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Merge pull request #2696 from peterjc/blast_datatypes
Returning Blast datatypes to Galaxy core (work-in-progress)
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| Original file line number | Diff line number | Diff line change |
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| # This file is now part of the Galaxy Project, but due to historical reasons | ||
| # reflecting time developed outside of the Galaxy Project, this file is under | ||
| # the MIT license. | ||
| # | ||
| # The MIT License (MIT) | ||
| # Copyright (c) 2012,2013,2014,2015,2016 Peter Cock | ||
| # Copyright (c) 2012 Edward Kirton | ||
| # Copyright (c) 2013 Nicola Soranzo | ||
| # Copyright (c) 2014 Bjoern Gruening | ||
| # | ||
| # Permission is hereby granted, free of charge, to any person obtaining a copy | ||
| # of this software and associated documentation files (the "Software"), to | ||
| # deal in the Software without restriction, including without limitation the | ||
| # rights to use, copy, modify, merge, publish, distribute, sublicense, and/or | ||
| # sell copies of the Software, and to permit persons to whom the Software is | ||
| # furnished to do so, subject to the following conditions: | ||
| # | ||
| # The above copyright notice and this permission notice shall be included in | ||
| # all copies or substantial portions of the Software. | ||
| # | ||
| # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR | ||
| # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, | ||
| # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL | ||
| # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER | ||
| # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING | ||
| # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER | ||
| # DEALINGS IN THE SOFTWARE. | ||
| # | ||
| """NCBI BLAST datatypes. | ||
| Covers the ``blastxml`` format and the BLAST databases. | ||
| """ | ||
|
|
||
| import logging | ||
| import os | ||
| from time import sleep | ||
|
|
||
| from galaxy.datatypes.data import get_file_peek | ||
| from galaxy.datatypes.data import Data, Text | ||
| from galaxy.datatypes.xml import GenericXml | ||
|
|
||
| log = logging.getLogger(__name__) | ||
|
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|
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| class BlastXml(GenericXml): | ||
| """NCBI Blast XML Output data""" | ||
| file_ext = "blastxml" | ||
| edam_format = "format_3331" | ||
| edam_data = "data_0857" | ||
|
|
||
| def set_peek(self, dataset, is_multi_byte=False): | ||
| """Set the peek and blurb text""" | ||
| if not dataset.dataset.purged: | ||
| dataset.peek = get_file_peek(dataset.file_name, is_multi_byte=is_multi_byte) | ||
| dataset.blurb = 'NCBI Blast XML data' | ||
| else: | ||
| dataset.peek = 'file does not exist' | ||
| dataset.blurb = 'file purged from disk' | ||
|
|
||
| def sniff(self, filename): | ||
| """Determines whether the file is blastxml | ||
| >>> from galaxy.datatypes.sniff import get_test_fname | ||
| >>> fname = get_test_fname('megablast_xml_parser_test1.blastxml') | ||
| >>> BlastXml().sniff(fname) | ||
| True | ||
| >>> fname = get_test_fname('tblastn_four_human_vs_rhodopsin.xml') | ||
| >>> BlastXml().sniff(fname) | ||
| True | ||
| >>> fname = get_test_fname('interval.interval') | ||
| >>> BlastXml().sniff(fname) | ||
| False | ||
| """ | ||
| # TODO - Use a context manager on Python 2.5+ to close handle | ||
| handle = open(filename) | ||
| line = handle.readline() | ||
| if line.strip() != '<?xml version="1.0"?>': | ||
| handle.close() | ||
| return False | ||
| line = handle.readline() | ||
| if line.strip() not in ['<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">', | ||
| '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">']: | ||
| handle.close() | ||
| return False | ||
| line = handle.readline() | ||
| if line.strip() != '<BlastOutput>': | ||
| handle.close() | ||
| return False | ||
| handle.close() | ||
| return True | ||
|
|
||
| def merge(split_files, output_file): | ||
| """Merging multiple XML files is non-trivial and must be done in subclasses.""" | ||
| if len(split_files) == 1: | ||
| # For one file only, use base class method (move/copy) | ||
| return Text.merge(split_files, output_file) | ||
| if not split_files: | ||
| raise ValueError("Given no BLAST XML files, %r, to merge into %s" | ||
| % (split_files, output_file)) | ||
| out = open(output_file, "w") | ||
| h = None | ||
| for f in split_files: | ||
| if not os.path.isfile(f): | ||
| log.warning("BLAST XML file %s missing, retry in 1s..." % f) | ||
| sleep(1) | ||
| if not os.path.isfile(f): | ||
| log.error("BLAST XML file %s missing" % f) | ||
| raise ValueError("BLAST XML file %s missing" % f) | ||
| h = open(f) | ||
| header = h.readline() | ||
| if not header: | ||
| out.close() | ||
| h.close() | ||
| # Retry, could be transient error with networked file system... | ||
| log.warning("BLAST XML file %s empty, retry in 1s..." % f) | ||
| sleep(1) | ||
| h = open(f) | ||
| header = h.readline() | ||
| if not header: | ||
| log.error("BLAST XML file %s was empty" % f) | ||
