Mercurial > repos > devteam > blast_datatypes
annotate blast.py @ 11:01b38f20197e draft default tip
v0.0.21 - Updated citation information with GigaScience paper
| author | peterjc |
|---|---|
| date | Fri, 04 Sep 2015 07:10:04 -0400 |
| parents | 5482a8cd0f36 |
| children |
| rev | line source |
|---|---|
| 3 | 1 """ |
| 2 BlastXml class | |
| 3 """ | |
| 4 | |
| 5 from galaxy.datatypes.data import get_file_peek | |
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6 from galaxy.datatypes.data import Text, Data, GenericAsn1 |
| 3 | 7 from galaxy.datatypes.xml import GenericXml |
| 4 | 8 from galaxy.datatypes.metadata import MetadataElement |
| 3 | 9 |
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10 from time import sleep |
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11 import os |
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12 import logging |
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13 |
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14 log = logging.getLogger(__name__) |
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15 |
| 3 | 16 class BlastXml( GenericXml ): |
| 17 """NCBI Blast XML Output data""" | |
| 18 file_ext = "blastxml" | |
| 19 | |
| 20 def set_peek( self, dataset, is_multi_byte=False ): | |
| 21 """Set the peek and blurb text""" | |
| 22 if not dataset.dataset.purged: | |
| 23 dataset.peek = get_file_peek( dataset.file_name, is_multi_byte=is_multi_byte ) | |
| 24 dataset.blurb = 'NCBI Blast XML data' | |
| 25 else: | |
| 26 dataset.peek = 'file does not exist' | |
| 27 dataset.blurb = 'file purged from disk' | |
| 4 | 28 |
| 3 | 29 def sniff( self, filename ): |
| 30 """ | |
| 31 Determines whether the file is blastxml | |
| 32 | |
| 33 >>> fname = get_test_fname( 'megablast_xml_parser_test1.blastxml' ) | |
| 34 >>> BlastXml().sniff( fname ) | |
| 35 True | |
| 36 >>> fname = get_test_fname( 'tblastn_four_human_vs_rhodopsin.xml' ) | |
| 37 >>> BlastXml().sniff( fname ) | |
| 38 True | |
| 39 >>> fname = get_test_fname( 'interval.interval' ) | |
| 40 >>> BlastXml().sniff( fname ) | |
| 41 False | |
| 42 """ | |
| 43 #TODO - Use a context manager on Python 2.5+ to close handle | |
| 44 handle = open(filename) | |
| 45 line = handle.readline() | |
| 46 if line.strip() != '<?xml version="1.0"?>': | |
| 47 handle.close() | |
| 48 return False | |
| 49 line = handle.readline() | |
| 50 if line.strip() not in ['<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">', | |
| 51 '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">']: | |
| 52 handle.close() | |
| 53 return False | |
| 54 line = handle.readline() | |
| 55 if line.strip() != '<BlastOutput>': | |
| 56 handle.close() | |
| 57 return False | |
| 58 handle.close() | |
| 59 return True | |
| 60 | |
| 61 def merge(split_files, output_file): | |
| 62 """Merging multiple XML files is non-trivial and must be done in subclasses.""" | |
| 63 if len(split_files) == 1: | |
| 64 #For one file only, use base class method (move/copy) | |
| 65 return Text.merge(split_files, output_file) | |
| 4 | 66 if not split_files: |
| 67 raise ValueError("Given no BLAST XML files, %r, to merge into %s" \ | |
| 68 % (split_files, output_file)) | |
| 3 | 69 out = open(output_file, "w") |
| 70 h = None | |
| 71 for f in split_files: | |
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72 if not os.path.isfile(f): |
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73 log.warning("BLAST XML file %s missing, retry in 1s..." % f) |
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74 sleep(1) |
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75 if not os.path.isfile(f): |
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76 log.error("BLAST XML file %s missing" % f) |
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77 raise ValueError("BLAST XML file %s missing" % f) |
| 3 | 78 h = open(f) |
| 79 header = h.readline() | |
| 80 if not header: | |
| 81 out.close() | |
| 82 h.close() | |
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83 #Retry, could be transient error with networked file system... |
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84 log.warning("BLAST XML file %s empty, retry in 1s..." % f) |
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85 sleep(1) |
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86 h = open(f) |
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87 header = h.readline() |
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88 if not header: |
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89 log.error("BLAST XML file %s was empty" % f) |
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90 raise ValueError("BLAST XML file %s was empty" % f) |
| 3 | 91 if header.strip() != '<?xml version="1.0"?>': |
| 92 out.write(header) #for diagnosis | |
| 93 out.close() | |
