Python PARAMSの例

コード例 #1

ファイル: RnaseqqcReport.py プロジェクト: sudlab/CGATPipelines

import random
from sklearn import manifold
from sklearn.metrics import euclidean_distances
from sklearn.preprocessing import scale as sklearn_scale
from sklearn.decomposition import PCA as sklearnPCA
from rpy2.robjects import r as R
import rpy2.robjects.pandas2ri as py2ri
from CGATReport.ResultBlock import ResultBlocks, ResultBlock
import seaborn
from CGATReport.Tracker import *
from CGATReport.Utils import PARAMS as P
import CGATPipelines.PipelineTracks as PipelineTracks
from CGATReport.Utils import PARAMS


DATABASE = PARAMS.get("readqc_backend", PARAMS.get("sql_backend", "sqlite:///./csvdb"))


class RnaseqqcTracker(TrackerSQL):

    """Define convenience tracks for plots"""

    def __init__(self, *args, **kwargs):
        TrackerSQL.__init__(self, *args, backend=DATABASE, **kwargs)


class SampleOverlap(RnaseqqcTracker):

    table = "sailfish_transcripts"

    def __call__(self, *args):

コード例 #2

ファイル: PeakcallingReport.py プロジェクト: CGATOxford/CGATPipelines

import itertools
import glob

from CGATReport.Tracker import *
from CGATReport.Utils import PARAMS as P
import CGATPipelines.Pipeline as Pipeline
import CGATPipelines.PipelineTracks as PipelineTracks
###################################################################
###################################################################
# parameterization

EXPORTDIR = P.get('calling_exportdir', P.get('exportdir', 'export'))
DATADIR = P.get('calling_datadir', P.get('datadir', '.'))
DATABASE = P.get('calling_backend', P.get('report_sql_backend', 'sqlite:///./csvdb'))

###################################################################
# cf. pipeline_chipseq.py
# This should be automatically gleaned from pipeline_chipseq.py
###################################################################
PARAMS_PIPELINE = Pipeline.peekParameters(".",
                                          "pipeline_chipseq.py")


Sample = PipelineTracks.Sample3

suffixes = ["export.txt.gz",
            "sra",
            "fastq.gz",
            "fastq.1.gz",
            "csfasta.gz"]

コード例 #3

ファイル: PeakcallingReport.py プロジェクト: Acribbs/CGATPipelines

import itertools
import glob

from CGATReport.Tracker import *
from CGATReport.Utils import PARAMS as P
import CGATPipelines.Pipeline as Pipeline
import CGATPipelines.PipelineTracks as PipelineTracks
###################################################################
###################################################################
# parameterization

EXPORTDIR = P.get('calling_exportdir', P.get('exportdir', 'export'))
DATADIR = P.get('calling_datadir', P.get('datadir', '.'))
DATABASE = P.get('calling_backend',
                 P.get('report_sql_backend', 'sqlite:///./csvdb'))

###################################################################
# cf. pipeline_chipseq.py
# This should be automatically gleaned from pipeline_chipseq.py
###################################################################
PARAMS_PIPELINE = Pipeline.peekParameters(".", "pipeline_chipseq.py")

Sample = PipelineTracks.Sample3

suffixes = ["export.txt.gz", "sra", "fastq.gz", "fastq.1.gz", "csfasta.gz"]

TRACKS = sum(
    itertools.chain([
        PipelineTracks.Tracks(Sample).loadFromDirectory([
            x for x in glob.glob("%s/*.%s" % (DATADIR, s)) if "input" not in x
        ], "%s/(\S+).%s" % (DATADIR, s)) for s in suffixes

コード例 #4

ファイル: Results.py プロジェクト: dormeight/CGATPipelines

import pandas as pd
import numpy as np
import sqlite3

from CGATReport.Tracker import SingleTableTrackerRows
from CGATReport.Tracker import SingleTableTrackerHistogram
from CGATReport.Tracker import *
from CGATReport.Utils import PARAMS as P

from IsoformReport import *

###############################################################################
# parse params
###############################################################################
DATABASE = P.get('', P.get('sql_backend', 'sqlite:///./csvdb'))
ANNOTATIONS_DATABASE = P.get('annotations_database')
###############################################################################
# trackers
###############################################################################


class SleuthResults(IsoformTracker):

    pattern = "(.*)_DEresults$"
    direction = ""
    where = "WHERE p_value NOT NULL"

    def __call__(self, track, slice=None):

        quantifier = track.split("_")[-2]

