mavis/constants

module responsible for small utility functions and constants used throughout the structural_variant package

PROGNAME

PROGNAME: str = 'mavis'

EXIT_OK

EXIT_OK: int = 0

EXIT_ERROR

EXIT_ERROR: int = 1

EXIT_INCOMPLETE

EXIT_INCOMPLETE: int = 2

COMPLETE_STAMP

COMPLETE_STAMP: str = 'MAVIS.COMPLETE'

CODON_SIZE

CODON_SIZE: int = 3

GAP

GAP: str = '-'

NA_MAPPING_QUALITY

NA_MAPPING_QUALITY: int = 255

DNA_ALPHABET

DNA_ALPHABET = alphabet = Gapped(ambiguous_dna, '-')

alphabet

DNA_ALPHABET = alphabet = Gapped(ambiguous_dna, '-')

DNA_ALPHABET.match

DNA_ALPHABET.match = lambda x, y: _match_ambiguous_dna(x, y)

START_AA

START_AA: str = 'M'

STOP_AA

STOP_AA: str = '*'

INTEGER_COLUMNS

INTEGER_COLUMNS = {
    COLUMNS.break1_position_end,
    COLUMNS.break1_position_start,
    COLUMNS.break2_position_end,
    COLUMNS.break2_position_start,

FLOAT_COLUMNS

FLOAT_COLUMNS = {
    COLUMNS.break1_ewindow_count,
    COLUMNS.break1_split_reads_forced,
    COLUMNS.break1_split_reads,
    COLUMNS.break2_ewindow_count,
    COLUMNS.break2_split_reads_forced,
    COLUMNS.break2_split_reads,
    COLUMNS.cluster_size,
    COLUMNS.contig_alignment_query_consumption,
    COLUMNS.contig_alignment_rank,
    COLUMNS.contig_alignment_score,
    COLUMNS.contig_break1_read_depth,
    COLUMNS.contig_break2_read_depth,
    COLUMNS.contig_build_score,
    COLUMNS.contig_read_depth,
    COLUMNS.contig_remap_score,
    COLUMNS.contig_remapped_reads,
    COLUMNS.contigs_assembled,
    COLUMNS.flanking_pairs_compatible,
    COLUMNS.flanking_pairs,
    COLUMNS.linking_split_reads,
    COLUMNS.raw_break1_half_mapped_reads,
    COLUMNS.raw_break1_split_reads,
    COLUMNS.raw_break2_half_mapped_reads,
    COLUMNS.raw_break2_split_reads,
    COLUMNS.raw_flanking_pairs,
    COLUMNS.raw_spanning_reads,
    COLUMNS.repeat_count,
    COLUMNS.spanning_reads,

BOOLEAN_COLUMNS

BOOLEAN_COLUMNS = {COLUMNS.opposing_strands, COLUMNS.stranded, COLUMNS.supplementary_call}

SUMMARY_LIST_COLUMNS

SUMMARY_LIST_COLUMNS = {
    COLUMNS.annotation_figure,
    COLUMNS.annotation_id,
    COLUMNS.break1_split_reads,
    COLUMNS.break2_split_reads,
    COLUMNS.call_method,
    COLUMNS.contig_alignment_score,
    COLUMNS.contig_remapped_reads,
    COLUMNS.contig_seq,
    COLUMNS.event_type,
    COLUMNS.flanking_pairs,
    COLUMNS.pairing,
    COLUMNS.product_id,
    COLUMNS.spanning_reads,
    COLUMNS.tools,
    COLUMNS.tools,
    COLUMNS.tracking_id,
    COLUMNS.dgv,
    COLUMNS.known_sv_count,

class SPLICE_TYPE

inherits MavisNamespace

holds controlled vocabulary for allowed splice type classification values

Attributes

RETAIN (str): an intron was retained
SKIP (str): an exon was skipped
NORMAL (str): no exons were skipped and no introns were retained. the normal/expected splicing pattern was followed
MULTI_RETAIN (str): multiple introns were retained
MULTI_SKIP (str): multiple exons were skipped
COMPLEX (str): some combination of exon skipping and intron retention