| 94 h.close() | |
| 95 raise ValueError("%s is not an XML file!" % f) | |
| 96 line = h.readline() | |
| 97 header += line | |
| 98 if line.strip() not in ['<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">', | |
| 99 '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">']: | |
| 100 out.write(header) #for diagnosis | |
| 101 out.close() | |
| 102 h.close() | |
| 103 raise ValueError("%s is not a BLAST XML file!" % f) | |
| 104 while True: | |
| 105 line = h.readline() | |
| 106 if not line: | |
| 107 out.write(header) #for diagnosis | |
| 108 out.close() | |
| 109 h.close() | |
| 110 raise ValueError("BLAST XML file %s ended prematurely" % f) | |
| 111 header += line | |
| 112 if "<Iteration>" in line: | |
| 113 break | |
| 114 if len(header) > 10000: | |
| 115 #Something has gone wrong, don't load too much into memory! | |
| 116 #Write what we have to the merged file for diagnostics | |
| 117 out.write(header) | |
| 118 out.close() | |
| 119 h.close() | |
| 120 raise ValueError("BLAST XML file %s has too long a header!" % f) | |
| 121 if "<BlastOutput>" not in header: | |
| 122 out.close() | |
| 123 h.close() | |
| 124 raise ValueError("%s is not a BLAST XML file:\n%s\n..." % (f, header)) | |
| 125 if f == split_files[0]: | |
| 126 out.write(header) | |
| 127 old_header = header | |
| 128 elif old_header[:300] != header[:300]: | |
| 129 #Enough to check <BlastOutput_program> and <BlastOutput_version> match | |
| 130 out.close() | |
| 131 h.close() | |
| 132 raise ValueError("BLAST XML headers don't match for %s and %s - have:\n%s\n...\n\nAnd:\n%s\n...\n" \ | |
| 133 % (split_files[0], f, old_header[:300], header[:300])) | |
| 134 else: | |
| 135 out.write(" <Iteration>\n") | |
| 136 for line in h: | |
| 137 if "</BlastOutput_iterations>" in line: | |
| 138 break | |
| 139 #TODO - Increment <Iteration_iter-num> and if required automatic query names | |
| 140 #like <Iteration_query-ID>Query_3</Iteration_query-ID> to be increasing? | |
| 141 out.write(line) | |
| 142 h.close() | |
| 143 out.write(" </BlastOutput_iterations>\n") | |
| 144 out.write("</BlastOutput>\n") | |
| 145 out.close() | |
| 146 merge = staticmethod(merge) | |
| 147 | |
| 4 | 148 |
| 149 class _BlastDb(object): | |
| 150 """Base class for BLAST database datatype.""" | |
| 151 | |
| 152 def set_peek( self, dataset, is_multi_byte=False ): | |
| 153 """Set the peek and blurb text.""" | |
| 154 if not dataset.dataset.purged: | |
| 155 dataset.peek = "BLAST database (multiple files)" | |
| 156 dataset.blurb = "BLAST database (multiple files)" | |
| 157 else: | |
| 158 dataset.peek = 'file does not exist' | |
| 159 dataset.blurb = 'file purged from disk' | |
| 160 | |
| 161 def display_peek( self, dataset ): | |
| 162 """Create HTML content, used for displaying peek.""" | |
| 163 try: | |
| 164 return dataset.peek | |
| 165 except: | |
| 166 return "BLAST database (multiple files)" | |
| 167 | |
| 168 def display_data(self, trans, data, preview=False, filename=None, | |
| 169 to_ext=None, size=None, offset=None, **kwd): | |
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170 """Documented as an old display method, but still gets called via tests etc |
| 4 | 171 |
| 172 This allows us to format the data shown in the central pane via the "eye" icon. | |
| 173 """ | |
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174 if filename is not None and filename != "index": |
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175 #Change nothing - important for the unit tests to access child files: |
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176 return Data.display_data(self, trans, data, preview, filename, |
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177 to_ext, size, offset, **kwd) |
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178 if self.file_ext == "blastdbn": |
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179 title = "This is a nucleotide BLAST database" |
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180 elif self.file_ext =="blastdbp": |
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181 title = "This is a protein BLAST database" |
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182 elif self.file_ext =="blastdbd": |
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183 title = "This is a domain BLAST database" |
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184 else: |
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185 #Error? |
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186 title = "This is a BLAST database." |
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187 msg = "" |
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188 try: |
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189 #Try to use any text recorded in the dummy index file: |
