()
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385 if not line or line.startswith( '#' ):
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386 continue
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387 if line[0] == '>':
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388 if first_entry == False:
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389 if keep_first_word:
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390 fasta_title = fasta_title.split()[0]
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391 out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) )
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392 else:
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393 first_entry = False
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394 fasta_title = line
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395 seq_len = 0
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396 else:
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397 seq_len += len(line)
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398
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399 # last fasta-entry
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400 if keep_first_word:
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401 fasta_title = fasta_title.split()[0]
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402 out.write( "%s\t%d\n" % ( fasta_title[ 1: ], seq_len ) )
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403 out.close()
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404
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405
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406 def _create_symlink( input_filename, target_directory, dbkey, dbkey_name, sequence_id, sequence_name ):
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407 fasta_base_filename = "%s.fa" % sequence_id
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408 fasta_filename = os.path.join( target_directory, fasta_base_filename )
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409 os.symlink( input_filename, fasta_filename )
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410
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411 dbkey_dict = None
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412 if dbkey_name:
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413 #do len calc here
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414 len_base_name = "%s.len" % ( dbkey )
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415 compute_fasta_length( fasta_filename, os.path.join( target_directory, len_base_name ), keep_first_word=True )
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416 dbkey_dict = dict( value=dbkey, name=dbkey_name, len_path=len_base_name )
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417
|
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|
418 return [ ( '__dbkeys__', dbkey_dict ), ( DATA_TABLE_NAME, dict( value=sequence_id, dbkey=dbkey, name=sequence_name, path=fasta_base_filename ) ) ]
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|
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419
|
|
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420
|
|
|
421 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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|
|
422
|
|
|
423 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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|
|
424
|
|
|
425
|
|
|
426 def main():
|
|
|
427 #Parse Command Line
|
|
|
428 parser = optparse.OptionParser()
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|
|
429 parser.add_option( '-d', '--dbkey_description', dest='dbkey_description', action='store', type="string", default=None, help='dbkey_description' )
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|
|
430 parser.add_option( '-t', '--type', dest='file_type', action='store', type='string', default=None, help='file_type')
|
|
|
431 (options, args) = parser.parse_args()
|
|
|
432
|
|
|
433 filename = args[0]
|
|
|
434 global DATA_TABLE_NAME
|
|
|
435 if options.file_type == 'representative':
|
|
|
436 DATA_TABLE_NAME= 'representative_gff'
|
|
|
437 params = loads( open( filename ).read() )
|
|
|
438 target_directory = params[ 'output_data' ][0]['extra_files_path']
|
|
|
439 os.mkdir( target_directory )
|
|
|
440 data_manager_dict = {}
|
|
|
441
|
|
|
442 dbkey, dbkey_name, sequence_id, sequence_name = get_dbkey_dbname_id_name( params, dbkey_description=options.dbkey_description )
|
|
|
443
|
|
|
444 if dbkey in [ None, '', '?' ]:
|
|
|
445 raise Exception( '"%s" is not a valid dbkey. You must specify a valid dbkey.' % ( dbkey ) )
|
|
|
446
|
|
|
447 # Create a tmp_dir, in case a zip file needs to be uncompressed
|
|
|
448 tmp_dir = tempfile.mkdtemp()
|
|
|
449 #Fetch the FASTA
|
|
|
450 try:
|
|
|
451 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 )
|
|
|
452 finally:
|
|
|
453 cleanup_before_exit(tmp_dir)
|
|
|
454 #save info to json file
|
|
|
455 open( filename, 'wb' ).write( dumps( data_manager_dict ).encode() )
|
|
|
456
|
|
|
457 if __name__ == "__main__":
|
|
|
458 main()
|
