def run(args=()): with open(TARGET, "w") as f: f.write("""\ ================================================== pbreports specifications (automatically generated) ================================================== """) for spec in os.listdir(SPEC_DIR): specfile = op.join(SPEC_DIR, spec) meta_rpt = MetaReport.from_json(specfile) if meta_rpt.id in blacklist: continue if meta_rpt.attributes: f.write("\n\n\n") f.write( "**{t}** ({d}):\n\n".format(t=meta_rpt.title, d=meta_rpt.id)) f.write("{n}\n\n".format(n=meta_rpt.description)) table = [] for attr in meta_rpt.attributes: row = [attr.id, attr.name, attr.description] table.append(row) HEADERS = ["Attribute ID", "Name", "Description"] f.write(tabulate(table, HEADERS, tablefmt="rst")) return 0
def setUp(self): self.meta_rpt = MetaReport.from_json(TEST_JSON) attributes = [] attributes.append( self.meta_rpt.get_meta_attribute("attribute1").as_attribute(1)) attributes.append( self.meta_rpt.get_meta_attribute("attribute2").as_attribute(2.2)) attributes.append( self.meta_rpt.get_meta_attribute("attribute3").as_attribute( "test_string")) plotgroups = [] plots = [] plots.append( self.meta_rpt.get_meta_plotgroup("plotgroup1").get_meta_plot( "plot1").as_plot(image=PLOT1_FILE, thumbnail=THUMBNAIL1_FILE)) plotgroups.append( self.meta_rpt.get_meta_plotgroup("plotgroup1").as_plotgroup( thumbnail=THUMBNAIL2_FILE, plots=plots)) tables = [] columns = [] columns.append( self.meta_rpt.get_meta_table("table1").get_meta_column( "column1").as_column(values=[1, 22, 142])) tables.append( self.meta_rpt.get_meta_table("table1").as_table(columns=columns)) columns = [] columns.append( self.meta_rpt.get_meta_table("table2").get_meta_column( "column1").as_column(values=[1.0, 2.1, 3.37])) columns.append( self.meta_rpt.get_meta_table("table2").get_meta_column( "column2").as_column(values=["string1", "string2", "string3"])) tables.append( self.meta_rpt.get_meta_table("table2").as_table(columns=columns)) self.rpt = self.meta_rpt.as_report(attributes=attributes, plotgroups=plotgroups, tables=tables) self.rpt = self.meta_rpt.apply_view(self.rpt)
def setUp(self): self.meta_rpt = MetaReport.from_json(TEST_JSON) attributes = [] attributes.append(self.meta_rpt.get_meta_attribute("attribute1").as_attribute(1)) attributes.append(self.meta_rpt.get_meta_attribute("attribute2").as_attribute(2.2)) attributes.append(self.meta_rpt.get_meta_attribute("attribute3").as_attribute("test_string")) plotgroups = [] plots = [] plots.append(self.meta_rpt.get_meta_plotgroup("plotgroup1").get_meta_plot("plot1").as_plot(image=PLOT1_FILE, thumbnail=THUMBNAIL1_FILE)) plotgroups.append(self.meta_rpt.get_meta_plotgroup("plotgroup1").as_plotgroup(thumbnail=THUMBNAIL2_FILE, plots=plots)) tables = [] columns = [] columns.append(self.meta_rpt.get_meta_table("table1").get_meta_column("column1").as_column(values=[1,22,142])) tables.append(self.meta_rpt.get_meta_table("table1").as_table(columns=columns)) columns = [] columns.append(self.meta_rpt.get_meta_table("table2").get_meta_column("column1").as_column(values=[1.0,2.1,3.37])) columns.append(self.meta_rpt.get_meta_table("table2").get_meta_column("column2").as_column(values=["string1","string2","string3"])) tables.append(self.meta_rpt.get_meta_table("table2").as_table(columns=columns)) self.rpt = self.meta_rpt.as_report(attributes=attributes,plotgroups=plotgroups,tables=tables)
