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# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Data conversion'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$... | [
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"__gluindex__ = True",
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"__license__ = 'See GLU license for terms by running: glu license'",
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# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Convert a GDAT file into series of BAFSegmentation input files'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
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# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Convert an Illumina Locus by DNA report file into a GLU genotype file'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license... | [
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"__license__ = 'See GLU license for ... |
# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Convert an Illumina Genotype Final Report (GFR) to a GLU raw genotype (GDAT) file'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N0... | [
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# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Convert a GDAT file into series of GADA input files'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See G... | [
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# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Estimate genetic admixture proportions from series of assumed ancestral populations'
__copyright__ = 'Copyright (c) 2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-C... | [
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# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Population structure'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
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"__license__ = 'See GLU license for terms by running: glu license'",
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# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Principle Components Analysis (PCA) to find large-scale correlations among samples based on genotype data'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-1240... | [
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# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Print information about a GLU genotype file'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu... | [
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"__license__ = 'See GLU license for terms by running: glu lice... |
# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Check concordance between a reference and comparison genotype set'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for... | [
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"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for term... |
# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Detect non-Mendelian inheritance among parents and their offspring'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license fo... | [
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"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for ter... |
# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Detect duplicate samples based on an all pairs-comparison of genotype concordance rates'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Con... | [
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# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Compute the genotype correlation between a reference and comparison genotype set'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-1... | [
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# -*- coding: utf-8 -*-
__gluindex__ = False
__abstract__ = 'Perform genotype-elimination on a set of genotypes based on their relationships'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
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# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Genotype quality control'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revisio... | [
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# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Compute IBS and IBD sharing for pairs of samples'
__copyright__ = 'Copyright (c) 2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU ... | [
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# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Compute a battery of genotype summary statistics'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
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# -*- coding: utf-8 -*-
__gluindex__ = False
__index__ = 'LD estimation and tagging'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
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# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Utility to merge rows with matching values from two files'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
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# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Utility modules'
__order__ = 90
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
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# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Manipulate delimited files, including filtering by column, value, and creating indicator variables based on a categorical variable'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI u... | [
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# -*- coding: utf-8 -*-
from __future__ import division
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__abstract__ = 'Perform quantile normalization and re-estimate LRR and BAF'
__copyright__ = 'Copyright (c) 2011, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ =... | [
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[
14,
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0.... | [
"from __future__ import division",
"__gluindex__ = True",
"__abstract__ = 'Perform quantile normalization and re-estimate LRR and BAF'",
"__copyright__ = 'Copyright (c) 2011, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = ... |
from __future__ import division
import sys
import numpy as np
import matplotlib.pyplot as plt
import matplotlib as mpl
import matplotlib.gridspec as gridspec
from matplotlib.ticker import NullFormatter
from scipy.stats import gaussian_kde
from glu.lib.recordtype import reco... | [
[
1,
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"from __future__ import division",
"import sys",
"import numpy as np",
"import matplotlib.pyplot as plt",
"import matplotlib as mpl",
"import matplotlib.gridspec as gridspec",
"from matplotlib.ticker import NullFormatter",
"from scipy.stats import gaussian_kde",
"fro... |
# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Generate statistics on LRR and BAF for original and renormalized values'
__copyright__ = 'Copyright (c) 2012, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__... | [
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"from __future__ import division",
"__gluindex__ = True",
"__abstract__ = 'Generate statistics on LRR and BAF for original and renormalized values'",
"__copyright__ = 'Copyright (c) 2012, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__l... |
# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Build GC/CpG model file (GCM) from an Illumina manifest file (BPM) and an indexed reference genome (FASTA)'
__copyright__ = 'Copyright (c) 2011, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by N... | [
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"from __future__ import division",
"__gluindex__ = True",