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190 handle = open(data.file_name, "rU") |
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191 msg = handle.read().strip() |
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192 handle.close() |
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193 except Exception, err: |
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194 #msg = str(err) |
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195 pass |
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196 if not msg: |
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197 msg = title |
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198 #Galaxy assumes HTML for the display of composite datatypes, |
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199 return "<html><head><title>%s</title></head><body><pre>%s</pre></body></html>" % (title, msg) |
| 4 | 200 |
| 201 def merge(split_files, output_file): | |
| 202 """Merge BLAST databases (not implemented for now).""" | |
| 203 raise NotImplementedError("Merging BLAST databases is non-trivial (do this via makeblastdb?)") | |
| 204 | |
| 205 def split( cls, input_datasets, subdir_generator_function, split_params): | |
| 206 """Split a BLAST database (not implemented for now).""" | |
| 207 if split_params is None: | |
| 208 return None | |
| 209 raise NotImplementedError("Can't split BLAST databases") | |
| 210 | |
| 211 | |
| 212 class BlastNucDb( _BlastDb, Data ): | |
| 213 """Class for nucleotide BLAST database files.""" | |
| 214 file_ext = 'blastdbn' | |
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215 allow_datatype_change = False |
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216 composite_type = 'basic' |
| 4 | 217 |
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218 def __init__(self, **kwd): |
| 4 | 219 Data.__init__(self, **kwd) |
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220 self.add_composite_file('blastdb.nhr', is_binary=True) # sequence headers |
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221 self.add_composite_file('blastdb.nin', is_binary=True) # index file |
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222 self.add_composite_file('blastdb.nsq', is_binary=True) # nucleotide sequences |
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223 self.add_composite_file('blastdb.nal', is_binary=False, optional=True) # alias ( -gi_mask option of makeblastdb) |
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224 self.add_composite_file('blastdb.nhd', is_binary=True, optional=True) # sorted sequence hash values ( -hash_index option of makeblastdb) |
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225 self.add_composite_file('blastdb.nhi', is_binary=True, optional=True) # index of sequence hash values ( -hash_index option of makeblastdb) |
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226 self.add_composite_file('blastdb.nnd', is_binary=True, optional=True) # sorted GI values ( -parse_seqids option of makeblastdb and gi present in the description lines) |
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227 self.add_composite_file('blastdb.nni', is_binary=True, optional=True) # index of GI values ( -parse_seqids option of makeblastdb and gi present in the description lines) |
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228 self.add_composite_file('blastdb.nog', is_binary=True, optional=True) # OID->GI lookup file ( -hash_index or -parse_seqids option of makeblastdb) |
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229 self.add_composite_file('blastdb.nsd', is_binary=True, optional=True) # sorted sequence accession values ( -hash_index or -parse_seqids option of makeblastdb) |
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230 self.add_composite_file('blastdb.nsi', is_binary=True, optional=True) # index of sequence accession values ( -hash_index or -parse_seqids option of makeblastdb) |
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231 # self.add_composite_file('blastdb.00.idx', is_binary=True, optional=True) # first volume of the MegaBLAST index generated by makembindex |
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232 # The previous line should be repeated for each index volume, with filename extensions like '.01.idx', '.02.idx', etc. |
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233 self.add_composite_file('blastdb.shd', is_binary=True, optional=True) # MegaBLAST index superheader (-old_style_index false option of makembindex) |
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234 # self.add_composite_file('blastdb.naa', is_binary=True, optional=True) # index of a WriteDB column for e.g. mask data |
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235 # self.add_composite_file('blastdb.nab', is_binary=True, optional=True) # data of a WriteDB column |
