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python-biopython  1.60
Classes | Namespaces | Functions | Variables
SffIO.py File Reference

Go to the source code of this file.

Classes

class  Bio.SeqIO.SffIO._AddTellHandle
class  Bio.SeqIO.SffIO.SffWriter

Namespaces

namespace  Bio.SeqIO.SffIO

Functions

def Bio.SeqIO.SffIO._sff_file_header
def Bio.SeqIO.SffIO._sff_do_slow_index
def Bio.SeqIO.SffIO._sff_find_roche_index
def Bio.SeqIO.SffIO._sff_read_roche_index_xml
def Bio.SeqIO.SffIO.ReadRocheXmlManifest
def Bio.SeqIO.SffIO._sff_read_roche_index
def Bio.SeqIO.SffIO._sff_read_seq_record
def Bio.SeqIO.SffIO._string_as_base_36
def Bio.SeqIO.SffIO._get_read_xy
def Bio.SeqIO.SffIO._get_read_time
def Bio.SeqIO.SffIO._get_read_region
def Bio.SeqIO.SffIO._sff_read_raw_record
def Bio.SeqIO.SffIO.SffIterator
def Bio.SeqIO.SffIO._SffTrimIterator

Variables

tuple Bio.SeqIO.SffIO._null = _as_bytes("\0")
tuple Bio.SeqIO.SffIO._sff = _as_bytes(".sff")
tuple Bio.SeqIO.SffIO._hsh = _as_bytes(".hsh")
tuple Bio.SeqIO.SffIO._srt = _as_bytes(".srt")
tuple Bio.SeqIO.SffIO._mft = _as_bytes(".mft")
tuple Bio.SeqIO.SffIO._flag = _as_bytes("\xff")
tuple Bio.SeqIO.SffIO._valid_UAN_read_name = re.compile(r'^[a-zA-Z0-9]{14}$')
list Bio.SeqIO.SffIO._powers_of_36 = [36**i for i in range(6)]
list Bio.SeqIO.SffIO._time_denominators
string Bio.SeqIO.SffIO.filename = "../../Tests/Roche/E3MFGYR02_random_10_reads.sff"
tuple Bio.SeqIO.SffIO.metadata = ReadRocheXmlManifest(open(filename, "rb"))
tuple Bio.SeqIO.SffIO.index1 = sorted(_sff_read_roche_index(open(filename, "rb")))
tuple Bio.SeqIO.SffIO.index2 = sorted(_sff_do_slow_index(open(filename, "rb")))
 Bio.SeqIO.SffIO.BytesIO = StringIO
tuple Bio.SeqIO.SffIO.sff = list(SffIterator(open(filename, "rb")))
tuple Bio.SeqIO.SffIO.sff2 = list(SffIterator(open("../../Tests/Roche/E3MFGYR02_alt_index_at_end.sff", "rb")))
tuple Bio.SeqIO.SffIO.sff_trim = list(SffIterator(open(filename, "rb"), trim=True))
tuple Bio.SeqIO.SffIO.fasta_no_trim = list(SeqIO.parse(open(filename,"rU"), "fasta"))
tuple Bio.SeqIO.SffIO.qual_no_trim = list(SeqIO.parse(open(filename,"rU"), "qual"))
tuple Bio.SeqIO.SffIO.fasta_trim = list(SeqIO.parse(open(filename,"rU"), "fasta"))
tuple Bio.SeqIO.SffIO.qual_trim = list(SeqIO.parse(open(filename,"rU"), "qual"))
tuple Bio.SeqIO.SffIO.handle = StringIO()
tuple Bio.SeqIO.SffIO.w = SffWriter(handle, xml=metadata)
tuple Bio.SeqIO.SffIO.data = handle.getvalue()
tuple Bio.SeqIO.SffIO.original = open(filename,"rb")