"__abstract__ = 'Build GC/CpG model file (GCM) from an Illumina manifest file (BPM) and an indexed reference genome (FASTA)'",
"__copyright__ = 'Copyright (c) 2011, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI und... |
import os
import sys
import h5py
import sqlite3
import numpy as np
import numpy.lib.recfunctions as rfn
from itertools import izip
from glu.lib.utils import is_str,namedtuple,lazy_property
from glu.lib.fileutils import parse_augmented_filename, compressed_filename, namefile
... | [
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"import os",
"import sys",
"import h5py",
"import sqlite3",
"import numpy as np",
"import numpy.lib.recfunctions as rfn",
"from itertools import izip",
"from glu.lib.utils import is_str,namedtuple,lazy_property",
"from glu.lib.fileutils import parse_augmente... |
# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Copy number and quantitative SNP probe analysis'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running:... | [
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"__gluindex__ = True",
"__abstract__ = 'Copy number and quantitative SNP probe analysis'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu ... |
# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Create an index of one or more GDAT files'
__copyright__ = 'Copyright (c) 2011, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu licens... | [
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[
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0,
0.6... | [
"__gluindex__ = True",
"__abstract__ = 'Create an index of one or more GDAT files'",
"__copyright__ = 'Copyright (c) 2011, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
... |
# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Resolve genomic metadata given feature names for SNPs, genes, and bounded regions'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See... | [
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[
14,
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0.... | [
"__gluindex__ = True",
"__abstract__ = 'Resolve genomic metadata given feature names for SNPs, genes, and bounded regions'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU ... |
# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Find SNPs near a set of genomic features (SNPs, genes or regions)'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for... | [
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0.6... | [
"__gluindex__ = True",
"__abstract__ = 'Find SNPs near a set of genomic features (SNPs, genes or regions)'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for term... |
# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Add columns of genomic annotation to a file containing a list of SNP names'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU li... | [
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14,
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0.... | [
"__gluindex__ = True",
"__abstract__ = 'Add columns of genomic annotation to a file containing a list of SNP names'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license... |
# -*- coding: utf-8 -*-
from __future__ import division
__abstract__ = 'Build a genedb database'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license... | [
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0.66... | [
"from __future__ import division",
"__abstract__ = 'Build a genedb database'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
... |
# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Genomic annotation database'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revi... | [
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"__gluindex__ = True",
"__abstract__ = 'Genomic annotation database'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revi... |
# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Convert Newbler 454PairAlign.txt and the corresponding SFF files into SAM/BAM format'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-... | [
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"__gluindex__ = True",
"__abstract__ = 'Convert Newbler 454PairAlign.txt and the corresponding SFF files into SAM/BAM format'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-124... |
# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Annotate genomic coordinates and nucleotide variation'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See... | [
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"__abstract__ = 'Annotate genomic coordinates and nucleotide variation'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See ... |
# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Filter SAM/BAM files'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running... | [
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"__gluindex__ = True",
"__abstract__ = 'Filter SAM/BAM files'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running:... |
# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Convert between sequence file formats'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for... | [
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"__abstract__ = 'Convert between sequence file formats'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for ... |
# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Annotate genomic coordinates and nucleotide variation'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See... | [
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"__abstract__ = 'Annotate genomic coordinates and nucleotide variation'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See ... |
# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Produce summary statistics from an annotated VCF file'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See... | [
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"__gluindex__ = True",
"__abstract__ = 'Produce summary statistics from an annotated VCF file'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See ... |
# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Convert a VCF file to an ldat file'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for te... | [
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"__gluindex__ = True",
"__abstract__ = 'Convert a VCF file to an ldat file'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for ter... |
# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Filter SAM/BAM files'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running... | [
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"__abstract__ = 'Filter SAM/BAM files'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running:... |
# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Compute summary statistics on SAM/BAM files'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU licen... | [
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"__abstract__ = 'Compute summary statistics on SAM/BAM files'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU licens... |
from __future__ import division
__gluindex__ = True
__abstract__ = 'Merge multiple CGI mastervar files together to create a unified list of variant individuals'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$Id$'
import os
import sys
from operator import... | [
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"from __future__ import division",
"__gluindex__ = True",
"__abstract__ = 'Merge multiple CGI mastervar files together to create a unified list of variant individuals'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id$'",
"import os",
"import sys",
"from ... |
# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Annotate genomic coordinates and nucleotide variation'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See... | [