from pbcommand.models.report import Report, Table, Column from pbreports.report.report_spec import (MetaAttribute, MetaPlotGroup, MetaPlot, MetaColumn, MetaTable, MetaReport) from pbcommand.models import TaskTypes, FileTypes, get_pbparser from pbcommand.cli import pbparser_runner from pbcommand.common_options import add_debug_option from pbcommand.utils import setup_log from pbcore.io import DataSet __version__ = '0.1.0' # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, 'specs/') LOADING_SPEC = op.join(SPEC_DIR, 'loading_xml.json') meta_rpt = MetaReport.from_json(LOADING_SPEC) class Constants(object): TOOL_ID = "pbreports.tasks.loading_report_xml" DRIVER_EXE = ("python -m pbreports.report.loading_xml " "--resolved-tool-contract ") DECIMALS = 3 T_LOADING = "loading_xml_table" C_CONTEXT = "collection_context" C_ZMWS = "productive_zmws" C_PROD_0 = "productivity_0" C_PROD_1 = "productivity_1" C_PROD_2 = "productivity_2" log = logging.getLogger(__name__)
MetaColumn, MetaTable, MetaReport) from pbcommand.validators import validate_dir, validate_file from pbcommand.cli.core import pacbio_args_runner from pbcommand.utils import setup_log from pbcore.io.FastqIO import FastqReader from pbreports.plot.helper import get_fig_axes_lpr log = logging.getLogger(__name__) __version__ = '1.2' # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, 'specs/') CCS_VAL_SPEC = op.join(SPEC_DIR, 'ccs_validator_report.json') meta_rpt = MetaReport.from_json(CCS_VAL_SPEC) class Constants(object): PG_CCS = "ccs_validator_group" P_RL = "readlength_hist" P_QV = "qv_hist" T_FASTQ = "fastq_table" C_FN = 'file_name' C_NREADS = 'n_reads' C_TOT_BASES = 'total_bases' C_READLENGTH = 'mean_readlength' C_QV = 'mean_qv'
from pbreports.plot.helper import (get_fig_axes_lpr, save_figure_with_thumbnail, set_tick_label_font_size, set_axis_label_font_size) from pbreports.util import add_base_and_plot_options log = logging.getLogger(__name__) __version__ = '0.1' # Import Mapping MetaReport _DIR_NAME = op.dirname(op.realpath(__file__)) SPEC_DIR = op.join(_DIR_NAME, 'specs/') CONTROL_SPEC = op.join(SPEC_DIR, 'control.json') meta_rpt = MetaReport.from_json(CONTROL_SPEC) CSV_COLUMN_MAP = { "ReadId": ("|S128", str), "Readlength": (int, int), "ReadScore": (float, float), "PassedFilter": (int, int) } class Constants(object): A_CONTROL_SEQ = "control_sequence" A_NCONTROL = "n_control_reads" A_FRAC_CONTROL = "frac_control_reads" A_ACCURACY = "control_subread_accuracy" A_N50 = "control_n50"
from pbcommand.cli import pbparser_runner from pbcommand.common_options import add_debug_option from pbcommand.utils import setup_log from pbreports.util import recfromcsv from pbreports.util import validate_nonempty_file log = logging.getLogger(__name__) __version__ = '0.3.1' # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, 'specs/') AAC_SPEC = op.join(SPEC_DIR, 'amplicon_analysis_consensus.json') meta_rpt = MetaReport.from_json(AAC_SPEC) class Constants(object): TOOL_ID = "pbreports.tasks.amplicon_analysis_consensus" def create_table(d, barcode): """Long Amplicon Analysis results table""" columns = [] if barcode: columns.append(Column("barcodename", header="")) columns.append(Column("coarsecluster", header=""))