| raise ValueError("BLAST XML file %s was empty" % f) | ||
| if header.strip() != '<?xml version="1.0"?>': | ||
| out.write(header) # for diagnosis | ||
| out.close() | ||
| h.close() | ||
| raise ValueError("%s is not an XML file!" % f) | ||
| line = h.readline() | ||
| header += line | ||
| if line.strip() not in ['<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">', | ||
| '<!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "NCBI_BlastOutput.dtd">']: | ||
| out.write(header) # for diagnosis | ||
| out.close() | ||
| h.close() | ||
| raise ValueError("%s is not a BLAST XML file!" % f) | ||
| while True: | ||
| line = h.readline() | ||
| if not line: | ||
| out.write(header) # for diagnosis | ||
| out.close() | ||
| h.close() | ||
| raise ValueError("BLAST XML file %s ended prematurely" % f) | ||
| header += line | ||
| if "<Iteration>" in line: | ||
| break | ||
| if len(header) > 10000: | ||
| # Something has gone wrong, don't load too much into memory! | ||
| # Write what we have to the merged file for diagnostics | ||
| out.write(header) | ||
| out.close() | ||
| h.close() | ||
| raise ValueError("The header in BLAST XML file %s is too long" % f) | ||
| if "<BlastOutput>" not in header: | ||
| out.close() | ||
| h.close() | ||
| raise ValueError("%s is not a BLAST XML file:\n%s\n..." % (f, header)) | ||
| if f == split_files[0]: | ||
| out.write(header) | ||
| old_header = header | ||
| elif old_header[:300] != header[:300]: | ||
| # Enough to check <BlastOutput_program> and <BlastOutput_version> match | ||
| out.close() | ||
| h.close() | ||
| raise ValueError("BLAST XML headers don't match for %s and %s - have:\n%s\n...\n\nAnd:\n%s\n...\n" | ||
| % (split_files[0], f, old_header[:300], header[:300])) | ||
| else: | ||
| out.write(" <Iteration>\n") | ||
| for line in h: | ||
| if "</BlastOutput_iterations>" in line: | ||
| break | ||
| # TODO - Increment <Iteration_iter-num> and if required automatic query names | ||
| # like <Iteration_query-ID>Query_3</Iteration_query-ID> to be increasing? | ||
| out.write(line) | ||
| h.close() | ||
| out.write(" </BlastOutput_iterations>\n") | ||
| out.write("</BlastOutput>\n") | ||
| out.close() | ||
| merge = staticmethod(merge) | ||
|
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|
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| class _BlastDb(object): | ||
| """Base class for BLAST database datatype.""" | ||
|
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| def set_peek(self, dataset, is_multi_byte=False): | ||
| """Set the peek and blurb text.""" | ||
| if not dataset.dataset.purged: | ||
| dataset.peek = "BLAST database (multiple files)" | ||
| dataset.blurb = "BLAST database (multiple files)" | ||
| else: | ||
| dataset.peek = 'file does not exist' | ||
| dataset.blurb = 'file purged from disk' | ||
|
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| def display_peek(self, dataset): | ||
| """Create HTML content, used for displaying peek.""" | ||
| try: | ||
| return dataset.peek | ||
| except Exception: | ||
| return "BLAST database (multiple files)" | ||
|
|
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| def display_data(self, trans, data, preview=False, filename=None, | ||
| to_ext=None, size=None, offset=None, **kwd): | ||
| """Documented as an old display method, but still gets called via tests etc | ||
| This allows us to format the data shown in the central pane via the "eye" icon. | ||
| """ | ||
| if filename is not None and filename != "index": | ||
| # Change nothing - important for the unit tests to access child files: | ||
| return Data.display_data(self, trans, data, preview, filename, | ||
| to_ext, size, offset, **kwd) | ||
| if self.file_ext == "blastdbn": | ||
| title = "This is a nucleotide BLAST database" | ||
| elif self.file_ext == "blastdbp": | ||
| title = "This is a protein BLAST database" | ||
| elif self.file_ext == "blastdbd": | ||
| title = "This is a domain BLAST database" | ||
| else: | ||
| # Error? | ||
| title = "This is a BLAST database." | ||
| msg = "" | ||
| try: | ||
| # Try to use any text recorded in the dummy index file: | ||
| handle = open(data.file_name, "rU") | ||
| msg = handle.read().strip() | ||
| handle.close() | ||
| except Exception: | ||
| pass | ||
| if not msg: | ||
| msg = title | ||
| # Galaxy assumes HTML for the display of composite datatypes, | ||
| return "<html><head><title>%s</title></head><body><pre>%s</pre></body></html>" % (title, msg) | ||
|
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| def merge(split_files, output_file): | ||
| """Merge BLAST databases (not implemented for now).""" | ||
| raise NotImplementedError("Merging BLAST databases is non-trivial (do this via makeblastdb?)") | ||
|
|
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| def split(cls, input_datasets, subdir_generator_function, split_params): | ||
| """Split a BLAST database (not implemented for now).""" | ||
| if split_params is None: | ||
| return None | ||
| raise NotImplementedError("Can't split BLAST databases") | ||
|
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|