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"__abstract__ = 'Annotate genomic coordinates and nucleotide variation'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See ... |
# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Next Generation Sequencing'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__... | [
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"__gluindex__ = True",
"__abstract__ = 'Next Generation Sequencing'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__... |
# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Partition reads by embedded barcode sequences'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU lic... | [
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"__abstract__ = 'Partition reads by embedded barcode sequences'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU lice... |
# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Query merged CGI variants'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by ru... | [
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"__abstract__ = 'Query merged CGI variants'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by run... |
# -*- coding: utf-8 -*-
__abstract__ = 'Data Management'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$Id$'
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"__abstract__ = 'Data Management'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id$'"
] |
# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Print a list of GLU modules'
__index__ = 'General modules'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for ter... | [
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"__gluindex__ = True",
"__abstract__ = 'Print a list of GLU modules'",
"__index__ = 'General modules'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for ter... |
# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'GLU copyright and license terms'
__index__ = 'General modules'
__order__ = 5
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'S... | [
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"__gluindex__ = True",
"__abstract__ = 'GLU copyright and license terms'",
"__index__ = 'General modules'",
"__order__ = 5",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ ... |
# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'New user quick start guide'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revis... | [
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"__gluindex__ = True",
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"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revis... |
# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Brief overview of GLU functionality'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license... | [
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"__gluindex__ = True",
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"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
... |
# -*- coding: utf-8 -*-
__gluindex__ = False
__abstract__ = 'Brief introduction to GLU for new users'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu li... | [
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"__gluindex__ = False",
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"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license... |
# -*- coding: utf-8 -*-
__gluindex__ = True
__index__ = 'Online introduction'
__order__ = 20
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu lice... | [
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"__gluindex__ = True",
"__index__ = 'Online introduction'",
"__order__ = 20",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu lice... |
# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Overview of GLU file formats'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__rev... | [
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"__gluindex__ = True",
"__abstract__ = 'Overview of GLU file formats'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__rev... |
# -*- coding: utf-8 -*-
__abstract__ = 'GLU package'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$Id$'
| [
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"__abstract__ = 'GLU package'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id$'"
] |
# -*- coding: utf-8 -*-
__abstract__ = 'Formula objects and parser for association testing'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__re... | [
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14,
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"__abstract__ = 'Formula objects and parser for association testing'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revisio... |
# -*- coding: utf-8 -*-
__abstract__ = 'Remap alleles'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$Id$'
import unittest
f... | [
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"__abstract__ = 'Remap alleles'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id$'",
"import unittest",
... |
# -*- coding: utf-8 -*-
__abstract__ = 'parser for region files'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$Id$'
import ... | [
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"__abstract__ = 'parser for region files'",
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"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id$'",
"import s... |
# -*- coding: utf-8 -*-
from __future__ import with_statement
__abstract__ = 'generic utility functions'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu... | [
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"__license__ = 'See GLU license for terms by running: glu licen... |
# -*- coding: utf-8 -*-
__abstract__ = 'implementation of the classical union-find algorithm'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__... | [
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"__license__ = 'See GLU license for terms by running: glu license'",
"__revis... |
# -*- coding: utf-8 -*-
from __future__ import division
__abstract__ = 'test for deviations from Hardy-Weinberg proportions'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for t... | [
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"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms b... |
# -*- coding: utf-8 -*-
from __future__ import division
__abstract__ = 'miscellaneous statistical functions'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running:... | [
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"__license__ = 'See GLU license for terms by running: glu l... |
# -*- coding: utf-8 -*-
from __future__ import division
__abstract__ = 'Compute triangular numbers, their inverses, and rectangular coordinate transformations'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__l... | [
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... | [
"from __future__ import division",
"__abstract__ = 'Compute triangular numbers, their inverses, and rectangular coordinate transformations'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license... |
# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Various edit distance algorithms'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for term... | [
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"from __future__ import division",
"__gluindex__ = True",
"__abstract__ = 'Various edit distance algorithms'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms... |
# -*- coding: utf-8 -*-
__abstract__ = 'Read and write multi-part file streams.'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ =... | [
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"__abstract__ = 'Read and write multi-part file streams.'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id... |