class ORIENT

inherits MavisNamespace

holds controlled vocabulary for allowed orientation values

Attributes

LEFT (str): left wrt to the positive/forward strand
RIGHT (str): right wrt to the positive/forward strand
NS (str): orientation is not specified

class PROTOCOL

inherits MavisNamespace

holds controlled vocabulary for allowed protocol values

Attributes

GENOME (str)
TRANS (str)

class DISEASE_STATUS

inherits MavisNamespace

holds controlled vocabulary for allowed disease status

Attributes

DISEASED (str)
NORMAL (str)

class STRAND

inherits MavisNamespace

holds controlled vocabulary for allowed strand values

Attributes

POS (str): the positive/forward strand
NEG (str): the negative/reverse strand
NS (str): strand is not specified

class SVTYPE

inherits MavisNamespace

holds controlled vocabulary for acceptable structural variant classifications

Attributes

ITRANS (str)
INV (str)
INS (str)
DUP (str)

class CIGAR

inherits MavisNamespace

Enum-like. For readable cigar values

Attributes

M: alignment match (can be a sequence match or mismatch)
I: insertion to the reference
D: deletion from the reference
N: skipped region from the reference
S: soft clipping (clipped sequences present in SEQ)
H: hard clipping (clipped sequences NOT present in SEQ)
P: padding (silent deletion from padded reference)
EQ: sequence match (=)
X: sequence mismatch

Note

descriptions are taken from the samfile documentation <https://samtools.github.io/hts-specs/SAMv1.pdf>_

class PYSAM_READ_FLAGS

inherits MavisNamespace

Enum-like. For readable PYSAM flag constants

Attributes

REVERSE (int): SEQ being reverse complemented
MATE_REVERSE (int): SEQ of the next segment in the template being reverse complemented
UNMAPPED (int): segment unmapped
MATE_UNMAPPED (int): next segment in the template unmapped
FIRST_IN_PAIR (int): the first segment in the template
LAST_IN_PAIR (int): the last segment in the template
SECONDARY (int): secondary alignment
MULTIMAP (int): template having multiple segments in sequencing
SUPPLEMENTARY (int): supplementary alignment
TARGETED_ALIGNMENT (str)
RECOMPUTED_CIGAR (str)
BLAT_RANK (str)
BLAT_SCORE (str)
BLAT_ALIGNMENTS (str)
BLAT_PERCENT_IDENTITY (str)
BLAT_PMS (str)

Note

descriptions are taken from the samfile documentation <https://samtools.github.io/hts-specs/SAMv1.pdf>_

class FLAGS

inherits MavisNamespace

Attributes

LQ (str)

class READ_PAIR_TYPE

inherits MavisNamespace

Attributes

RR (str)
LL (str)
RL (str)
LR (str)

class CALL_METHOD

inherits MavisNamespace

holds controlled vocabulary for allowed call methods

Attributes

CONTIG (str): a contig was assembled and aligned across the breakpoints
SPLIT (str): the event was called by split read
FLANK (str): the event was called by flanking read pair
SPAN (str): the event was called by spanning read
INPUT (str)

class GENE_PRODUCT_TYPE

inherits MavisNamespace

controlled vocabulary for gene products

Attributes

SENSE (str): the gene product is a sense fusion
ANTI_SENSE (str): the gene product is anti-sense

class PRIME

inherits MavisNamespace

Attributes

FIVE (int): five prime
THREE (int): three prime

class GIEMSA_STAIN

inherits MavisNamespace

holds controlled vocabulary relating to stains of chromosome bands

Attributes

GNEG (str)
GPOS33 (str)
GPOS50 (str)
GPOS66 (str)
GPOS75 (str)
GPOS25 (str)
GPOS100 (str)
ACEN (str)
GVAR (str)
STALK (str)