コード例 #5

ファイル: CaputreCTracker.py プロジェクト: sudlab/Capture_C

from CGATReport.Tracker import *
from CGATReport.Utils import PARAMS as P

PIPELINE_DB = P.get("capturec_database", P.get("database_name", None))


class CaptureCTracker(TrackerSQL):
    def __init__(self, *args, **kwags):

        if PIPELINE_DB is not None:
            self.backend = PIPELINE_DB

        TrackerSQL.__init__(self, *args, **kwargs)

コード例 #6

ファイル: IntervalReport.py プロジェクト: kevinrue/cgat-flow

from CGATReport.Tracker import *
from CGATReport.Utils import PARAMS as P

EXPORTDIR = P.get('motifs_exportdir',
                  P.get('report_exportdir', "export"))
DATADIR = P.get('motifs_datadir',
                P.get('report_datadir', "."))
DATABASE = P.get('motifs_backend',
                 P.get('report_backend', "sqlite:///./csvdb"))


class IntervalTracker(TrackerSQL):
    '''Define convenience tracks for plots'''

    def __init__(self, *args, **kwargs):
        TrackerSQL.__init__(self,
                            *args,
                            backend=DATABASE,
                            **kwargs)

コード例 #7

ファイル: RnaseqDiffExpressionReport.py プロジェクト: Charlie-George/cgat

import glob

from CGATReport.Tracker import *
from CGATReport.Utils import PARAMS as P
from collections import OrderedDict as odict

from CGATPipelines.PipelineGeneset import mapUCSCToEnsembl

# get from config file
UCSC_DATABASE = P["genome"]

###################################################################
###################################################################
# parameterization

EXPORTDIR = P.get(
    'rnaseqdiffexpression_exportdir', P.get('exportdir', 'export'))
DATADIR = P.get('rnaseqdiffexpression_datadir', P.get('datadir', '.'))
DATABASE = P.get('rnaseqdiffexpression_backend', P.get(
    'sql_backend', 'sqlite:///./csvdb'))

DATABASE_ANNOTATIONS = P['annotations_database']

###################################################################
# cf. pipeline_rnaseq.py
# This should be automatically gleaned from pipeline_rnaseq.py
###################################################################
import CGATPipelines.PipelineTracks as PipelineTracks

TRACKS = PipelineTracks.Tracks(PipelineTracks.Sample).loadFromDirectory(
    glob.glob("%s/*.bam" % DATADIR), "(\S+).bam")

コード例 #8

ファイル: RnaseqqcReport.py プロジェクト: wbyu/CGATPipelines

import itertools
import random
from sklearn import manifold
from sklearn.metrics import euclidean_distances
from sklearn.preprocessing import scale as sklearn_scale
from sklearn.decomposition import PCA as sklearnPCA
from rpy2.robjects import r as R
import rpy2.robjects.pandas2ri as py2ri
from CGATReport.ResultBlock import ResultBlocks, ResultBlock
import seaborn
from CGATReport.Tracker import *
from CGATReport.Utils import PARAMS
import CGATPipelines.Pipeline as Pipeline
import matplotlib.pyplot as plt

DATABASE = PARAMS.get('readqc_backend',
                      PARAMS.get('sql_backend', 'sqlite:///./csvdb'))


class imagesTracker(TrackerImages):
    '''Convience Tracker for globbing images for gallery plot'''
    def __init__(self, *args, **kwargs):
        Tracker.__init__(self, *args, **kwargs)
        if "glob" not in kwargs:
            raise ValueError("TrackerImages requires a:glob: parameter")
        self.glob = kwargs["glob"]


class RnaseqqcTracker(TrackerSQL):
    '''Define convenience tracks for plots'''
    def __init__(self, *args, **kwargs):
        TrackerSQL.__init__(self, *args, backend=DATABASE, **kwargs)

コード例 #9

ファイル: IntervalReport.py プロジェクト: kevinrue/cgat-flow

from CGATReport.Tracker import *
from CGATReport.Utils import PARAMS as P


###################################################################
###################################################################
# parameterization
EXPORTDIR = P.get('intervals_exportdir',
                  P.get('exportdir', 'export'))
DATADIR = P.get('intervals_datadir',
                P.get('datadir', '.'))
DATABASE = P.get('intervals_backend',
                 P.get('sql_backend', 'sqlite:///./csvdb'))


class IntervalTracker(TrackerSQL):

    '''Define convenience tracks for plots'''

    def __init__(self, *args, **kwargs):
        TrackerSQL.__init__(self, *args, backend=DATABASE, **kwargs)