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| class BlastNucDb(_BlastDb, Data): | ||
| """Class for nucleotide BLAST database files.""" | ||
| file_ext = 'blastdbn' | ||
| allow_datatype_change = False | ||
| composite_type = 'basic' | ||
|
|
||
| def __init__(self, **kwd): | ||
| Data.__init__(self, **kwd) | ||
| self.add_composite_file('blastdb.nhr', is_binary=True) # sequence headers | ||
| self.add_composite_file('blastdb.nin', is_binary=True) # index file | ||
| self.add_composite_file('blastdb.nsq', is_binary=True) # nucleotide sequences | ||
| self.add_composite_file('blastdb.nal', is_binary=False, optional=True) # alias ( -gi_mask option of makeblastdb) | ||
| self.add_composite_file('blastdb.nhd', is_binary=True, optional=True) # sorted sequence hash values ( -hash_index option of makeblastdb) | ||
| self.add_composite_file('blastdb.nhi', is_binary=True, optional=True) # index of sequence hash values ( -hash_index option of makeblastdb) | ||
| 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) | ||
| 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) | ||
| self.add_composite_file('blastdb.nog', is_binary=True, optional=True) # OID->GI lookup file ( -hash_index or -parse_seqids option of makeblastdb) | ||
| self.add_composite_file('blastdb.nsd', is_binary=True, optional=True) # sorted sequence accession values ( -hash_index or -parse_seqids option of makeblastdb) | ||
| self.add_composite_file('blastdb.nsi', is_binary=True, optional=True) # index of sequence accession values ( -hash_index or -parse_seqids option of makeblastdb) | ||
| # self.add_composite_file('blastdb.00.idx', is_binary=True, optional=True) # first volume of the MegaBLAST index generated by makembindex | ||
| # The previous line should be repeated for each index volume, with filename extensions like '.01.idx', '.02.idx', etc. | ||
| self.add_composite_file('blastdb.shd', is_binary=True, optional=True) # MegaBLAST index superheader (-old_style_index false option of makembindex) | ||
| # self.add_composite_file('blastdb.naa', is_binary=True, optional=True) # index of a WriteDB column for e.g. mask data | ||
| # self.add_composite_file('blastdb.nab', is_binary=True, optional=True) # data of a WriteDB column | ||
| # self.add_composite_file('blastdb.nac', is_binary=True, optional=True) # multiple byte order for a WriteDB column | ||
| # The previous 3 lines should be repeated for each WriteDB column, with filename extensions like ('.nba', '.nbb', '.nbc'), ('.nca', '.ncb', '.ncc'), etc. | ||
|
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| class BlastProtDb(_BlastDb, Data): | ||
| """Class for protein BLAST database files.""" | ||
| file_ext = 'blastdbp' | ||
| allow_datatype_change = False | ||
| composite_type = 'basic' | ||
|
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| def __init__(self, **kwd): | ||
| Data.__init__(self, **kwd) | ||
| # Component file comments are as in BlastNucDb except where noted | ||
| self.add_composite_file('blastdb.phr', is_binary=True) | ||
| self.add_composite_file('blastdb.pin', is_binary=True) | ||
| self.add_composite_file('blastdb.psq', is_binary=True) # protein sequences | ||
| self.add_composite_file('blastdb.phd', is_binary=True, optional=True) | ||
| self.add_composite_file('blastdb.phi', is_binary=True, optional=True) | ||
| self.add_composite_file('blastdb.pnd', is_binary=True, optional=True) | ||
| self.add_composite_file('blastdb.pni', is_binary=True, optional=True) | ||
| self.add_composite_file('blastdb.pog', is_binary=True, optional=True) | ||
| self.add_composite_file('blastdb.psd', is_binary=True, optional=True) | ||
| self.add_composite_file('blastdb.psi', is_binary=True, optional=True) | ||
| # self.add_composite_file('blastdb.paa', is_binary=True, optional=True) | ||
| # self.add_composite_file('blastdb.pab', is_binary=True, optional=True) | ||
| # self.add_composite_file('blastdb.pac', is_binary=True, optional=True) | ||
| # 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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|
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| class BlastDomainDb(_BlastDb, Data): | ||
| """Class for domain BLAST database files.""" | ||
| file_ext = 'blastdbd' | ||
| allow_datatype_change = False | ||
| composite_type = 'basic' | ||
|
|
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| def __init__(self, **kwd): | ||
| Data.__init__(self, **kwd) | ||
| self.add_composite_file('blastdb.phr', is_binary=True) | ||
| self.add_composite_file('blastdb.pin', is_binary=True) | ||
| self.add_composite_file('blastdb.psq', is_binary=True) | ||
| self.add_composite_file('blastdb.freq', is_binary=True, optional=True) | ||
| self.add_composite_file('blastdb.loo', is_binary=True, optional=True) | ||
| self.add_composite_file('blastdb.psd', is_binary=True, optional=True) | ||
| self.add_composite_file('blastdb.psi', is_binary=True, optional=True) | ||
| self.add_composite_file('blastdb.rps', is_binary=True, optional=True) | ||
| self.add_composite_file('blastdb.aux', is_binary=True, optional=True) |
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