How to use the multiqc.modules.base_module.BaseMultiqcModule function in multiqc

from multiqc.modules.base_module import BaseMultiqcModule
import logging
from collections import OrderedDict
from multiqc import config
from multiqc.plots import bargraph

log = logging.getLogger(__name__)


class MultiqcModule(BaseMultiqcModule):
    def __init__(self):
        # Initialise the parent object
        super(MultiqcModule, self).__init__(name='HiCExplorer', anchor='hicexplorer',
                                            href="https://hicexplorer.readthedocs.io",
                                            info=" addresses the common tasks of Hi-C analysis from processing to visualization.")

        self.mod_data = dict()
        for file in self.find_log_files('hicexplorer'):
            if file['s_name'] != "QC_table":
                s_name = file['root'] + "_" + file['s_name']
                
                self.mod_data[s_name] = self.parse_logs(file['f'])
                self.mod_data[s_name]['File'][0] = self.clean_s_name(file['root'] + "_" + s_name + "_" + self.mod_data[s_name]['File'][0], file['root'])
            
                self.add_data_source(file)

#!/usr/bin/env python

""" MultiQC module to parse output from Flexbar """

from __future__ import print_function
from collections import OrderedDict
import logging
import re

from multiqc.plots import bargraph
from multiqc.modules.base_module import BaseMultiqcModule

# Initialise the logger
log = logging.getLogger(__name__)

class MultiqcModule(BaseMultiqcModule):

    def __init__(self):

        # Initialise the parent object
        super(MultiqcModule, self).__init__(name='Flexbar', anchor='flexbar',
        href='https://github.com/seqan/flexbar',
        info="is a barcode and adapter removal tool.")

        # Parse logs
        self.flexbar_data = dict()
        for f in self.find_log_files('flexbar', filehandles=True):
            self.parse_flexbar(f)

        # Filter to strip out ignored sample names
        self.flexbar_data = self.ignore_samples(self.flexbar_data)

""" MultiQC module to parse output from methylQA """

from __future__ import print_function
from collections import OrderedDict
import logging
import os
import re

from multiqc.plots import linegraph
from multiqc.modules.base_module import BaseMultiqcModule

# Initialise the logger
log = logging.getLogger(__name__)

class MultiqcModule(BaseMultiqcModule):

    def __init__(self):

        # Initialise the parent object
        super(MultiqcModule, self).__init__(name='methylQA', anchor='methylqa',
        target='methylQA', href="http://methylqa.sourceforge.net/",
        info=" - a methylation sequencing data quality assessment tool.")

        # Find and load any methylQA reports
        self.methylqa_data = dict()
        self.methylqa_coverage_counts = dict()
        self.methylqa_coverage_percentages = dict()
        for f in self.find_log_files('methylQA'):
            self.parse_methylqa_logs(f)

        # Filter to strip out ignored sample names

#!/usr/bin/env python

""" MultiQC module to parse output from HiCUP """

from __future__ import print_function
from collections import OrderedDict
import logging

from multiqc import config
from multiqc.plots import bargraph
from multiqc.modules.base_module import BaseMultiqcModule

# Initialise the logger
log = logging.getLogger(__name__)

class MultiqcModule(BaseMultiqcModule):
    """ HiCUP module, parses log files saved by HiCUP. """

    def __init__(self):

        # Initialise the parent object
        super(MultiqcModule, self).__init__(name='HiCUP', anchor='hicup',
        href='http://www.bioinformatics.babraham.ac.uk/projects/hicup/',
        info="(Hi-C User Pipeline) is a tool for mapping and performing "\
         "quality control on Hi-C data.")

        # Find and load any HiCUP summary reports
        self.hicup_data = dict()
        for f in self.find_log_files('hicup'):
            self.parse_hicup_logs(f)

        # Filter to strip out ignored sample names

#!/usr/bin/env python
""" MultiQC module to parse output from sequana"""
import logging
import os
import re

from multiqc import config
from multiqc.modules.base_module import BaseMultiqcModule
from multiqc.plots import linegraph, table, heatmap, bargraph

log = logging.getLogger('multiqc.sequana/quality_control')


class MultiqcModule(BaseMultiqcModule):

    def __init__(self):

        # Initialise the parent object
        super(MultiqcModule, self).__init__(
            name='Sequana/quality_control',
            anchor='sequana_quality_control',
            target='sequana_quality_control',
            href='http://github.com/sequana/sequana/',
            info="(sequana pipelines)")

        self.data = {}
        for myfile in self.find_log_files("sequana/quality_control"):
            thisdata =  self.parse_logs(myfile["f"])
            name = thisdata["project"]
            self.data[name] = self.parse_logs(myfile["f"])

""" MultiQC module to parse output from Samblaster """

from __future__ import print_function
import os
from collections import OrderedDict
import logging
import re
from multiqc.plots import bargraph
from multiqc.modules.base_module import BaseMultiqcModule