from pbcommand.common_options import add_debug_option from pbcommand.models import FileTypes, get_pbparser from pbcommand.cli import pbparser_runner from pbcommand.utils import setup_log from pbcore.io import SubreadSet from pbreports.plot.helper import (get_fig_axes_lpr, save_figure_with_thumbnail, get_green) __version__ = '0.1.0' # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, 'specs/') ADAPTER_SPEC = op.join(SPEC_DIR, 'adapter_xml.json') meta_rpt = MetaReport.from_json(ADAPTER_SPEC) class Constants(object): TOOL_ID = "pbreports.tasks.adapter_report_xml" DRIVER_EXE = ("python -m pbreports.report.adapter_xml " "--resolved-tool-contract ") A_DIMERS = "adapter_dimers" A_SHORT_INSERTS = "short_inserts" PG_ADAPTER = "adapter_xml_plot_group" P_ADAPTER = "adapter_xml_plot" log = logging.getLogger(__name__)
from pbcommand.models import TaskTypes, FileTypes, get_pbparser from pbcommand.cli import pbparser_runner from pbcommand.common_options import add_debug_option from pbcore.io import SubreadSet from pbreports.plot.helper import (get_fig_axes_lpr, save_figure_with_thumbnail, get_green) from pbreports.util import compute_n50, continuous_dist_shaper __version__ = '0.1.0' # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, 'specs/') FILTER_SPEC = op.join(SPEC_DIR, 'filter_stats_xml.json') meta_rpt = MetaReport.from_json(FILTER_SPEC) class Constants(object): TOOL_ID = "pbreports.tasks.filter_stats_report_xml" DRIVER_EXE = ("python -m pbreports.report.filter_stats_xml " "--resolved-tool-contract ") A_NBASES = "nbases" A_NREADS = "nreads" A_READ_N50 = "read_n50" A_READ_LENGTH = "read_length" # A_READ_QUALITY = "read_quality" A_INSERT_LENGTH = "insert_length" # A_INSERT_QUALITY = "insert_quality"
def test_read_specs(self): for spec in os.listdir(SPEC_DIR): specfile = op.join(SPEC_DIR, spec) tmp_meta_rpt = MetaReport.from_json(specfile)
from pbcore.io import ContigSet from pbreports.plot.helper import (get_fig_axes_lpr, apply_histogram_data, get_blue) from pbreports.util import validate_file log = logging.getLogger(__name__) __version__ = '0.1.0.132615' # The last 6 digits is changelist # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, 'specs/') ISOSEQ_CLASSIFY_SPEC = op.join(SPEC_DIR, 'isoseq_classify.json') meta_rpt = MetaReport.from_json(ISOSEQ_CLASSIFY_SPEC) class Constants(object): TOOL_ID = "pbreports.tasks.isoseq_classify" DRIVER_EXE = "python -m pbreports.report.isoseq_classify --resolved-tool-contract " """Names used within plot groups.""" R_ID = meta_rpt.id # PlotGroup PG_READLENGTH = "fulllength_nonchimeric_readlength_group" # Plots P_READLENGTH = "fulllength_nonchimeric_readlength_hist" # Table
from pbcommand.models import get_pbparser, FileTypes from pbreports.report.streaming_utils import PlotViewProperties from pbreports.plot.helper import (get_fig_axes_lpr, apply_line_data, Line) from pbreports.report.mapping_stats import * from pbreports.report.mapping_stats import Constants as BaseConstants from pbreports.report.ccs import create_plot from pbreports.report.report_spec import (MetaAttribute, MetaPlotGroup, MetaPlot, MetaColumn, MetaTable, MetaReport) # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, 'specs/') MAPPING_STATS_CCS_SPEC = op.join(SPEC_DIR, 'mapping_stats_ccs.json') meta_rpt = MetaReport.from_json(MAPPING_STATS_CCS_SPEC) class Constants(BaseConstants): TOOL_ID = "pbreports.tasks.mapping_stats_ccs" DRIVER_EXE = "python -m pbreports.report.mapping_stats_ccs --resolved-tool-contract" T_STATS = "mapping_stats_table" PG_READ_CONCORDANCE = "ccs_read_concordance_group" P_READ_CONCORDANCE = "concordance_plot" PG_READLENGTH = "ccs_readlength_group" PG_QV_CALIBRATION = "qv_calibration_group" P_QV_CALIBRATION = "qv_calibration_plot" A_NREADS = "mapped_reads_n" A_READLENGTH = "mapped_readlength_mean"
from pbcommand.cli import pbparser_runner from pbcommand.common_options import add_debug_option from pbcommand.utils import setup_log from pbcore.io.GffIO import GffReader import pbreports.plot.helper as PH __version__ = '2.0' log = logging.getLogger() # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, 'specs/') MOTIF_SPEC = op.join(SPEC_DIR, 'motifs.json') meta_rpt = MetaReport.from_json(MOTIF_SPEC) class Constants(object): R_ID = meta_rpt.id T_ID = "motif_records" # Plot Groups PG_MOD_QV = 'modification_qvs' P_MOD_QV = "motifs" PG_MOD = 'modifications' P_MOD_COV = 'mod_qv_coverage' P_MOD_HIST = 'qmod_hist'
from pbcommand.models import FileTypes, get_pbparser from pbcommand.cli import pbparser_runner from pbcommand.utils import setup_log from pbcore.io import openDataSet, BamReader from pbreports.util import movie_to_cell, path_to_movie log = logging.getLogger(__name__) __version__ = '2.0' # Import Mapping MetaReport _DIR_NAME = op.dirname(op.realpath(__file__)) SPEC_DIR = op.join(_DIR_NAME, 'specs/') OV_SPEC = op.join(SPEC_DIR, 'overview.json') meta_rpt = MetaReport.from_json(OV_SPEC) class Constants(object): TOOL_ID = "pbreports.tasks.overview" TOOL_NAME = "Overview report" DRIVER_EXE = "python -m pbreports.report.overview --resolved-tool-contract " A_NCELLS = "ncells" A_NMOVIES = "nmovies" def run(dataset_file): """Reads in the input.fofn and counts movies and cells. Outputs in XML.""" with openDataSet(dataset_file) as ds: movies = None
from pbreports.util import compute_n50 from pbreports.report.streaming_utils import (PlotViewProperties, to_plot_groups, custom_subread_length_histogram) from pbreports.model.aggregators import (BaseAggregator, SumAggregator, HistogramAggregator, MaxAggregator, MeanAggregator, CountAggregator) log = logging.getLogger(__name__) __version__ = '1.2' # Import Mapping MetaReport _DIR_NAME = op.dirname(op.realpath(__file__)) SPEC_DIR = op.join(_DIR_NAME, 'specs/') FS_SPEC = op.join(SPEC_DIR, 'filter_subread.json') meta_rpt = MetaReport.from_json(FS_SPEC) class Constants(object): """Ids used for Report, Table, PlotGroup, Plot, Attributes, Using an a prefix for autocomplete """ R_ID = meta_rpt.id # Table #T_MY_ID = '' # Plot Groups PG_SUBREAD_LENGTH = 'subread'
def setUp(self): self.meta_rpt = MetaReport.from_json(TEST_JSON)