#!/usr/bin/python
# -*- coding: iso-8859-1 -*-
#
# progressbar - Text progressbar library for python.
# Copyright (c) 2005 Nilton Volpato
# Copyright (c) 2009, BioInformed LLC
#
# Modified extensively for inclusion in GLU by Kevin Jacobs
#
# This library is free software; you can redistribute it and/or
# modify it und... | [
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"from __future__ import division",
"'''Text progressbar library for python.\n\nThis library provides a text mode progressbar. This is typically used\nto display the progress of a long running operation, providing a\nvisual clue that processing is underway.\n\nThe ProgressBar class manages the progress, and the fo... |
# -*- coding: utf-8 -*-
__abstract__ = 'Query genedb database'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$Id$'
import r... | [
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"__abstract__ = 'Query genedb database'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id$'",
"import re"... |
# -*- coding: utf-8 -*-
__gluindex__ = True
__abstract__ = 'Genomic annotation database'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revi... | [
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"__gluindex__ = True",
"__abstract__ = 'Genomic annotation database'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revi... |
# -*- coding: utf-8 -*-
__abstract__ = 'efficiently merge sorted iterables'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$Id... | [
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"__abstract__ = 'efficiently merge sorted iterables'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id$'",
... |
# -*- coding: utf-8 -*-
__abstract__ = 'Functions to perform cross-tabulations of data'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revisi... | [
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"__abstract__ = 'Functions to perform cross-tabulations of data'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ ... |
# -*- coding: utf-8 -*-
__abstract__ = 'GLU library modules'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$Id$'
| [
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"__abstract__ = 'GLU library modules'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id$'"
] |
# -*- coding: utf-8 -*-
__abstract__ = 'GLU argument parser'
__copyright__ = 'Copyright (c) 2011, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
import sys
import argparse
from gettex... | [
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"__abstract__ = 'GLU argument parser'",
"__copyright__ = 'Copyright (c) 2011, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"import sys",
"import argparse",
"from get... |
# -*- coding: utf-8 -*-
from __future__ import division
import pysam
from glu.lib.fileutils import list_reader
class ReferenceVariants(object):
def __init__(self, refvariant, ingroupfile=None):
self.vars = pysam.Tabixfile(refvariant,cache_size=128*1024*1024)
self.ingroup = set(s.strip() for ... | [
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"from __future__ import division",
"import pysam",
"from glu.lib.fileutils import list_reader",
"class ReferenceVariants(object):\n def __init__(self, refvariant, ingroupfile=None):\n self.vars = pysam.Tabixfile(refvariant,cache_size=128*1024*1024)\n self.ingroup = set(s.strip() for s in li... |
# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Annotate genomic coordinates and nucleotide variation'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See... | [
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"from __future__ import division",
"__gluindex__ = True",
"__abstract__ = 'Annotate genomic coordinates and nucleotide variation'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See ... |
# -*- coding: utf-8 -*-
from __future__ import with_statement, division
__abstract__ = 'functions for alignment filtering'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by... | [
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"from __future__ import with_statement, division",
"__abstract__ = 'functions for alignment filtering'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by runni... |
# -*- coding: utf-8 -*-
from __future__ import division
__abstract__ = 'Annotate genomic coordinates and nucleotide variation'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for term... | [
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"from __future__ import division",