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236 # self.add_composite_file('blastdb.nac', is_binary=True, optional=True) # multiple byte order for a WriteDB column |
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237 # The previous 3 lines should be repeated for each WriteDB column, with filename extensions like ('.nba', '.nbb', '.nbc'), ('.nca', '.ncb', '.ncc'), etc. |
| 4 | 238 |
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239 |
| 4 | 240 class BlastProtDb( _BlastDb, Data ): |
| 241 """Class for protein BLAST database files.""" | |
| 242 file_ext = 'blastdbp' | |
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243 allow_datatype_change = False |
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244 composite_type = 'basic' |
| 4 | 245 |
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246 def __init__(self, **kwd): |
| 4 | 247 Data.__init__(self, **kwd) |
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248 # Component file comments are as in BlastNucDb except where noted |
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249 self.add_composite_file('blastdb.phr', is_binary=True) |
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250 self.add_composite_file('blastdb.pin', is_binary=True) |
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251 self.add_composite_file('blastdb.psq', is_binary=True) # protein sequences |
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252 self.add_composite_file('blastdb.phd', is_binary=True, optional=True) |
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253 self.add_composite_file('blastdb.phi', is_binary=True, optional=True) |
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254 self.add_composite_file('blastdb.pnd', is_binary=True, optional=True) |
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255 self.add_composite_file('blastdb.pni', is_binary=True, optional=True) |
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256 self.add_composite_file('blastdb.pog', is_binary=True, optional=True) |
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257 self.add_composite_file('blastdb.psd', is_binary=True, optional=True) |
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258 self.add_composite_file('blastdb.psi', is_binary=True, optional=True) |
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259 # self.add_composite_file('blastdb.paa', is_binary=True, optional=True) |
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260 # self.add_composite_file('blastdb.pab', is_binary=True, optional=True) |
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261 # self.add_composite_file('blastdb.pac', is_binary=True, optional=True) |
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262 # The last 3 lines should be repeated for each WriteDB column, with filename extensions like ('.pba', '.pbb', '.pbc'), ('.pca', '.pcb', '.pcc'), etc. |
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263 |
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264 |
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265 class BlastDomainDb( _BlastDb, Data ): |
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266 """Class for domain BLAST database files.""" |
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267 file_ext = 'blastdbd' |
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268 allow_datatype_change = False |
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269 composite_type = 'basic' |
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270 |
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271 def __init__(self, **kwd): |
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272 Data.__init__(self, **kwd) |
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273 self.add_composite_file('blastdb.phr', is_binary=True) |
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274 self.add_composite_file('blastdb.pin', is_binary=True) |
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275 self.add_composite_file('blastdb.psq', is_binary=True) |
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276 self.add_composite_file('blastdb.freq', is_binary=True, optional=True) |
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277 self.add_composite_file('blastdb.loo', is_binary=True, optional=True) |
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278 self.add_composite_file('blastdb.psd', is_binary=True, optional=True) |
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279 self.add_composite_file('blastdb.psi', is_binary=True, optional=True) |
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280 self.add_composite_file('blastdb.rps', is_binary=True, optional=True) |
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281 self.add_composite_file('blastdb.aux', is_binary=True, optional=True) |