- sctools package
- Submodules
- sctools.bam module
- Tools for Manipulating SAM/BAM format files
AlignmentSortOrder
QueryNameSortOrder
SortError
SubsetAlignments
TagSortableRecord
Tagger
get_barcode_for_alignment()
get_barcodes_from_bam()
get_tag_or_default()
iter_cell_barcodes()
iter_genes()
iter_molecule_barcodes()
iter_tag_groups()
merge_bams()
sort_by_tags_and_queryname()
split()
verify_sort()
write_barcodes_to_bins()
- sctools.barcode module
- sctools.encodings module
- sctools.fastq module
- sctools.gtf module
- sctools.platform module
- sctools.reader module
- sctools.stats module
- sctools.bam module
- Submodules
- sctools.metrics package
- Submodules
- sctools.metrics.aggregator module
- sctools.metrics.gatherer module
- Sequence Metric Gatherers
GatherCellMetrics
- sctools.metrics.gatherer.MetricGatherer
- sctools.metrics.gatherer.GatherCellMetrics
- sctools.metrics.gatherer.GatherGeneMetrics
GatherGeneMetrics
- sctools.metrics.gatherer.MetricGatherer
- sctools.metrics.gatherer.GatherCellMetrics
- sctools.metrics.gatherer.GatherGeneMetrics
MetricGatherer
- sctools.metrics.merge module
- sctools.metrics.writer module
- Submodules
- sctools.test package
- Submodules
- sctools.test.test_bam module
bamfile()
indices()
make_records_from_values()
n_nonspecific()
n_specific()
sa_object()
tagged_bam()
test_chromosome_19_comes_before_21()
test_correct_number_of_indices_are_extracted()
test_get_barcode_for_alignment()
test_get_barcode_for_alignment_raises_error_for_missing_tag()
test_get_barcodes_from_bam()
test_get_barcodes_from_bam_with_raise_missing_true_raises_warning_without_cr_barcode_passed()
test_incorrect_extension_does_not_raise_when_open_mode_is_specified()
test_incorrect_extension_without_open_mode_raises_value_error()
test_indices_are_all_greater_than_zero()
test_sort_by_tags_and_queryname_sorts_correctly_from_file()
test_sort_by_tags_and_queryname_sorts_correctly_from_file_no_tag_keys()
test_sort_by_tags_and_queryname_sorts_correctly_no_tag_keys()
test_split_bam_raises_value_error_when_passed_bam_without_barcodes()
test_split_on_tagged_bam()
test_split_succeeds_with_raise_missing_false_and_no_cr_barcode_passed()
test_split_with_large_chunk_size_generates_one_file()
test_split_with_raise_missing_true_raises_warning_without_cr_barcode_passed()
test_str_and_int_chromosomes_both_function()
test_tag_sortable_record_eq_is_false_when_any_difference_exists()
test_tag_sortable_record_eq_is_true_for_identical_records()
test_tag_sortable_record_lt_empty_query_name_is_smaller()
test_tag_sortable_record_lt_empty_tag_is_smaller()
test_tag_sortable_record_lt_is_false_for_equal_records()
test_tag_sortable_record_lt_is_true_for_smaller_query_name()
test_tag_sortable_record_lt_is_true_for_smaller_tag()
test_tag_sortable_record_lt_is_true_for_smaller_tag_regardless_of_query_name()
test_tag_sortable_record_missing_tag_value_is_empty_string()
test_tag_sortable_records_compare_correctly()
test_tag_sortable_records_raises_error_on_different_tag_lists()
test_tag_sortable_records_sort_correctly()
test_tag_sortable_records_sort_correctly_when_already_sorted()
test_tag_sortable_records_str()
test_verify_sort_on_unsorted_records_raises_error()
test_verify_sort_raises_no_error_on_sorted_records()
test_write_barcodes_to_bins()
- sctools.test.test_barcode module
barcode_set()
short_barcode_set_from_encoded()
short_barcode_set_from_iterable()
tagged_bamfile()
test_barcode_diversity_is_in_range()
test_base_frequency_sums_are_all_equal_to_barcode_set_length()
test_correct_bam_produces_cb_tags()