# Initialise the logger
log = logging.getLogger(__name__)


class MultiqcModule(BaseMultiqcModule):
    """ Samblaster """

    def __init__(self):
        # Initialise the parent object
        super(MultiqcModule, self).__init__(name='Samblaster', anchor='samblaster',
                                            href="https://github.com/GregoryFaust/samblaster",
                                            info="is a tool to mark duplicates and extract discordant and split reads from sam files.")

        self.samblaster_data = dict()
        for f in self.find_log_files('samblaster', filehandles=True):
            self.parse_samblaster(f)

        # Filter to strip out ignored sample names
        self.samblaster_data = self.ignore_samples(self.samblaster_data)

        if len(self.samblaster_data) == 0:

import logging
import os
import re
from collections import defaultdict
import yaml

from multiqc import config
from multiqc.modules.base_module import BaseMultiqcModule
from multiqc.plots import linegraph, table, heatmap, bargraph
#from multiqc_sequana import srna

# Initialise the logger
log = logging.getLogger('multiqc.sequana/pacbio_qc')


class MultiqcModule(BaseMultiqcModule):

    def __init__(self):

        # Initialise the parent object
        super(MultiqcModule, self).__init__(
            name='Sequana/pacbio',    # name that appears at the top
            anchor='sequana',  # ??
            target='sequana',  # Name show that link to the following href
            href='http://github.com/sequana/sequana/',
            info="pipelines multi Summary")

        self.sequana_data = {}
        for myfile in self.find_log_files("sequana/pacbio_qc"):
            #print( myfile['f'] )       # File contents
            #print( myfile['s_name'] )  # Sample name (from cleaned filename)
            #print( myfile['fn'] )      # Filename

else:
                log.info("{}: Found {} samples ({})".format(module_id, len(mod['data']), mod['config'].get('plot_type')))

    # Sort sections if we have a config option for order
    mod_order = getattr(config, 'custom_content', {}).get('order', [])
    sorted_modules = [parsed_mod for parsed_mod in parsed_modules if parsed_mod.anchor not in mod_order ]
    sorted_modules.extend([parsed_mod for mod_id in mod_order for parsed_mod in parsed_modules if parsed_mod.anchor == mod_id ])

    # If we only have General Stats columns then there are no module outputs
    if len(sorted_modules) == 0:
        raise UserWarning

    return sorted_modules


class MultiqcModule(BaseMultiqcModule):
    """ Module class, used for each custom content type """

    def __init__(self, c_id, mod):

        modname = mod['config'].get('section_name', c_id.replace('_', ' ').title())
        if modname == '' or modname is None:
            modname = 'Custom Content'

        # Initialise the parent object
        super(MultiqcModule, self).__init__(
            name = modname,
            anchor = mod['config'].get('section_anchor', c_id),
            href = mod['config'].get('section_href'),
            info = mod['config'].get('description')
        )

#!/usr/bin/env python

""" MultiQC module to parse output from Preseq """

from __future__ import print_function
import logging
import numpy as np

from multiqc import config
from multiqc.plots import linegraph
from multiqc.modules.base_module import BaseMultiqcModule

# Initialise the logger
log = logging.getLogger(__name__)

class MultiqcModule(BaseMultiqcModule):

    def __init__(self):

        # Initialise the parent object
        super(MultiqcModule, self).__init__(name='Preseq', anchor='preseq',
        href='http://smithlabresearch.org/software/preseq/',
        info="""estimates the complexity of a library, showing how many additional
         unique reads are sequenced for increasing total read count.
         A shallow curve indicates complexity saturation. The dashed line
         shows a perfectly complex library where total reads = unique reads.""")

        # Find and load any Preseq reports
        self.preseq_data = dict()
        self.axis_label = ''
        self.counts_in_1x = None
        for f in self.find_log_files('preseq'):

""" MultiQC module to parse output from HOMER """
from __future__ import print_function
from collections import OrderedDict
import logging

from multiqc.modules.base_module import BaseMultiqcModule

# Import the HOMER submodules
from .findpeaks import FindPeaksReportMixin
from .tagdirectory import TagDirReportMixin

# Initialise the logger
log = logging.getLogger(__name__)


class MultiqcModule(BaseMultiqcModule, FindPeaksReportMixin, TagDirReportMixin):
    """ HOMER has a number of different commands and outputs.
    This MultiQC module supports some but not all. The code for
    each script is split into its own file and adds a section to
    the module output if logs are found. """

    def __init__(self):

        # Initialise the parent object
        super(MultiqcModule, self).__init__(name='HOMER', anchor='homer',
            href='http://homer.ucsd.edu/homer/',
            info="is a suite of tools for Motif Discovery and next-gen sequencing analysis.")


        # Set up class objects to hold parsed data
        self.general_stats_headers = OrderedDict()
        self.general_stats_data = dict()