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src/q/i/qiime-1.8.0/qiime/split_libraries_fastq.py   qiime(Download)
from numpy import log10, arange, histogram
from cogent import DNA
from cogent.parse.fastq import MinimalFastqParser
from qiime.format import (format_histogram_one_count,
                          format_split_libraries_fastq_log,
    sequence_lengths = []
    seqs_per_sample_counts = {}
    for bc_data,read_data in izip(MinimalFastqParser(fastq_barcode_f,strict=False),
                                  MinimalFastqParser(fastq_read_f,strict=False)):
        input_sequence_count += 1

src/q/i/qiime-1.8.0/qiime/join_paired_ends.py   qiime(Download)
__email__ = "robesonms@ornl.gov"
 
from cogent.parse.fastq import MinimalFastqParser
from qiime.pycogent_backports.fastq_join import FastqJoin,join_paired_end_reads_fastqjoin
from qiime.pycogent_backports.seqprep import SeqPrep,join_paired_end_reads_seqprep
 
    # Set up iterators
    index_fastq_iter = MinimalFastqParser(ih, strict=False)
    joined_fastq_iter = MinimalFastqParser(jh, strict=False) 
    # Write barcodes / index reads that we observed within

src/q/i/qiime-1.8.0/qiime/extract_barcodes.py   qiime(Download)
from re import compile
 
from cogent.parse.fastq import MinimalFastqParser
from cogent import DNA
 
    header_index = 0
 
    for read1_data, read2_data in izip(MinimalFastqParser(fastq1,strict=False),
                                       MinimalFastqParser(fastq2,strict=False)):
        if not disable_header_match:

src/q/i/qiime-1.8.0/qiime/parse.py   qiime(Download)
from cogent.parse.fasta import FastaFinder
from cogent.parse.tree import DndParser
from cogent.parse.fastq import MinimalFastqParser as MinimalFastqParserCogent
from cogent.core.tree import PhyloNode
from cogent import DNA
from qiime.quality import ascii_to_phred33, ascii_to_phred64
from types import GeneratorType
 
def MinimalFastqParser(data,strict=False):
    return MinimalFastqParserCogent(data,strict=strict)

src/q/i/qiime-1.8.0/scripts/filter_fasta.py   qiime(Download)
from qiime.util import make_option
from cogent.parse.fasta import MinimalFastaParser
from cogent.parse.fastq import MinimalFastqParser
from qiime.util import parse_command_line_parameters, get_options_lookup
from qiime.parse import fields_to_dict
def filter_fastq_fp(input_seqs_fp,output_seqs_fp,seqs_to_keep,negate=False):
    """Filter a fastq file to include only sequences listed in seqs_to_keep """
    input_seqs = MinimalFastqParser(open(input_seqs_fp,'U'),strict=False)
    output_f = open(output_seqs_fp,'w')
    return filter_fastq(input_seqs,output_f,seqs_to_keep,negate)

src/q/i/qiime-1.8.0/qiime/convert_fastaqual_fastq.py   qiime(Download)
from qiime.parse import QiimeParseError, MinimalQualParser
from cogent.parse.fasta import MinimalFastaParser
from cogent.parse.fastq import MinimalFastqParser
 
def convert_fastaqual_fastq(fasta_file_path, qual_file_path, 
        qual_out_lookup = defaultdict(str)
 
    for header, sequence, qual in MinimalFastqParser(open(fastq_fp, 'U'),
                                                     strict=False):
        label = header.split()[0]

src/q/i/qiime-1.8.0/scripts/join_paired_ends.py   qiime(Download)
__email__ = "robesonms@ornl.gov"
 
from cogent.parse.fastq import MinimalFastqParser
from qiime.join_paired_ends import (join_method_names,
                                    join_method_constructors,

src/p/y/pycogent-HEAD/tests/test_parse/test_fastq.py   pycogent(Download)
#!/usr/bin/env python
from cogent.util.unit_test import TestCase, main
 
from cogent.parse.fastq import MinimalFastqParser
 
    def test_parse(self):
        """sequence and info objects should correctly match"""
        for label, seq, qual in MinimalFastqParser('data/fastq.txt'):
            self.assertTrue(label in data)
            self.assertEqual(seq, data[label]["seq"])

src/c/o/cogent-1.5.3/tests/test_parse/test_fastq.py   cogent(Download)
#!/usr/bin/env python
from cogent.util.unit_test import TestCase, main
 
from cogent.parse.fastq import MinimalFastqParser
 
    def test_parse(self):
        """sequence and info objects should correctly match"""
        for label, seq, qual in MinimalFastqParser('data/fastq.txt'):
            self.assertTrue(label in data)
            self.assertEqual(seq, data[label]["seq"])