"__abstract__ = 'Annotate genomic coordinates and nucleotide variation'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by r... |
# -*- coding: utf-8 -*-
from __future__ import division
from collections import defaultdict, namedtuple
import pysam
from glu.lib.recordtype import recordtype
VarInfo = namedtuple('VarInfo', 'exact_vars inexact_vars common_score function_info')
VarRecord = recordtype('VarRecord', 'chromosome... | [
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"from __future__ import division",
"from collections import defaultdict, namedtuple",
"import pysam",
"from glu.lib.recordtype import recordtype",
"VarInfo = namedtuple('VarInfo', 'exact_vars inexact_vars common_score function_info')",
"VarRecord = recordtype('VarRecord', 'chromosome ... |
# -*- coding: utf-8 -*-
from __future__ import division
__abstract__ = 'Read and process features from BED files'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running:... | [
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... | [
"from __future__ import division",
"__abstract__ = 'Read and process features from BED files'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu l... |
# -*- coding: utf-8 -*-
from __future__ import division
__gluindex__ = True
__abstract__ = 'Various edit distance algorithms'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for term... | [
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0... | [
"from __future__ import division",
"__gluindex__ = True",
"__abstract__ = 'Various edit distance algorithms'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms... |
import sys
import xml.etree.cElementTree as etree
from collections import defaultdict
import numpy as np
from Bio import SeqIO
try:
from Bio.SeqIO.SffIO import ReadRocheXmlManifest as sff_manifest
except ImportError:
from Bio.SeqIO.SffIO import _sff_read_roche_index_xml a... | [
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... | [
"import sys",
"import xml.etree.cElementTree as etree",
"from collections import defaultdict",
"import numpy as np",
"from Bio import SeqIO",
"try:\n from Bio.SeqIO.SffIO import ReadRocheXmlManifest as sff_manifest\nexcept ImportError:\n from Bio.SeqIO.SffIO import... |
# -*- coding: utf-8 -*-
__abstract__ = '''\
Implements sequence alphabet, manipulation, and mapping of top/bottom
sequence normalization and A/B SNP allele canonical mappings based on
Illumina and dbSNP standards documented at
ftp://ftp.ncbi.nih.gov/snp/database/Illumina_top_bot_strand.note.txt'''
__copyright__ = 'Co... | [
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"__abstract__ = '''\\\nImplements sequence alphabet, manipulation, and mapping of top/bottom\nsequence normalization and A/B SNP allele canonical mappings based on\nIllumina and dbSNP standards documented at\nftp://ftp.ncbi.nih.gov/snp/database/Illumina_top_bot_strand.note.txt'''",
"__copyright__ = 'Copyright (c... |
# -*- coding: utf-8 -*-
__abstract__ = '''\
Implements sequence alphabet, manipulation, and mapping of top/bottom
sequence normalization and A/B SNP allele canonical mappings based on
Illumina and dbSNP standards documented at
ftp://ftp.ncbi.nih.gov/snp/database/Illumina_top_bot_strand.note.txt'''
__copyright__ = 'Co... | [
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"__abstract__ = '''\\\nImplements sequence alphabet, manipulation, and mapping of top/bottom\nsequence normalization and A/B SNP allele canonical mappings based on\nIllumina and dbSNP standards documented at\nftp://ftp.ncbi.nih.gov/snp/database/Illumina_top_bot_strand.note.txt'''",
"__copyright__ = 'Copyright (c... |
# -*- coding: utf-8 -*-
__abstract__ = 'GLU library modules'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$Id$'
| [
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"__abstract__ = 'GLU library modules'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id$'"
] |
# -*- coding: utf-8 -*-
from __future__ import division
__abstract__ = 'Variant Call Format parser'
__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
... | [
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"from __future__ import division",
"__abstract__ = 'Variant Call Format parser'",
"__copyright__ = 'Copyright (c) 2010, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"i... |
from operator import getitem, itemgetter