from pbcommand.models import TaskTypes, FileTypes, get_pbparser from pbcommand.cli import pbparser_runner from pbcommand.common_options import add_debug_option from pbcore.io import SubreadSet from pbreports.plot.helper import (get_fig_axes_lpr, save_figure_with_thumbnail, get_green) from pbreports.util import compute_n50, continuous_dist_shaper __version__ = '0.1.0' # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, 'specs/') FILTER_SPEC = op.join(SPEC_DIR, 'filter_stats_xml.json') meta_rpt = MetaReport.from_json(FILTER_SPEC) class Constants(object): TOOL_ID = "pbreports.tasks.filter_stats_report_xml" DRIVER_EXE = ("python -m pbreports.report.filter_stats_xml " "--resolved-tool-contract ") A_NBASES = "nbases" A_NREADS = "nreads" A_READ_N50 = "read_n50" A_READ_LENGTH = "read_length" # A_READ_QUALITY = "read_quality" A_INSERT_LENGTH = "insert_length" # A_INSERT_QUALITY = "insert_quality" READ_ATTR = [A_NBASES, A_NREADS, A_READ_LENGTH, A_READ_N50]
from pbcommand.models import get_pbparser, FileTypes from pbreports.report.streaming_utils import PlotViewProperties from pbreports.plot.helper import get_fig_axes_lpr, apply_line_data, Line from pbreports.report.mapping_stats import * from pbreports.report.mapping_stats import Constants as BaseConstants from pbreports.report.ccs import create_plot from pbreports.report.report_spec import MetaAttribute, MetaPlotGroup, MetaPlot, MetaColumn, MetaTable, MetaReport # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, "specs/") MAPPING_STATS_CCS_SPEC = op.join(SPEC_DIR, "mapping_stats_ccs.json") meta_rpt = MetaReport.from_json(MAPPING_STATS_CCS_SPEC) class Constants(BaseConstants): TOOL_ID = "pbreports.tasks.mapping_stats_ccs" DRIVER_EXE = "python -m pbreports.report.mapping_stats_ccs --resolved-tool-contract" T_STATS = "mapping_stats_table" PG_READ_CONCORDANCE = "ccs_read_concordance_group" P_READ_CONCORDANCE = "concordance_plot" PG_READLENGTH = "ccs_readlength_group" PG_QV_CALIBRATION = "qv_calibration_group" P_QV_CALIBRATION = "qv_calibration_plot" A_NREADS = "mapped_reads_n" A_READLENGTH = "mapped_readlength_mean"
from pbreports.report.coverage import ContigCoverage from pbreports.util import compute_n50 import pbreports.plot.helper as PH log = logging.getLogger(__name__) __version__ = '0.4' __all__ = ['make_polished_assembly_report', 'ContigInfo', 'get_parser'] # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, 'specs/') POLISHED_ASSEMBLY_SPEC = op.join(SPEC_DIR, 'polished_assembly.json') meta_rpt = MetaReport.from_json(POLISHED_ASSEMBLY_SPEC) class Constants(object): TOOL_ID = "pbreports.tasks.polished_assembly" A_N_CONTIGS = "polished_contigs" A_MAX_LEN = "max_contig_length" A_N50_LEN = "n_50_contig_length" A_SUM_LEN = "sum_contig_lengths" PG_COVERAGE = "coverage_based" P_COVERAGE = "cov_vs_qual" def make_polished_assembly_report(report, gff, fastq, output_dir): """ Entry to report. :param gff: (str) path to alignment_summary.gff :param fastq: (str) path to polished fastq file
from pbcommand.cli import pbparser_runner from pbcommand.models.report import Report, Table, Column from pbreports.report.report_spec import MetaAttribute, MetaPlotGroup, MetaPlot, MetaColumn, MetaTable, MetaReport from pbcommand.models import FileTypes, get_pbparser from pbcommand.utils import setup_log from pbcore.io import openDataSet, BarcodeSet log = logging.getLogger(__name__) __version__ = "0.6" # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, "specs/") BC_SPEC = op.join(SPEC_DIR, "barcode.json") meta_rpt = MetaReport.from_json(BC_SPEC) class Constants(object): TOOL_ID = "pbreports.tasks.barcode_report" TOOL_NAME = "barcode_report" DRIVER_EXE = "python -m pbreports.report.barcode --resolved-tool-contract" C_BARCODE = "barcode" C_NREADS = "number_of_reads" C_NBASES = "number_of_bases" def _labels_reads_iterator(reads, barcodes, subreads=True): with openDataSet(reads) as ds: for er in ds.externalResources: if er.barcodes != barcodes:
from pbcommand.utils import setup_log import pbreports.plot.helper as PH from pbreports.util import (add_base_and_plot_options, add_base_options_pbcommand) from pbreports.util import Constants as BaseConstants log = logging.getLogger(__name__) __version__ = '2.1' # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, 'specs/') MOD_SPEC = op.join(SPEC_DIR, 'modifications.json') meta_rpt = MetaReport.from_json(MOD_SPEC) class Constants(BaseConstants): TOOL_ID = "pbreports.tasks.modifications_report" DRIVER_EXE = "python -m pbreports.report.modifications --resolved-tool-contract" PG_KIN = "kinetic_detections" P_SCAT = "kinetic_scatter" P_HIST = "kinetic_histogram" def _create_fig_template(dims=(8, 6), facecolor='#ffffff', gridcolor='#e0e0e0'): fig, ax = PH.get_fig_axes_lpr(dims=dims) ax = fig.add_subplot(111) ax.axesPatch.set_facecolor(facecolor) ax.grid(color=gridcolor, linewidth=0.5, linestyle='-') ax.set_axisbelow(True)
from pbcore.io import GffReader, ReferenceSet from pbreports.util import (openReference, add_base_options_pbcommand, get_top_contigs_from_ref_entry) import pbreports.plot.helper as PH log = logging.getLogger(__name__) __version__ = '0.1' # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, 'specs/') VARIANTS_SPEC = op.join(SPEC_DIR, 'variants.json') meta_rpt = MetaReport.from_json(VARIANTS_SPEC) class Constants(object): TOOL_ID = "pbreports.tasks.variants_report" DRIVER_EXE = "python -m pbreports.report.variants --resolved-tool-contract " MAX_CONTIGS_ID = "pbreports.task_options.max_contigs" MAX_CONTIGS_DEFAULT = 25 MEAN_CONTIG_LENGTH = "mean_contig_length" MEAN_BASES_CALLED = "weighted_mean_bases_called" MEAN_CONCORDANCE = "weighted_mean_concordance" MEAN_COVERAGE = "weighted_mean_coverage" LONGEST_CONTIG = "longest_contig_name" T_STATS = "consensus_table" C_CONTIG_NAME = "contig_name" C_CONTIG_LEN = "contig_len" C_BASES_CALLED = "bases_called"
from pbcommand.common_options import add_debug_option from pbcommand.cli import pbparser_runner from pbcommand.utils import setup_log from pbcore.io import AlignmentSet from pbreports.util import movie_to_cell, add_base_options_pbcommand log = logging.getLogger(__name__) __version__ = '0.1' # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, 'specs/') SAT_SPEC = op.join(SPEC_DIR, 'sat.json') meta_rpt = MetaReport.from_json(SAT_SPEC) class Constants(object): TOOL_ID = "pbreports.tasks.sat_report" DRIVER_EXE = "python -m pbreports.report.sat --resolved-tool-contract " A_INSTRUMENT = "instrument" A_COVERAGE = "coverage" A_CONCORDANCE = "concordance" A_READLENGTH = "mapped_readlength_mean" A_READS = "reads_in_cell" V_COVERAGE = "weighted_mean_bases_called" V_CONCORDANCE = "weighted_mean_concordance" M_READLENGTH = "mapped_readlength_mean"