class COLUMNS

inherits MavisNamespace

Column names for i/o files used throughout the pipeline

see column descriptions

Attributes

tracking_id (str)
library (str)
cluster_id (str)
cluster_size (str)
dgv (str)
validation_id (str)
annotation_id (str)
product_id (str)
event_type (str)
pairing (str)
inferred_pairing (str)
gene1 (str)
gene1_direction (str)
gene2 (str)
gene2_direction (str)
gene1_aliases (str)
gene2_aliases (str)
gene_product_type (str)
transcript1 (str)
transcript2 (str)
fusion_splicing_pattern (str)
fusion_cdna_coding_start (str)
fusion_cdna_coding_end (str)
fusion_mapped_domains (str)
fusion_sequence_fasta_id (str)
fusion_sequence_fasta_file (str)
fusion_protein_hgvs (str)
annotation_figure (str)
annotation_figure_legend (str)
genes_encompassed (str)
genes_overlapping_break1 (str)
genes_overlapping_break2 (str)
genes_proximal_to_break1 (str)
genes_proximal_to_break2 (str)
break1_chromosome (str)
break1_position_start (str)
break1_position_end (str)
break1_orientation (str)
exon_last_5prime (str)
exon_first_3prime (str)
break1_strand (str)
break1_seq (str)
break2_chromosome (str)
break2_position_start (str)
break2_position_end (str)
break2_orientation (str)
break2_strand (str)
break2_seq (str)
opposing_strands (str)
stranded (str)
protocol (str)
disease_status (str)
tools (str)
call_method (str)
break1_ewindow (str)
break1_ewindow_count (str)
break1_homologous_seq (str)
break1_split_read_names (str)
break1_split_reads (str)
break1_split_reads_forced (str)
break2_ewindow (str)
break2_ewindow_count (str)
break2_homologous_seq (str)
break2_split_read_names (str)
break2_split_reads (str)
break2_split_reads_forced (str)
contig_alignment_query_consumption (str)
contig_alignment_score (str)
contig_alignment_query_name (str)
contig_read_depth (str)
contig_break1_read_depth (str)
contig_break2_read_depth (str)
contig_alignment_rank (str)
contig_build_score (str)
contig_remap_score (str)
contig_remap_coverage (str)
contig_remapped_read_names (str)
contig_remapped_reads (str)
contig_seq (str)
contig_strand_specific (str)
contigs_assembled (str)
call_sequence_complexity (str)
known_sv_count (str)
spanning_reads (str)
spanning_read_names (str)
flanking_median_fragment_size (str)
flanking_pairs (str)
flanking_pairs_compatible (str)
flanking_pairs_read_names (str)
flanking_pairs_compatible_read_names (str)
flanking_stdev_fragment_size (str)
linking_split_read_names (str)
linking_split_reads (str)
raw_break1_half_mapped_reads (str)
raw_break1_split_reads (str)
raw_break2_half_mapped_reads (str)
raw_break2_split_reads (str)
raw_flanking_pairs (str)
raw_spanning_reads (str)
untemplated_seq (str)
filter_comment (str)
cdna_synon (str)
protein_synon (str)
supplementary_call (str)
net_size (str)
repeat_count (str)
assumed_untemplated (str)

float_fraction()

cast input to a float

def float_fraction(num):

Args

num: input to cast

Returns

: float

Raises

TypeError: if the input cannot be cast to a float or the number is not between 0 and 1

reverse_complement()

wrapper for the Bio.Seq reverse_complement method

def reverse_complement(s: str) -> str:

Args

s (str): the input DNA sequence

Returns

str: the reverse complement of the input sequence

Examples

>>> reverse_complement('ATCCGGT')
'ACCGGAT'

Warning

assumes the input is a DNA sequence

translate()

given a DNA sequence, translates it and returns the protein amino acid sequence

def translate(s: str, reading_frame: int = 0) -> str:

Args

s (str): the input DNA sequence
reading_frame (int): where to start translating the sequence

Returns

str: the amino acid sequence