comparison varscan.py @ 6:2c66c4025db2 draft

planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c

5:d37adcc2ec03

    def _add_indel_info_flag_to_header(self, header):
        header.info.add(
            'INDEL', 0, 'Flag', 'Indicates that the variant is an INDEL'
        )

    def _compile_common_header(self, varcall_template, no_filters=False):
        # fix the header generated by VarScan
        # by adding reference and contig information
        common_header = pysam.VariantHeader()
        common_header.add_meta('reference', value=self.ref_genome)

            self._add_filters_to_header(common_header)
        # change the source information
        common_header.add_meta('source', value='varscan.py')
        # declare an INDEL flag for record INFO fields
        self._add_indel_info_flag_to_header(common_header)
        # take the remaining metadata from the template header produced by
        # VarScan
        with pysam.VariantFile(varcall_template, 'r') as original_data:
            varscan_header = original_data.header
        for sample in varscan_header.samples:
            common_header.samples.add(sample)
        common_header.merge(varscan_header)
        return common_header

    def pileup_masker(self, mask):
        def apply_mask_on_pileup(piled_items):
            for item, status in zip(piled_items, mask):
                if status:

                        # to avoid Warnings from htslib about missing contig
                        # info
                        self._add_ref_contigs_to_header(snp_invcf.header)
                        self._add_filters_to_header(snp_invcf.header)
                        self._add_indel_info_flag_to_header(snp_invcf.header)
                        with pysam.VariantFile(indel_f, 'r') as indel_invcf:
                            # fix the input header on the fly
                            # to avoid Warnings from htslib about missing
                            # contig info
                            self._add_ref_contigs_to_header(indel_invcf.header)
                            self._add_filters_to_header(indel_invcf.header)
                            self._add_indel_info_flag_to_header(
                                indel_invcf.header
                            )
                            for record in apply_filters(
                                self._merge_generator(
                                    snp_invcf,
                                    self._indel_flagged_records(indel_invcf)
                                ),
                                **filter_args
                            ):
                                o.write(str(record))
                    try:
                        os.remove(snp_f)
                    except Exception:
                        pass

                        # to avoid Warnings from htslib about missing
                        # contig info and errors because of undeclared
                        # filters
                        self._add_ref_contigs_to_header(invcf.header)
                        self._add_filters_to_header(invcf.header)
                        for record in apply_filters(
                            invcf, **filter_args
                        ):
                            o.write(str(record))
                    try:
                        os.remove(f)
                    except Exception:
                        pass

                        # contig info and errors because of undeclared
                        # filters
                        self._add_ref_contigs_to_header(invcf.header)
                        self._add_filters_to_header(invcf.header)
                        self._add_indel_info_flag_to_header(invcf.header)
                        for record in apply_filters(
                            self._indel_flagged_records(invcf), **filter_args
                        ):
                            o.write(str(record))
                    try:
                        os.remove(f)
                    except Exception:
                        pass

6:2c66c4025db2

    def _add_indel_info_flag_to_header(self, header):
        header.info.add(
            'INDEL', 0, 'Flag', 'Indicates that the variant is an INDEL'
        )

    def _standardize_format_fields(self, header):
        """Add standard FORMAT key declarations to a VCF header."""

        format_field_specs = [
            ('GT', '1', 'String', 'Genotype'),
            ('GQ', '1', 'Integer', 'Genotype quality'),
            ('DP', '1', 'Integer', 'Read depth'),
            ('AD', 'R', 'Integer', 'Read depth for each allele'),
            ('ADF', 'R', 'Integer',
             'Read depth for each allele on the forward strand'),
            ('ADR', 'R', 'Integer',
             'Read depth for each allele on the reverse strand')
        ]
        # Existing FORMAT declarations cannot be overwritten.
        # The only viable strategy is to mark them as removed,
        # then merge the header with another one containing the
        # correct declarations. This is what is implemented below.
        temp_header = pysam.VariantHeader()
        for spec in format_field_specs:
            temp_header.formats.add(*spec)
            if spec[0] in header.formats:
                header.formats.remove_header(spec[0])
        header.merge(temp_header)

