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src/b/i/biopython-1.63/Bio/SeqIO/_convert.py   biopython(Download)
def _fastq_generic(in_handle, out_handle, mapping):
    """FASTQ helper function where can't have data loss by truncation (PRIVATE)."""
    from Bio.SeqIO.QualityIO import FastqGeneralIterator
    #For real speed, don't even make SeqRecord and Seq objects!
    count = 0
    null = chr(0)
    for title, seq, old_qual in FastqGeneralIterator(in_handle):
def _fastq_generic2(in_handle, out_handle, mapping, truncate_char, truncate_msg):
    """FASTQ helper function where there could be data loss by truncation (PRIVATE)."""
    from Bio.SeqIO.QualityIO import FastqGeneralIterator
    #For real speed, don't even make SeqRecord and Seq objects!
    count = 0
    null = chr(0)
    for title, seq, old_qual in FastqGeneralIterator(in_handle):
    are valid!
    """
    from Bio.SeqIO.QualityIO import FastqGeneralIterator
    #For real speed, don't even make SeqRecord and Seq objects!
    count = 0

src/b/i/biopython-HEAD/Bio/SeqIO/_convert.py   biopython(Download)
def _fastq_generic(in_handle, out_handle, mapping):
    """FASTQ helper function where can't have data loss by truncation (PRIVATE)."""
    from Bio.SeqIO.QualityIO import FastqGeneralIterator
    #For real speed, don't even make SeqRecord and Seq objects!
    count = 0
    null = chr(0)
    for title, seq, old_qual in FastqGeneralIterator(in_handle):
def _fastq_generic2(in_handle, out_handle, mapping, truncate_char, truncate_msg):
    """FASTQ helper function where there could be data loss by truncation (PRIVATE)."""
    from Bio.SeqIO.QualityIO import FastqGeneralIterator
    #For real speed, don't even make SeqRecord and Seq objects!
    count = 0
    null = chr(0)
    for title, seq, old_qual in FastqGeneralIterator(in_handle):
    are valid!
    """
    from Bio.SeqIO.QualityIO import FastqGeneralIterator
    #For real speed, don't even make SeqRecord and Seq objects!
    count = 0

src/b/c/bcbb-HEAD/align/adaptor_trim.py   bcbb(Download)
from Bio.Seq import Seq
from Bio import SeqIO
from Bio.SeqIO.QualityIO import FastqGeneralIterator
 
def main(in_file, out_file, adaptor_seq, num_errors, min_size=1, max_size=None):
    with open(in_file) as in_handle:
        with open(out_file, "w") as out_handle:
            for title, seq, qual in FastqGeneralIterator(in_handle):
                cur_adaptor = (adaptor_seq[:(len(rec) - max_size)] if max_size
                        else adaptor_seq)

src/p/i/picobio-HEAD/blooming_reads/interlace_fastq.py   picobio(Download)
 
try:
    from Bio.SeqIO.QualityIO import FastqGeneralIterator
except ImportError:
    sys_exit("Missing FastqGeneralIterator from Biopython")
out_handle = sys.stdout
 
iter1 = FastqGeneralIterator(handle1)
iter2 = FastqGeneralIterator(handle2)
 

src/b/c/bcbb-HEAD/nextgen/bcbio/variation/cortex.py   bcbb(Download)
import pysam
from Bio import Seq
from Bio.SeqIO.QualityIO import FastqGeneralIterator
 
from bcbio import broad
    with open(in_fastq) as in_handle:
        items = list(itertools.takewhile(lambda i : i <= min_reads,
                                         (i for i, _ in enumerate(FastqGeneralIterator(in_handle)))))
    return len(items)
 

src/b/c/bcbb-HEAD/nextgen/bcbio/pipeline/demultiplex.py   bcbb(Download)
 
from Bio import SeqIO
from Bio.SeqIO.QualityIO import FastqGeneralIterator
 
from bcbio import utils
        with open(trim_file, "w") as out_handle:
            with open(work_file) as in_handle:
                for name, seq, qual in FastqGeneralIterator(in_handle):
                    out_handle.write("@%s\n%s\n+\n%s\n" % (name, trimmer(seq),
                                                           trimmer(qual)))

src/b/c/bcbb-HEAD/nextgen/bcbio/pipeline/alignment.py   bcbb(Download)
from collections import namedtuple
 
from Bio.SeqIO.QualityIO import FastqGeneralIterator
 
from bcbio import utils, broad
            with open(in_file) as in_handle:
                with open(tx_out_file, "w") as out_handle:
                    for i, (name, seq, qual) in enumerate(FastqGeneralIterator(in_handle)):
                        if i == 0 and not name.endswith("/1"):
                            out_file = in_file

src/b/c/bcbb-HEAD/nextgen/bcbio/ngsalign/split.py   bcbb(Download)
import pysam
from Bio import Seq
from Bio.SeqIO.QualityIO import FastqGeneralIterator
 
from bcbio.bam.trim import _save_diskspace
    out_files = [out_fname]
    with open(in_fastq) as in_handle:
        for name, seq, qual in FastqGeneralIterator(in_handle):
            if cur_count < split_size:
                cur_count += 1

src/b/c/bcbb-HEAD/nextgen/bcbio/bam/trim.py   bcbb(Download)
from bcbio.utils import file_exists, save_diskspace, safe_makedir
 
from Bio.SeqIO.QualityIO import FastqGeneralIterator
 
def _trim_quality(seq, qual, to_trim, min_length):
def _trim_by_read(in_handles, to_trim, min_length):
    """Lazy generator for trimmed reads for all input files.
    """
    iterators = [(f, FastqGeneralIterator(h)) for f, h in in_handles.iteritems()]
    f1, x1 = iterators[0]

src/p/a/paired_sequence_utils-0.1/paired_sequence_match.py   paired_sequence_utils(Download)
import fileinput
import gzip
from Bio.SeqIO.QualityIO import FastqGeneralIterator
from Bio import SeqIO
 
    f_file = fileinput.FileInput(args[0], openhook=fileinput.hook_compressed)
    r_file = fileinput.FileInput(args[1], openhook=fileinput.hook_compressed)
    f_fastq = FastqGeneralIterator(f_file)
    r_fastq = FastqGeneralIterator(r_file)
    matched_pair_count = 0

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