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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
                line = handle.readline()
                if marker_re.match(line) or not line:
                    yield _bytes_to_string(id), start_offset, length
                    start_offset = end_offset
                    break
                        raise ValueError(
                            "Did not find ACCESSION/VERSION lines")
                    yield _bytes_to_string(key), start_offset, length
                    start_offset = end_offset
                    break
                if marker_re.match(line) or not line:
                    end_offset = handle.tell() - len(line)
                    yield _bytes_to_string(key), start_offset, length
                    start_offset = end_offset
                    break
                line = handle.readline()
                if marker_re.match(line) or not line:
                    yield _bytes_to_string(key), start_offset, length
                    start_offset = end_offset
                    break

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
                line = handle.readline()
                if marker_re.match(line) or not line:
                    yield _bytes_to_string(id), start_offset, length
                    start_offset = end_offset
                    break
                        raise ValueError(
                            "Did not find ACCESSION/VERSION lines")
                    yield _bytes_to_string(key), start_offset, length
                    start_offset = end_offset
                    break
                if marker_re.match(line) or not line:
                    end_offset = handle.tell() - len(line)
                    yield _bytes_to_string(key), start_offset, length
                    start_offset = end_offset
                    break
                line = handle.readline()
                if marker_re.match(line) or not line:
                    yield _bytes_to_string(key), start_offset, length
                    start_offset = end_offset
                    break

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
 
 
                if curr_key != qresult_key:
                    yield _bytes_to_string(qresult_key), start_offset, \
                            end_offset - start_offset
                    qresult_key = curr_key
                    start_offset = end_offset - len(line)
 
            line = handle.readline()
            if not line:
                yield _bytes_to_string(qresult_key), start_offset, \

src/b/i/biopython-HEAD/Bio/SearchIO/BlatIO.py   biopython(Download)
from math import log
 
from Bio._py3k import _as_bytes, _bytes_to_string
from Bio._py3k import zip
 
 
                if curr_key != qresult_key:
                    yield _bytes_to_string(qresult_key), start_offset, \
                            end_offset - start_offset
                    qresult_key = curr_key
                    start_offset = end_offset - len(line)
 
            line = handle.readline()
            if not line:
                yield _bytes_to_string(qresult_key), start_offset, \

src/b/i/biopython-1.63/Bio/SearchIO/HmmerIO/hmmer3_tab.py   biopython(Download)
from itertools import chain
 
from Bio._py3k import _as_bytes, _bytes_to_string
from Bio.Alphabet import generic_protein
from Bio.SearchIO._index import SearchIndexer
                if curr_key != qresult_key:
                    adj_end = end_offset - len(line)
                    yield _bytes_to_string(qresult_key), start_offset, \
                            adj_end - start_offset
                    qresult_key = curr_key
                    start_offset = adj_end
 
            line = handle.readline()
            if not line:
                yield _bytes_to_string(qresult_key), start_offset, \

src/b/i/biopython-1.63/Bio/SearchIO/HmmerIO/hmmer2_text.py   biopython(Download)
import re
 
from Bio._py3k import _as_bytes, _bytes_to_string
from Bio._utils import read_forward
from Bio.Alphabet import generic_protein
                start_offset = end_offset - len(line)
            elif line.startswith(self.qresult_end):
                yield _bytes_to_string(qresult_key), start_offset, 0
                start_offset = end_offset
            elif not line:
                # HACK: since hmmsearch can only have one query result
                if is_hmmsearch:
                    yield _bytes_to_string(qresult_key), start_offset, 0

src/b/i/biopython-HEAD/Bio/SearchIO/HmmerIO/hmmer3_tab.py   biopython(Download)
from itertools import chain
 
from Bio._py3k import _as_bytes, _bytes_to_string
from Bio.Alphabet import generic_protein
from Bio.SearchIO._index import SearchIndexer
                if curr_key != qresult_key:
                    adj_end = end_offset - len(line)
                    yield _bytes_to_string(qresult_key), start_offset, \
                            adj_end - start_offset
                    qresult_key = curr_key
                    start_offset = adj_end
 
            line = handle.readline()
            if not line:
                yield _bytes_to_string(qresult_key), start_offset, \

src/b/i/biopython-HEAD/Bio/SearchIO/HmmerIO/hmmer2_text.py   biopython(Download)
import re
 
from Bio._py3k import _as_bytes, _bytes_to_string
from Bio._utils import read_forward
from Bio.Alphabet import generic_protein
                start_offset = end_offset - len(line)
            elif line.startswith(self.qresult_end):
                yield _bytes_to_string(qresult_key), start_offset, 0
                start_offset = end_offset
            elif not line:
                # HACK: since hmmsearch can only have one query result
                if is_hmmsearch:
                    yield _bytes_to_string(qresult_key), start_offset, 0

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("")
 
            if qstart_id.startswith(blast_id_mark):
                qstart_id = qstart_desc.split(_as_bytes(' '), 1)[0]
            yield _bytes_to_string(qstart_id), start_offset, len(block)
            counter += 1
 

src/b/i/biopython-1.63/Bio/SeqIO/AbiIO.py   biopython(Download)
from Bio.SeqRecord import SeqRecord
 
from Bio._py3k import _bytes_to_string, _as_bytes
from Bio._py3k import zip
 
        index += 1
        # only parse desired dirs
        key = _bytes_to_string(dir_entry[0])
        key += str(dir_entry[1])
        if key in (list(_EXTRACT) + _SPCTAGS):
            tag_name = _bytes_to_string(dir_entry[0])
        # account for different data types
        if elem_code == 2:
            return _bytes_to_string(data)
        elif elem_code == 10:
            return str(datetime.date(*data))
            return bool(data)
        elif elem_code == 18:
            return _bytes_to_string(data[1:])
        elif elem_code == 19:
            return _bytes_to_string(data[:-1])

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