from pbcommand.utils import setup_log from pbcore.io import ContigSet from pbreports.plot.helper import (get_fig_axes_lpr, apply_histogram_data, get_blue) from pprint import pformat log = logging.getLogger(__name__) __version__ = '0.1.0.132615' # The last 6 digits is changelist # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, 'specs/') ISOSEQ_CLUSTER_SPEC = op.join(SPEC_DIR, 'isoseq_cluster.json') meta_rpt = MetaReport.from_json(ISOSEQ_CLUSTER_SPEC) class Constants(object): TOOL_ID = "pbreports.tasks.isoseq_cluster" DRIVER_EXE = "python -m pbreports.report.isoseq_cluster --resolved-tool-contract" """Names used within plot groups.""" R_ID = meta_rpt.id # Attributes A_LENGTH = "avg_consensus_isoform_length" A_CONSENSUS = "num_consensus_isoforms" A_BASES = "num_total_bases" # PlotGroup PG_READLENGTH = "consensus_isoforms_readlength_group"
from pbcommand.models import FileTypes, get_pbparser from pbcommand.cli import pbparser_runner from pbcommand.utils import setup_log from pbcore.io import openDataSet, BamReader from pbreports.util import movie_to_cell, path_to_movie log = logging.getLogger(__name__) __version__ = '2.0' # Import Mapping MetaReport _DIR_NAME = op.dirname(op.realpath(__file__)) SPEC_DIR = op.join(_DIR_NAME, 'specs/') OV_SPEC = op.join(SPEC_DIR, 'overview.json') meta_rpt = MetaReport.from_json(OV_SPEC) class Constants(object): TOOL_ID = "pbreports.tasks.overview" TOOL_NAME = "Overview report" DRIVER_EXE = "python -m pbreports.report.overview --resolved-tool-contract " A_NCELLS = "ncells" A_NMOVIES = "nmovies" def run(dataset_file): """Reads in the input.fofn and counts movies and cells. Outputs in XML.""" with openDataSet(dataset_file) as ds: movies = None movies = set([]) for file_name in ds.toExternalFiles():
from pbreports.report.report_spec import (MetaAttribute, MetaPlotGroup, MetaPlot, MetaColumn, MetaTable, MetaReport) from pbcommand.models import TaskTypes, FileTypes, get_pbparser from pbcommand.cli import pbparser_runner from pbcommand.common_options import add_debug_option from pbcommand.utils import setup_log from pbcore.io import DataSet __version__ = '0.1.0' # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, 'specs/') LOADING_SPEC = op.join(SPEC_DIR, 'loading_xml.json') meta_rpt = MetaReport.from_json(LOADING_SPEC) class Constants(object): TOOL_ID = "pbreports.tasks.loading_report_xml" DRIVER_EXE = ("python -m pbreports.report.loading_xml " "--resolved-tool-contract ") DECIMALS = 3 T_LOADING = "loading_xml_table" C_CONTEXT = "collection_context" C_ZMWS = "productive_zmws" C_PROD_0 = "productivity_0" C_PROD_1 = "productivity_1" C_PROD_2 = "productivity_2"
save_figure_with_thumbnail, set_tick_label_font_size, set_axis_label_font_size) from pbreports.util import add_base_and_plot_options log = logging.getLogger(__name__) __version__ = '0.1' # Import Mapping MetaReport _DIR_NAME = op.dirname(op.realpath(__file__)) SPEC_DIR = op.join(_DIR_NAME, 'specs/') CONTROL_SPEC = op.join(SPEC_DIR, 'control.json') meta_rpt = MetaReport.from_json(CONTROL_SPEC) CSV_COLUMN_MAP = {"ReadId": ("|S128", str), "Readlength": (int, int), "ReadScore": (float, float), "PassedFilter": (int, int)} class Constants(object): A_CONTROL_SEQ = "control_sequence" A_NCONTROL = "n_control_reads" A_FRAC_CONTROL = "frac_control_reads" A_ACCURACY = "control_subread_accuracy" A_N50 = "control_n50" A_PCT95 = "control_95_percentile_readlength" A_LENGTH = "control_mean_readlength"