test_correct_barcode_finds_and_corrects_1_base_errors()
test_correct_barcode_raises_keyerror_when_barcode_has_more_than_one_error()
test_correct_barcode_raises_keyerror_when_barcode_not_correct_length()
test_incorrect_input_raises_errors()
test_iterable_produces_correct_barcodes()
test_reads_barcodes_from_file()
test_summarize_hamming_distances_gives_reasonable_results()
trivial_whitelist()
truncated_whitelist_from_10x()
- sctools.test.test_encodings module
encoder()
encoder_2bit()
encoder_3bit()
sequence()
simple_barcodes()
simple_hamming_distances()
test_encoded_hamming_distance_is_accurate()
test_three_bit_encode_decode_produces_same_string()
test_three_bit_encoder_gets_correct_gc_content()
test_three_bit_encodes_unknown_nucleotides_as_N()
test_two_bit_encode_decode_produces_same_string_except_for_N()
test_two_bit_encoder_gets_correct_gc_content()
test_two_bit_throws_errors_when_asked_to_encode_unknown_nucleotide()
- sctools.test.test_entrypoints module
test_Attach10XBarcodes_entrypoint()
test_Attach10XBarcodes_entrypoint_with_whitelist()
test_AttachBarcodes_entrypoint_with_whitelist()
test_count_merge()
test_split_bam()
test_tag_sort_bam()
test_tag_sort_bam_dash_t_specified_multiple_times()
test_tag_sort_bam_no_tags()
test_verify_bam_sort()
test_verify_bam_sort_raises_error_on_unsorted()
- sctools.test.test_fastq module
barcode_generator_with_corrected_cell_barcodes()
bytes_fastq_record()
embedded_barcode_generator()
i7_files_compressions_and_modes()
reader_all_compressions()
string_fastq_record()
test_bytes_fastq_record_quality_score_parsing()
test_corrects_barcodes()
test_embedded_barcode_generator_produces_outputs_of_expected_size()
test_fastq_returns_correct_filesize_for_single_and_multiple_files()
test_fields_populate_properly()
test_invalid_open_mode_raises_valueerror()
test_mixed_filetype_read_gets_correct_record_number()
test_non_string_filename_in_iterable_raises_typeerror()
test_non_string_filename_raises_typeerror()
test_printing_bytes_record_generates_valid_fastq_record()
test_printing_string_record_generates_valid_fastq_record()
test_reader_properly_subsets_based_on_indices()
test_reader_reads_correct_number_of_records_across_multiple_files()
test_reader_reads_first_record()
test_reader_skips_header_character_raises_value_error()
test_reader_stores_filenames()
test_string_fastq_record_quality_score_parsing()
test_zipping_readers_generates_expected_output()
test_zipping_readers_with_indices_generates_expected_output()
- sctools.test.test_gtf module
- sctools.test.test_metrics module
mergeable_cell_metrics()
mergeable_gene_metrics()
split_metrics_file()
test_calculate_cell_metrics_cli()
test_calculate_gene_metrics_cli()
test_cell_metrics_mean_n_genes_observed()
test_duplicate_records()
test_fragments_number_is_greater_than_molecule_number()
test_gene_metrics_n_genes()
test_gzip_compression()
test_higher_order_metrics_by_gene()
test_merge_cell_metrics_cli()
test_merge_cell_metrics_does_not_correct_duplicates()
test_merge_gene_metrics_averages_over_multiply_detected_genes()
test_merge_gene_metrics_cli()
test_metrics_highest_expression_class()
test_metrics_highest_read_count()
test_metrics_n_fragments()
test_metrics_n_molecules()
test_metrics_n_reads()
test_metrics_number_perfect_cell_barcodes()
test_metrics_number_perfect_molecule_barcodes()
test_reads_mapped_exonic()
test_reads_mapped_intronic()
test_reads_mapped_uniquely()
test_reads_mapped_utr()
test_single_read_evidence()
test_spliced_reads()
- sctools.test.test_stats module
- sctools.test.test_bam module
- Submodules