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src/b/i/biopython-1.63/Bio/SeqIO/_index.py   biopython(Download)
import re
from Bio._py3k import StringIO
from Bio._py3k import _bytes_to_string, _as_bytes
 
from Bio import SeqIO
                  }[format]
        self._marker = marker
        self._marker_re = re.compile(_as_bytes("^%s" % marker))
 
    def __iter__(self):
    def __iter__(self):
        handle = self._handle
        handle.seek(0)
        marker_re = self._marker_re
        dot_char = _as_bytes(".")
        accession_marker = _as_bytes("ACCESSION ")
        version_marker = _as_bytes("VERSION ")

src/b/i/biopython-HEAD/Bio/SeqIO/_index.py   biopython(Download)
import re
from Bio._py3k import StringIO
from Bio._py3k import _bytes_to_string, _as_bytes
 
from Bio import SeqIO
                  }[format]
        self._marker = marker
        self._marker_re = re.compile(_as_bytes("^%s" % marker))
 
    def __iter__(self):
    def __iter__(self):
        handle = self._handle
        handle.seek(0)
        marker_re = self._marker_re
        dot_char = _as_bytes(".")
        accession_marker = _as_bytes("ACCESSION ")
        version_marker = _as_bytes("VERSION ")

src/b/i/biopython-1.63/Bio/Blast/NCBIWWW.py   biopython(Download)
 
from Bio._py3k import StringIO
from Bio._py3k import _as_string, _as_bytes
from Bio._py3k import urlopen as _urlopen
from Bio._py3k import urlencode as _urlencode
        ]
    query = [x for x in parameters if x[1] is not None]
    message = _as_bytes(_urlencode(query))
 
    # Send off the initial query to qblast.
        ]
    query = [x for x in parameters if x[1] is not None]
    message = _as_bytes(_urlencode(query))
 
    # Poll NCBI until the results are ready.  Use a 3 second wait

src/b/i/biopython-1.63/Bio/SearchIO/BlastIO/blast_xml.py   biopython(Download)
 
 
from Bio._py3k import _as_bytes, _bytes_to_string, unicode
_empty_bytes_string = _as_bytes("")
 
class BlastXmlIndexer(SearchIndexer):
    """Indexer class for BLAST XML output."""
 
    _parser = BlastXmlParser
    qstart_mark = _as_bytes('<Iteration>')
    qend_mark = _as_bytes('</Iteration>')
    def __iter__(self):
        qstart_mark = self.qstart_mark
        qend_mark = self.qend_mark
        blast_id_mark = _as_bytes('Query_')
        block_size = self.block_size

src/b/i/biopython-HEAD/Bio/SearchIO/BlastIO/blast_xml.py   biopython(Download)
 
 
from Bio._py3k import _as_bytes, _bytes_to_string, unicode
_empty_bytes_string = _as_bytes("")
 
class BlastXmlIndexer(SearchIndexer):
    """Indexer class for BLAST XML output."""
 
    _parser = BlastXmlParser
    qstart_mark = _as_bytes('<Iteration>')
    qend_mark = _as_bytes('</Iteration>')
    def __iter__(self):
        qstart_mark = self.qstart_mark
        qend_mark = self.qend_mark
        blast_id_mark = _as_bytes('Query_')
        block_size = self.block_size

src/b/i/biopython-HEAD/Bio/Blast/NCBIWWW.py   biopython(Download)
 
from Bio._py3k import StringIO
from Bio._py3k import _as_string, _as_bytes
from Bio._py3k import urlopen as _urlopen
from Bio._py3k import urlencode as _urlencode
        ]
    query = [x for x in parameters if x[1] is not None]
    message = _as_bytes(_urlencode(query))
 
    # Send off the initial query to qblast.
        ]
    query = [x for x in parameters if x[1] is not None]
    message = _as_bytes(_urlencode(query))
 
    # Poll NCBI until the results are ready.  Use a backoff delay from 2 - 120 second wait

src/b/i/biopython-1.63/Bio/TogoWS/__init__.py   biopython(Download)
 
import time
from Bio._py3k import _binary_to_string_handle, _as_bytes
 
#Importing these functions with leading underscore as not intended for reuse
    #print(url)
    if post:
        handle = _urlopen(url, _as_bytes(_urlencode(post)))
    else:
        handle = _urlopen(url)

src/b/i/biopython-1.63/Bio/Entrez/__init__.py   biopython(Download)
from Bio._py3k import HTTPError as _HTTPError
 
from Bio._py3k import _binary_to_string_handle, _as_bytes
 
email = None
        if post:
            #HTTP POST
            handle = _urlopen(cgi, data=_as_bytes(options))
        else:
            #HTTP GET

src/b/i/biopython-HEAD/Bio/Entrez/__init__.py   biopython(Download)
from Bio._py3k import HTTPError as _HTTPError
 
from Bio._py3k import _binary_to_string_handle, _as_bytes
 
email = None
        if post:
            #HTTP POST
            handle = _urlopen(cgi, data=_as_bytes(options))
        else:
            #HTTP GET

src/b/i/biopython-1.63/Bio/SearchIO/BlatIO.py   biopython(Download)
from math import log
 
from Bio._py3k import _as_bytes, _bytes_to_string
from Bio._py3k import zip
 
_PTR_ROW_CHECK = r'^\d+\s+\d+\s+\d+\s+\d+'
_RE_ROW_CHECK = re.compile(_PTR_ROW_CHECK)
_RE_ROW_CHECK_IDX = re.compile(_as_bytes(_PTR_ROW_CHECK))
 
 
        query_id_idx = 9
        qresult_key = None
        tab_char = _as_bytes('\t')
 
        start_offset = handle.tell()
        query_id_idx = 9
        qresult_key = None
        qresult_raw = _as_bytes('')
        tab_char = _as_bytes('\t')
 

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