Overview

• Single Cell Tools

API References

• 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
      • Nucleotide Barcode Manipulation Tools
      • Barcodes
      • ErrorsToCorrectBarcodesMap
    • sctools.encodings module
      • Compressed Barcode Encoding Methods
      • Encoding
      • ThreeBit
      • TwoBit
    • sctools.fastq module
      • Efficient Fastq Iterators and Representations
      • BarcodeGeneratorWithCorrectedCellBarcodes
      • EmbeddedBarcode
      • EmbeddedBarcodeGenerator
      • Reader
      • Record
      • StrRecord
      • extract_barcode()
    • sctools.gtf module
      • GTF Records and Iterators
      • GTFRecord
      • Reader
      • extract_extended_gene_names()
      • extract_gene_exons()
      • extract_gene_names()
      • get_mitochondrial_gene_names()
    • sctools.platform module
      • Command Line Interface for SC Tools:
      • BarcodePlatform
      • GenericPlatform
      • TenXV2
    • sctools.reader module
      • Sequence File Iterators
      • Reader
      • infer_open()
      • zip_readers()
    • sctools.stats module
      • Statistics Functions for Sequence Data Analysis
      • OnlineGaussianSufficientStatistic
      • base4_entropy()
• sctools.metrics package
  • Submodules
    • sctools.metrics.aggregator module
      • Sequence Metric Aggregators
      • CellMetrics
      • GeneMetrics
      • MetricAggregator
    • 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
      • Merge Sequence Metrics
      • MergeCellMetrics
      • MergeGeneMetrics
      • MergeMetrics
    • sctools.metrics.writer module
      • Metric Writers
      • MetricCSVWriter
• 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
      • files()
      • test_opens_file_parses_size()
      • test_opens_file_populates_fields_properly()
      • test_opens_file_reads_first_line()
      • test_set_attribute_verify_included_in_output_string()
    • 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
      • test_balanced_data_produces_entropy_1()
      • test_balanced_unnormalized_data_produces_entropy_1()
      • test_concentrated_data_produces_entropy_0()
      • test_concentrated_unnormalized_data_produces_entropy_0()

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