コード例 #10

ファイル: Results.py プロジェクト: CGATOxford/CGATPipelines

import pandas as pd
import numpy as np
import sqlite3

from CGATReport.Tracker import SingleTableTrackerRows
from CGATReport.Tracker import SingleTableTrackerHistogram
from CGATReport.Tracker import *
from CGATReport.Utils import PARAMS as P

from IsoformReport import *

###############################################################################
# parse params
###############################################################################
DATABASE = P.get('', P.get('sql_backend', 'sqlite:///./csvdb'))
ANNOTATIONS_DATABASE = P.get('annotations_database')
###############################################################################
# trackers
###############################################################################


class SleuthResults(IsoformTracker):

    pattern = "(.*)_DEresults$"
    direction = ""
    where = "WHERE p_value NOT NULL"

    def __call__(self, track, slice=None):

        quantifier = track.split("_")[-2]

コード例 #11

ファイル: IntervalReport.py プロジェクト: Charlie-George/cgat

import os
import sys
import re
import types
import itertools
import glob

from CGATReport.Tracker import *
from CGATReport.Utils import PARAMS as P
from collections import OrderedDict as odict

EXPORTDIR = P.get('motifs_exportdir',
                  P.get('report_exportdir', "export"))
DATADIR = P.get('motifs_datadir',
                P.get('report_datadir', "."))
DATABASE = P.get('motifs_backend',
                 P.get('report_backend', "sqlite:///./csvdb"))


class IntervalTracker(TrackerSQL):
    '''Define convenience tracks for plots'''

    def __init__(self, *args, **kwargs):
        TrackerSQL.__init__(self,
                            *args,
                            backend=DATABASE,
                            **kwargs)

コード例 #12

ファイル: AnnotationReport.py プロジェクト: santayana/cgat

from CGATReport.Tracker import *
from CGATReport.Utils import PARAMS as P
from collections import OrderedDict as odict

###################################################################
# parameterization

EXPORTDIR = P.get('annotations_exportdir', P.get('exportdir', 'export'))
DATADIR = P.get('annotations_datadir', P.get('datadir', '.'))
DATABASE = P.get('annotations_backend',
                 P.get('sql_backend', 'sqlite:///./csvdb'))


class AnnotationTracker(TrackerSQL):
    '''Define convenience tracks for plots'''
    def __init__(self, *args, **kwargs):
        TrackerSQL.__init__(self, *args, backend=DATABASE, **kwargs)


class BedSummaryIntervals(TrackerSQL):
    pattern = '(.*)_bedsummary'

    def __call__(self, track):
        return self.getValue(
            "SELECT sum(nintervals) FROM %(track)s_bedsummary")


class BedSummaryIntervalsPerContig(TrackerSQL):
    pattern = '(.*)_bedsummary'

    def __call__(self, track):

コード例 #13

ファイル: Results.py プロジェクト: hainm/CGATPipelines

import pandas as pd
import numpy as np

from CGATReport.Tracker import SingleTableTrackerRows
from CGATReport.Tracker import SingleTableTrackerHistogram
from CGATReport.Tracker import *
from CGATReport.Utils import PARAMS as P

from IsoformReport import *

###############################################################################
# parse params
###############################################################################
DATABASE = P.get('', P.get('sql_backend', 'sqlite:///./csvdb'))


###############################################################################
# trackers
###############################################################################

class SleuthResults(IsoformTracker):

    pattern = "(.*)_DEresults$"
    direction = ""
    where = ""

    def __call__(self, track, slice=None):

        statement = '''
        SELECT A.gene_name, A.gene_id, A.transcript_id, A.transcript_biotype,
        A.control_mean AS expression, A.fold, A.l2fold AS log2_fold,

コード例 #14

ファイル: CaptureCTracker.py プロジェクト: sudlab/Capture_C

from CGATReport.Tracker import *
from CGATReport.Utils import PARAMS as P

PIPELINE_DB = P.get("capturec_database",
                    P.get("database_name",
                          None))

class CaptureCTracker(TrackerSQL):
    
    def __init__(self, *args, **kwargs):

        print PIPELINE_DB
        if PIPELINE_DB is not None:
            self.backend = "sqlite:///" + PIPELINE_DB

        TrackerSQL.__init__(self, *args,
                            **kwargs)

    

コード例 #15

ファイル: exomeReport.py プロジェクト: BioXiao/CGATPipelines

import re
from CGATReport.Tracker import *
from CGATReport.Utils import PARAMS as P

