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src/q/i/qiime-1.8.0/qiime/make_otu_table.py   qiime(Download)
from sys import stderr
from numpy import array, zeros
from cogent.util.misc import flatten, InverseDict
from qiime.format import format_otu_table
from qiime.parse import parse_otu_map
def seqids_from_otu_to_seqid(otu_to_seqid):
    """Returns set of all seq ids from libs"""
    return set(flatten(otu_to_seqid.values()))
 
def make_otu_table(otu_map_f,

src/c/o/cogent-1.5.3/cogent/struct/rna2d.py   cogent(Download)
from cogent.util.transform import make_trans, float_from_string
from cogent.core.tree import TreeNode, TreeError
from cogent.util.misc import not_none, flatten
 
__author__ = "Rob Knight"
        """
        if self.Length > 1:
            return flatten([p.extract(seq) for p in self])
        else:
            if self.Start is not None:

src/p/y/pycogent-HEAD/cogent/struct/rna2d.py   pycogent(Download)
from cogent.util.transform import make_trans, float_from_string
from cogent.core.tree import TreeNode, TreeError
from cogent.util.misc import not_none, flatten
 
__author__ = "Rob Knight"
        """
        if self.Length > 1:
            return flatten([p.extract(seq) for p in self])
        else:
            if self.Start is not None:

src/c/o/cogent-1.5.3/cogent/db/ensembl/genome.py   cogent(Download)
                                    CpGisland, Repeat, Est
from cogent.db.ensembl.feature_level import FeatureCoordLevels
from cogent.util.misc import flatten
 
 
        if result:
            try:
                symbol = flatten(result)[0]
            except IndexError:
                symbol = None

src/c/o/cogent-1.5.3/cogent/db/ensembl/database.py   cogent(Download)
import sqlalchemy as sql
 
from cogent.util import table as cogent_table
from cogent.db.ensembl.host import DbConnection, get_db_name
from cogent.util.misc import flatten
                type(record[0]) not in string_types:
                # multi-dimensioned list/tuple
                record = flatten(record)
            elif type(record) not in string_types:
                # list/tuple of strings

src/p/y/pycogent-HEAD/cogent/db/ensembl/genome.py   pycogent(Download)
                                    CpGisland, Repeat, Est
from cogent.db.ensembl.feature_level import FeatureCoordLevels
from cogent.util.misc import flatten
 
 
        if result:
            try:
                symbol = flatten(result)[0]
            except IndexError:
                symbol = None

src/p/y/pycogent-HEAD/cogent/db/ensembl/database.py   pycogent(Download)
import sqlalchemy as sql
 
from cogent.util import table as cogent_table
from cogent.db.ensembl.host import DbConnection, get_db_name
from cogent.util.misc import flatten
                type(record[0]) not in string_types:
                # multi-dimensioned list/tuple
                record = flatten(record)
            elif type(record) not in string_types:
                # list/tuple of strings

src/q/i/qiime-1.8.0/qiime/pick_otus.py   qiime(Download)
from cogent import LoadSeqs, DNA, Alignment
from cogent.util.trie import build_prefix_map
from cogent.util.misc import flatten
 
from qiime.util import FunctionWithParams, get_tmp_filename, get_qiime_temp_dir
def expand_otu_map_seq_ids(otu_map,seq_id_map):
    for otu_id, seq_ids in otu_map.items():
        mapped_seq_ids = flatten(\
         [seq_id_map[seq_id] for seq_id in seq_ids])
        otu_map[otu_id] = mapped_seq_ids

src/q/i/qiime-1.8.0/qiime/make_3d_plots.py   qiime(Download)
from biplots import make_mage_taxa
from numpy import abs as numpy_abs
from cogent.util.misc import flatten
from qiime.format import format_coords
from cogent.maths.stats.util import Numbers
    if len(mins) < num_coords:
        num_coords = len(mins)
    min_maxes = flatten(zip(mins,maxes))
 
    if custom_axes:

src/q/i/qiime-HEAD/qiime/make_otu_table.py   qiime(Download)
from sys import stderr
from numpy import array, zeros
from cogent.util.misc import flatten
from qiime.format import format_otu_table
from qiime.parse import parse_otu_map
def seqids_from_otu_to_seqid(otu_to_seqid):
    """Returns set of all seq ids from libs"""
    return set(flatten(otu_to_seqid.values()))
 
 

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