from itertools import izip, imap, groupby, repeat
CIGAR_map = { ('-','-'):'P' }
for a in 'NACGTacgt':
CIGAR_map[a,'-'] = 'I'
CIGAR_map['-',a] = 'D'
for b in 'NACGTacgt':
CIGAR_map[a,b] = 'M'
NDIFF_map = { ('-','-'): ('P',None) }
for a in 'NACGTacgt':
NDIFF_m... | [
[
1,
0,
0.0125,
0.0125,
0,
0.66,
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4,
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0,
808,
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0
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[
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... | [
"from operator import getitem, itemgetter",
"from itertools import izip, imap, groupby, repeat",
"CIGAR_map = { ('-','-'):'P' }",
"for a in 'NACGTacgt':\n CIGAR_map[a,'-'] = 'I'\n CIGAR_map['-',a] = 'D'\n for b in 'NACGTacgt':\n CIGAR_map[a,b] = 'M'",
" CIGAR_map[a,'-'] = 'I'",
" CIGAR_map['-... |
from __future__ import division
import sys
import csv
from operator import itemgetter
from itertools import groupby
from collections import namedtuple
from glu.lib.utils import unique, is_str
from glu.lib.fileutils import autofile, hyphen
from glu.lib.recordtype import r... | [
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0... | [
"from __future__ import division",
"import sys",
"import csv",
"from operator import itemgetter",
"from itertools import groupby",
"from collections import namedtuple",
"from glu.lib.utils import unique, is_str",
"from glu.lib.fileutils import autofile, hyph... |
# -*- coding: utf-8 -*-
from __future__ import division
__abstract__ = 'library for association testing'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu... | [
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0
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[
14,
0,
0.0066,
0.0011,
0,
0... | [
"from __future__ import division",
"__abstract__ = 'library for association testing'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu licen... |
# -*- coding: utf-8 -*-
__abstract__ = 'file related utility functions'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$Id$'
... | [
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0,
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0.0038,
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929,
1,
0,
0,
0,
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0
],
[
14,
0,
0.015,
0.0038,
0,
0.66,
0.0667,
200,
1,
0,
0,
0,
0,
3,
0
],
[
14,
0,
0.0188,
0.0038,
0,
0.... | [
"__abstract__ = 'file related utility functions'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id$'",
"i... |
# -*- coding: utf-8 -*-
__abstract__ = 'file related utility functions'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$Id$'
... | [
[
14,
0,
0.0037,
0.0012,
0,
0.66,
0,
929,
1,
0,
0,
0,
0,
3,
0
],
[
14,
0,
0.005,
0.0012,
0,
0.66,
0.0385,
200,
1,
0,
0,
0,
0,
3,
0
],
[
14,
0,
0.0062,
0.0012,
0,
0.... | [
"__abstract__ = 'file related utility functions'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id$'",
"f... |
# -*- coding: utf-8 -*-
__abstract__ = 'GLU fileutils package'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$Id$'
from glu... | [
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[
14,
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0.0667,
0,
0.66... | [
"__abstract__ = 'GLU fileutils package'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id$'",
"from glu.l... |
# -*- coding: utf-8 -*-
__abstract__ = 'file related utility functions'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$Id$'
... | [
[
14,
0,
0.0026,
0.0009,
0,
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1,
0,
0,
0,
0,
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],
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200,
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0,
0,
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],
[
14,
0,
0.0044,
0.0009,
0,
0... | [
"__abstract__ = 'file related utility functions'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id$'",
"i... |
# -*- coding: utf-8 -*-
__abstract__ = 'fileutils Stata file support'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$Id$'
''... | [
[
14,
0,
0.0073,
0.0024,
0,
0.66,
0,
929,
1,
0,
0,
0,
0,
3,
0
],
[
14,
0,
0.0097,
0.0024,
0,
0.66,
0.0769,
200,
1,
0,
0,
0,
0,
3,
0
],
[
14,
0,
0.0121,
0.0024,
0,
0... | [
"__abstract__ = 'fileutils Stata file support'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id$'",