# get from config file
UCSC_DATABASE = "hg19"
EXPORTDIR = "export"

###################################################################
###################################################################
###################################################################
###################################################################
# Run configuration script
EXPORTDIR = P.get('exome_exportdir', P.get('exportdir', 'export'))
DATADIR = P.get('exome_datadir', P.get('datadir', '.'))
DATABASE = P.get('exome_backend', P.get('sql_backend', 'sqlite:///./csvdb'))

TRACKS = ['WTCHG_10997_01', 'WTCHG_10997_02']


###########################################################################
def splitLocus(locus):
    if ".." in locus:
        contig, start, end = re.match("(\S+):(\d+)\.\.(\d+)", locus).groups()
    elif "-" in locus:
        contig, start, end = re.match("(\S+):(\d+)\-(\d+)", locus).groups()

    return contig, int(start), int(end)


def linkToUCSC(contig, start, end):

コード例 #16

ファイル: RnaseqqcReport.py プロジェクト: gjaime/CGATPipelines

import random
from sklearn import manifold
from sklearn.metrics import euclidean_distances
from sklearn.preprocessing import scale as sklearn_scale
from sklearn.decomposition import PCA as sklearnPCA
from rpy2.robjects import r as R
import rpy2.robjects.pandas2ri as py2ri
from CGATReport.ResultBlock import ResultBlocks, ResultBlock
import seaborn
from CGATReport.Tracker import *
from CGATReport.Utils import PARAMS as P
import CGATPipelines.PipelineTracks as PipelineTracks
from CGATReport.Utils import PARAMS


DATABASE = PARAMS.get('readqc_backend', PARAMS.get('sql_backend', 'sqlite:///./csvdb'))


class RnaseqqcTracker(TrackerSQL):

    '''Define convenience tracks for plots'''

    def __init__(self, *args, **kwargs):
        TrackerSQL.__init__(self, *args, backend=DATABASE, **kwargs)


class SampleOverlap(RnaseqqcTracker):

    table = "sailfish_transcripts"

    def __call__(self, *args):

コード例 #17

ファイル: ReadqcReport.py プロジェクト: santayana/cgat

import types
import itertools
import glob

from CGATReport.Tracker import *
from CGATReport.Utils import PARAMS as P
from collections import OrderedDict as odict

from CGATReport.ResultBlock import ResultBlock, ResultBlocks
from CGATReport import Utils

###################################################################
###################################################################
# parameterization

EXPORTDIR = P.get('readqc_exportdir', P.get('exportdir', 'export'))
DATADIR = P.get('readqc_datadir', P.get('datadir', '.'))
DATABASE = P.get('readqc_backend', P.get('sql_backend', 'sqlite:///./csvdb'))

###################################################################
# cf. pipeline_rnaseq.py
# This should be automatically gleaned from pipeline_rnaseq.py
###################################################################
import CGATPipelines.PipelineTracks as PipelineTracks

TRACKS = PipelineTracks.Tracks(PipelineTracks.Sample).loadFromDirectory(
    glob.glob("%s/*.sra" % DATADIR), "(\S+).sra") +\
    PipelineTracks.Tracks(PipelineTracks.Sample).loadFromDirectory(
        glob.glob("%s/*.fastq.gz" % DATADIR), "(\S+).fastq.gz") +\
    PipelineTracks.Tracks(PipelineTracks.Sample).loadFromDirectory(
        glob.glob("%s/*.fastq.1.gz" % DATADIR), "(\S+).fastq.1.gz") +\

コード例 #18

ファイル: RnaseqDiffExpressionReport.py プロジェクト: santayana/cgat

import glob

from CGATReport.Tracker import *
from CGATReport.Utils import PARAMS as P
from collections import OrderedDict as odict

from CGATPipelines.PipelineGeneset import mapUCSCToEnsembl

# get from config file
UCSC_DATABASE = P["genome"]

###################################################################
###################################################################
# parameterization

EXPORTDIR = P.get('rnaseqdiffexpression_exportdir',
                  P.get('exportdir', 'export'))
DATADIR = P.get('rnaseqdiffexpression_datadir', P.get('datadir', '.'))
DATABASE = P.get('rnaseqdiffexpression_backend',
                 P.get('sql_backend', 'sqlite:///./csvdb'))

DATABASE_ANNOTATIONS = P['annotations_database']

###################################################################
# cf. pipeline_rnaseq.py
# This should be automatically gleaned from pipeline_rnaseq.py
###################################################################
import CGATPipelines.PipelineTracks as PipelineTracks

TRACKS = PipelineTracks.Tracks(PipelineTracks.Sample).loadFromDirectory(
    glob.glob("%s/*.bam" % DATADIR), "(\S+).bam")