Python SearchIndexer Examples

Example #1

    def __init__(self, filename, comments=False, fields=_DEFAULT_FIELDS):
        SearchIndexer.__init__(self, filename, comments=comments, fields=fields)

        # if the file doesn't have comments,
        # get index of column used as the key (qseqid / qacc / qaccver)
        if not self._kwargs['comments']:
            if 'qseqid' in fields:
                self._key_idx = fields.index('qseqid')
            elif 'qacc' in fields:
                self._key_idx = fields.index('qacc')
            elif 'qaccver' in fields:
                self._key_idx = fields.index('qaccver')
            else:
                raise ValueError("Custom fields is missing an ID column. "
                        "One of these must be present: 'qseqid', 'qacc', or 'qaccver'.")

Example #2

File: blast_tab.py Project: JulianNymark/blendergame

    def __init__(self, filename, comments=False, fields=_DEFAULT_FIELDS):
        SearchIndexer.__init__(self, filename, comments=comments, fields=fields)

        # if the file doesn't have comments,
        # get index of column used as the key (qseqid / qacc / qaccver)
        if not self._kwargs['comments']:
            if 'qseqid' in fields:
                self._key_idx = fields.index('qseqid')
            elif 'qacc' in fields:
                self._key_idx = fields.index('qacc')
            elif 'qaccver' in fields:
                self._key_idx = fields.index('qaccver')
            else:
                raise ValueError("Custom fields is missing an ID column. "
                        "One of these must be present: 'qseqid', 'qacc', or 'qaccver'.")

Example #3

File: blast_tab.py Project: xm1490/biopython

    def __init__(self, filename, comments=False, fields=_DEFAULT_FIELDS):
        """Initialize the class."""
        SearchIndexer.__init__(self, filename, comments=comments, fields=fields)

        # if the file doesn't have comments,
        # get index of column used as the key (qseqid / qacc / qaccver)
        if not self._kwargs["comments"]:
            if "qseqid" in fields:
                self._key_idx = fields.index("qseqid")
            elif "qacc" in fields:
                self._key_idx = fields.index("qacc")
            elif "qaccver" in fields:
                self._key_idx = fields.index("qaccver")
            else:
                raise ValueError(
                    "Custom fields is missing an ID column. One of these must be "
                    "present: 'qseqid', 'qacc', or 'qaccver'."
                )

Example #4

 def __init__(self, filename):
     """Initialize the class."""
     SearchIndexer.__init__(self, filename)
     self._handle = UndoHandle(self._handle)

Example #5

File: blast_xml.py Project: stxinsite/biopython

 def __init__(self, filename, **kwargs):
     """Initialize the class."""
     SearchIndexer.__init__(self, filename)
     # TODO: better way to do this?
     iter_obj = self._parser(self._handle, **kwargs)
     self._meta, self._fallback = iter_obj._meta, iter_obj._fallback

Example #6

File: blast_xml.py Project: harshberia93/biopython

 def __init__(self, filename):
     SearchIndexer.__init__(self, filename)
     # TODO: better way to do this?
     iter_obj = self._parser(self._handle)
     self._meta, self._fallback = iter_obj._meta, iter_obj._fallback

Example #7

 def __init__(self, filename):
     SearchIndexer.__init__(self, filename)
     self._handle = UndoHandle(self._handle)

Example #8

File: BlatIO.py Project: olgabot/biopython

 def __init__(self, filename, pslx=False):
     SearchIndexer.__init__(self, filename, pslx=pslx)

Example #9

File: FastaIO.py Project: guru1982/biopython

 def __init__(self, filename):
     SearchIndexer.__init__(self, filename)
     self._handle = UndoHandle(self._handle)

Example #10

File: blast_xml.py Project: umbrr/biopython

 def __init__(self, filename, **kwargs):
     """Initialize the class."""
     SearchIndexer.__init__(self, filename)
     # TODO: better way to do this?
     iter_obj = self._parser(self._handle, **kwargs)
     self._meta, self._fallback = iter_obj._meta, iter_obj._fallback

Example #11

 def __init__(self, filename, pslx=False):
     """Initialize the class."""
     SearchIndexer.__init__(self, filename, pslx=pslx)

Example #12

File: BlatIO.py Project: JoaoRodrigues/biopython

 def __init__(self, filename, pslx=False):
     """Initialize the class."""
     SearchIndexer.__init__(self, filename, pslx=pslx)

Example #13

File: blast_xml.py Project: troyxmccall/biopython

 def __init__(self, filename):
     SearchIndexer.__init__(self, filename)
     # TODO: better way to do this?
     iter_obj = self._parser(self._handle)
     self._meta, self._fallback = iter_obj._meta, iter_obj._fallback

Example #14

File: BlatIO.py Project: xirect/textgraver

 def __init__(self, filename, pslx=False):
     SearchIndexer.__init__(self, filename, pslx=pslx)

Example #15

File: FastaIO.py Project: umbrr/biopython

 def __init__(self, filename):
     """Initialize the class."""
     SearchIndexer.__init__(self, filename)
     self._handle = UndoHandle(self._handle)

Example #16

 def __init__(self, filename):
     """Initialize the class."""
     SearchIndexer.__init__(self, filename)