    def _compile_common_header(self, varcall_template, no_filters=False):
        # fix the header generated by VarScan
        # by adding reference and contig information
        common_header = pysam.VariantHeader()
        common_header.add_meta('reference', value=self.ref_genome)

            self._add_filters_to_header(common_header)
        # change the source information
        common_header.add_meta('source', value='varscan.py')
        # declare an INDEL flag for record INFO fields
        self._add_indel_info_flag_to_header(common_header)
        # generate standard FORMAT field declarations
        # including a correct AD declaration to prevent VarScan's
        # non-standard one from getting propagated
        self._standardize_format_fields(common_header)
        # take the remaining metadata from the template header produced by
        # VarScan
        with pysam.VariantFile(varcall_template, 'r') as original_data:
            varscan_header = original_data.header
        for sample in varscan_header.samples:
            common_header.samples.add(sample)
        common_header.merge(varscan_header)
        # don't propagate non-standard and redundant FORMAT keys written
        # by VarScan
        common_header.formats.remove_header('FREQ')
        common_header.formats.remove_header('RD')
        common_header.formats.remove_header('DP4')
        return common_header

    def _fix_read_gt_fields(self, read):
        """Migrate non-standard genotype fields to standard ones."""

        for gt_field in read.samples.values():
            # generate a standard AD field by combining VarScan's
            # RD and non-standard AD fields
            gt_field['AD'] = (gt_field['RD'], gt_field['AD'][0])
            # split VarScan's DP4 field into the standard fields
            # ADF and ADR
            gt_field['ADF'] = (
                int(gt_field['DP4'][0]), int(gt_field['DP4'][2])
            )
            gt_field['ADR'] = (
                int(gt_field['DP4'][1]), int(gt_field['DP4'][3])
            )
        # remove redundant fields
        # FREQ is easy to calculate from AD
        del read.format['FREQ']
        del read.format['RD']
        del read.format['DP4']

    def pileup_masker(self, mask):
        def apply_mask_on_pileup(piled_items):
            for item, status in zip(piled_items, mask):
                if status:

                        # to avoid Warnings from htslib about missing contig
                        # info
                        self._add_ref_contigs_to_header(snp_invcf.header)
                        self._add_filters_to_header(snp_invcf.header)
                        self._add_indel_info_flag_to_header(snp_invcf.header)
                        self._standardize_format_fields(snp_invcf.header)
                        with pysam.VariantFile(indel_f, 'r') as indel_invcf:
                            # fix the input header on the fly
                            # to avoid Warnings from htslib about missing
                            # contig info
                            self._add_ref_contigs_to_header(indel_invcf.header)
                            self._add_filters_to_header(indel_invcf.header)
                            self._add_indel_info_flag_to_header(
                                indel_invcf.header
                            )
                            self._standardize_format_fields(indel_invcf.header)
                            for record in apply_filters(
                                self._merge_generator(
                                    snp_invcf,
                                    self._indel_flagged_records(indel_invcf)
                                ),
                                **filter_args
                            ):
                                self._fix_read_gt_fields(record)
                                o.write(str(record))
                    try:
                        os.remove(snp_f)
                    except Exception:
                        pass

                        # to avoid Warnings from htslib about missing
                        # contig info and errors because of undeclared
                        # filters
                        self._add_ref_contigs_to_header(invcf.header)
                        self._add_filters_to_header(invcf.header)
                        self._standardize_format_fields(invcf.header)
                        for record in apply_filters(
                            invcf, **filter_args
                        ):
                            self._fix_read_gt_fields(record)
                            o.write(str(record))
                    try:
                        os.remove(f)
                    except Exception:
                        pass

                        # contig info and errors because of undeclared
                        # filters
                        self._add_ref_contigs_to_header(invcf.header)
                        self._add_filters_to_header(invcf.header)
                        self._add_indel_info_flag_to_header(invcf.header)
                        self._standardize_format_fields(invcf.header)
                        for record in apply_filters(
                            self._indel_flagged_records(invcf), **filter_args
                        ):
                            self._fix_read_gt_fields(record)
                            o.write(str(record))
                    try:
                        os.remove(f)
                    except Exception:
                        pass