from pbcommand.cli import pbparser_runner from pbcommand.utils import setup_log from pbcore.io import GffReader, ReferenceSet from pbreports.util import add_base_options, openReference, \ add_base_options_pbcommand log = logging.getLogger(__name__) __version__ = '0.1' # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, 'specs/') VARS_SPEC = op.join(SPEC_DIR, 'top_variants.json') meta_rpt = MetaReport.from_json(VARS_SPEC) class Constants(object): R_ID = meta_rpt.id TOOL_ID = "pbreports.tasks.top_variants" DRIVER_EXE = "python -m pbreports.report.top_variants --resolved-tool-contract" HOW_MANY_ID = "pbreports.task_options.how_many" BATCH_SORT_SIZE_ID = "pbreports.task_options.batch_sort_size" HOW_MANY_DEFAULT = 100 BATCH_SORT_SIZE_DEFAULT = 10000 T_MINOR = "top_minor_variants_table" C_SEQ = 'sequence' C_POS = 'position' C_VAR = 'variant' C_TYP = 'type'
from pbcommand.cli import pbparser_runner from pbcommand.utils import setup_log from pbcore.io import ConsensusReadSet, BarcodeSet from pbreports.plot.helper import (get_fig_axes_lpr, apply_histogram_data, get_blue, get_green, Line, apply_line_data) from pbreports.util import accuracy_as_phred_qv log = logging.getLogger(__name__) __version__ = '0.44' # Import MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, 'specs/') CCS_SPEC = op.join(SPEC_DIR, 'ccs.json') meta_rpt = MetaReport.from_json(CCS_SPEC) class Constants(object): """ ids for the core Report objects (e.g., Plot, PlotGroup, etc...)""" TOOL_ID = "pbreports.tasks.ccs_report" TOOL_NAME = "ccs_report" DRIVER_EXE = "python -m pbreports.report.ccs --resolved-tool-contract" R_ID = meta_rpt.id # PlotGroup PG_READLENGTH = 'readlength_group' PG_ACCURACY = "accuracy_group" PG_NPASSES = "npasses_hist"
apply_line_fill_data, apply_histogram_data, LineFill, save_figure_with_thumbnail) from pbreports.report.report_spec import (MetaAttribute, MetaPlotGroup, MetaPlot, MetaColumn, MetaTable, MetaReport) log = logging.getLogger(__name__) __version__ = '0.1' # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, 'specs/') COVERAGE_SPEC = op.join(SPEC_DIR, 'coverage.json') meta_rpt = MetaReport.from_json(COVERAGE_SPEC) class Constants(object): TOOL_ID = "pbreports.tasks.coverage_report" DRIVER_EXE = "python -m pbreports.report.coverage --resolved-tool-contract " MAX_CONTIGS_ID = "pbreports.task_options.max_contigs" MAX_CONTIGS_DEFAULT = 25 COLOR_STEEL_BLUE_DARK = '#226F96' COLOR_STEEL_BLUE_LIGHT = '#2B8CBE' A_COVERAGE = "depth_coverage_mean" A_MISSING = "missing_bases_pct" PG_COVERAGE = "coverage_plots"
from pbreports.plot.helper import (get_fig_axes_lpr, apply_line_data, apply_line_fill_data, apply_histogram_data, LineFill, save_figure_with_thumbnail) from pbreports.report.report_spec import (MetaAttribute, MetaPlotGroup, MetaPlot, MetaColumn, MetaTable, MetaReport) log = logging.getLogger(__name__) __version__ = '0.1' # Import Mapping MetaReport _DIR_NAME = os.path.dirname(os.path.realpath(__file__)) SPEC_DIR = os.path.join(_DIR_NAME, 'specs/') COVERAGE_SPEC = op.join(SPEC_DIR, 'coverage.json') meta_rpt = MetaReport.from_json(COVERAGE_SPEC) class Constants(object): TOOL_ID = "pbreports.tasks.coverage_report" DRIVER_EXE = "python -m pbreports.report.coverage --resolved-tool-contract " MAX_CONTIGS_ID = "pbreports.task_options.max_contigs" MAX_CONTIGS_DEFAULT = 25 COLOR_STEEL_BLUE_DARK = '#226F96' COLOR_STEEL_BLUE_LIGHT = '#2B8CBE' A_COVERAGE = "depth_coverage_mean" A_MISSING = "missing_bases_pct" PG_COVERAGE = "coverage_plots"