"'''... |
# -*- coding: utf-8 -*-
__abstract__ = 'fileutils Excel file support'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$Id$'
f... | [
[
14,
0,
0.0116,
0.0039,
0,
0.66,
0,
929,
1,
0,
0,
0,
0,
3,
0
],
[
14,
0,
0.0154,
0.0039,
0,
0.66,
0.0769,
200,
1,
0,
0,
0,
0,
3,
0
],
[
14,
0,
0.0193,
0.0039,
0,
0... | [
"__abstract__ = 'fileutils Excel file support'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id$'",
"fro... |
# -*- coding: utf-8 -*-
__abstract__ = 'fileutils XLSX file support'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$Id$'
fr... | [
[
14,
0,
0.0169,
0.0056,
0,
0.66,
0,
929,
1,
0,
0,
0,
0,
3,
0
],
[
14,
0,
0.0226,
0.0056,
0,
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0.1111,
200,
1,
0,
0,
0,
0,
3,
0
],
[
14,
0,
0.0282,
0.0056,
0,
0... | [
"__abstract__ = 'fileutils XLSX file support'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id$'",
"from... |
# -*- coding: utf-8 -*-
__abstract__ = 'GLU fileutils table input/output formats'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ ... | [
[
14,
0,
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0,
0.66,
0,
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0,
0,
0,
3,
0
],
[
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0.6667,
0.1667,
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0.3333,
200,
1,
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0,
0,
3,
0
],
[
14,
0,
0.8333,
0.1667,
0,
0.66... | [
"__abstract__ = 'GLU fileutils table input/output formats'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$I... |
# -*- coding: utf-8 -*-
__abstract__ = 'fileutils sqlite format support'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$Id$'
... | [
[
14,
0,
0.0147,
0.0049,
0,
0.66,
0,
929,
1,
0,
0,
0,
0,
3,
0
],
[
14,
0,
0.0196,
0.0049,
0,
0.66,
0.0833,
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1,
0,
0,
0,
0,
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0
],
[
14,
0,
0.0245,
0.0049,
0,
0... | [
"__abstract__ = 'fileutils sqlite format support'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id$'",
"... |
# -*- coding: utf-8 -*-
__abstract__ = 'fileutils delimited text file support'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '... | [
[
14,
0,
0.0242,
0.0081,
0,
0.66,
0,
929,
1,
0,
0,
0,
0,
3,
0
],
[
14,
0,
0.0323,
0.0081,
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0.66,
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1,
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0,
0,
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3,
0
],
[
14,
0,
0.0403,
0.0081,
0,
0... | [
"__abstract__ = 'fileutils delimited text file support'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id$'... |
# -*- coding: utf-8 -*-
__abstract__ = 'file related utility functions'
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license__ = 'See GLU license for terms by running: glu license'
__revision__ = '$Id$'
... | [
[
14,
0,
0.0101,
0.0034,
0,
0.66,
0,
929,
1,
0,
0,
0,
0,
3,
0
],
[
14,
0,
0.0135,
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0,
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1,
0,
0,
0,
0,
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0
],
[
14,
0,
0.0168,
0.0034,
0,
0... | [
"__abstract__ = 'file related utility functions'",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ = 'See GLU license for terms by running: glu license'",
"__revision__ = '$Id$'",
"i... |
# -*- coding: utf-8 -*-
from __future__ import division
__abstract__ = '''\
Fast linkage disequilibrium (LD) estimation for allelic
SNP genotype data'''
__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'
__license_... | [
[
1,
0,
0.0077,
0.0026,
0,
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0,
777,
0,
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0,
0,
777,
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],
[
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],
[
14,
0,
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0.0026,
0,
0.... | [
"from __future__ import division",
"__abstract__ = '''\\\nFast linkage disequilibrium (LD) estimation for allelic\nSNP genotype data'''",
"__copyright__ = 'Copyright (c) 2007-2009, BioInformed LLC and the U.S. Department of Health & Human Services. Funded by NCI under Contract N01-CO-12400.'",
"__license__ ... |
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