constants module

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

mavis.constants.CALL_METHOD = <vocab.vocab.Vocab object>

Vocab – holds controlled vocabulary for allowed call methods

mavis.constants.CIGAR = <vocab.vocab.Vocab object>

Vocab – Enum-like. For readable cigar values

  • 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

mavis.constants.CODON_SIZE = 3

int – the number of bases making up a codon

mavis.constants.COLUMNS = <vocab.vocab.Vocab object>

Vocab – Column names for i/o files used throughout the pipeline

annotation_figure
File path to the svg drawing representing the annotation
annotation_figure_legend
JSON - JSON data for the figure legend
annotation_id
Identifier for the annotation step
break1_call_method
CALL_METHOD - The method used to call the first breakpoint
break1_chromosome
str - The name of the chromosome on which breakpoint 1 is situated
break1_ewindow
Window where evidence was gathered for the first breakpoint
break1_ewindow_count
int - Number of reads processed/looked-at in the first evidence window
break1_ewindow_practical_coverage
float - break2_ewindow_practical_coverage, break1_ewindow_count / len(break1_ewindow). Not the actual coverage as bins are sampled within and there is a read limit cutoff
break1_homologous_seq
str - Sequence in common at the first breakpoint and other side of the second breakpoint
break1_orientation
ORIENT - The side of the breakpoint wrt the positive/forward strand that is retained.
break1_position_end
int - End integer inclusive 1-based of the range representing breakpoint 1
break1_position_start
int - Start integer inclusive 1-based of the range representing breakpoint 1
break1_seq
str - The sequence up to and including the breakpoint. Always given wrt to the positive/forward strand
break1_split_reads
int - Number of split reads that call the exact breakpoint given
break1_split_reads_forced
int - Number of split reads which were aligned to the opposite breakpoint window using a targeted alignment
break1_strand
STRAND - The strand wrt to the reference positive/forward strand at this breakpoint.
break2_call_method
CALL_METHOD - The method used to call the second breakpoint
break2_chromosome
The name of the chromosome on which breakpoint 2 is situated
break2_ewindow
Window where evidence was gathered for the second breakpoint
break2_ewindow_count
int - Number of reads processed/looked-at in the second evidence window
break2_ewindow_practical_coverage
float - break2_ewindow_practical_coverage, break2_ewindow_count / len(break2_ewindow). Not the actual coverage as bins are sampled within and there is a read limit cutoff
break2_homologous_seq
str - Sequence in common at the second breakpoint and other side of the first breakpoint
break2_orientation
ORIENT - The side of the breakpoint wrt the positive/forward strand that is retained.
break2_position_end
int - End integer inclusive 1-based of the range representing breakpoint 2
break2_position_start
int - Start integer inclusive 1-based of the range representing breakpoint 2
break2_seq
str - The sequence up to and including the breakpoint. Always given wrt to the positive/forward strand
break2_split_reads
int - Number of split reads that call the exact breakpoint given
break2_split_reads_forced
int - Number of split reads which were aligned to the opposite breakpoint window using a targeted alignment
break2_strand
STRAND - The strand wrt to the reference positive/forward strand at this breakpoint.
cluster_id
Identifier for the merging/clustering step
cluster_size
The number of breakpoint pair calls that were grouped in creating the cluster
contig_alignment_query_name
The query name for the contig alignment. Should match the ‘read’ name(s) in the .contigs.bam output file
contig_alignment_score
float - A rank based on the alignment tool blat etc. of the alignment being used. An average if split alignments were used. Lower numbers indicate a better alignment. If it was the best alignment possible then this would be zero.
contig_build_score
int - Score representing the edge weights of all edges used in building the sequence
contig_remap_score
float - Score representing the number of sequences from the set of sequences given to the assembly algorithm that were aligned to the resulting contig with an acceptable scoring based on user-set thresholds. For any sequence its contribution to the score is divided by the number of mappings to give less weight to multimaps
contig_remapped_read_names
read query names for the reads that were remapped. A -1 or -2 has been appended to the end of the name to indicate if this is the first or second read in the pair
contig_remapped_reads
int - the number of reads from the input bam that map to the assembled contig
contig_seq
str - Sequence of the current contig wrt to the positive forward strand if not strand specific
contig_strand_specific
bool - A flag to indicate if it was possible to resolve the strand for this contig
contigs_aligned
int - Number of contigs that were able to align
contigs_assembled
int - Number of contigs that were built from split read sequences
event_type
SVTYPE - The classification of the event
flanking_median_fragment_size
int - The median fragment size of the flanking reads being used as evidence
flanking_pairs
int - Number of read-pairs where one read aligns to the first breakpoint window and the second read aligns to the other. The count here is based on the number of unique query names
flanking_pairs_compatible
int - Number of flanking pairs of a compatible orientation type. This applies to insertions and duplications. Flanking pairs supporting an insertion will be compatible to a duplication and flanking pairs supporting a duplication will be compatible to an insertion (possibly indicating an internal translocation)
flanking_stdev_fragment_size
float - The standard deviation in fragment size of the flanking reads being used as evidence
fusion_cdna_coding_end
Position wrt the 5’ end of the fusion transcript where coding ends last base of the stop codon
fusion_cdna_coding_start
Position wrt the 5’ end of the fusion transcript where coding begins first base of the Met amino acid.
fusion_mapped_domains
JSON - List of domains in JSON format where each domain start and end positions are given wrt to the fusion transcript and the mapping quality is the number of matching amino acid positions over the total number of amino acids. The sequence is the amino acid sequence of the domain on the reference/original transcript
fusion_sequence_fasta_file
Path to the corresponding fasta output file
fusion_sequence_fasta_id
The sequence identifier for the cdna sequence output fasta file
fusion_splicing_pattern
SPLICE_TYPE - Type of splicing pattern used to create the fusion cDNA.
gene1
Gene for the current annotation at the first breakpoint
gene1_direction
PRIME - The direction/prime of the gene
gene2
Gene for the current annotation at the second breakpoint
gene2_direction
PRIME - The direction/prime of the gene. Has the following possible values
gene_product_type
GENE_PRODUCT_TYPE - Describes if the putative fusion product will be sense or anti-sense
genes_encompassed
Applies to intrachromosomal events only. List of genes which overlap any region that occurs between both breakpoints. For example in a deletion event these would be deleted genes.
genes_overlapping_break1
list of genes which overlap the first breakpoint
genes_overlapping_break2
list of genes which overlap the second breakpoint
genes_proximal_to_break1
list of genes near the breakpoint and the distance away from the breakpoint
genes_proximal_to_break2
list of genes near the breakpoint and the distance away from the breakpoint
library
Identifier for the library/source
linking_split_reads
int - Number of split reads that align to both breakpoints
opposing_strands
bool - Specifies if breakpoints are on opposite strands wrt to the reference. Expects a boolean
pairing
A semi colon delimited of event identifiers i.e. <annotation_id>_<splicing pattern>_<cds start>_<cds end>
product_id
Unique identifier of the final fusion including splicing and ORF decision from the annotation step
protocol
PROTOCOL - Specifies the type of library
raw_break1_split_reads
int - Number of split reads before calling the breakpoint
raw_break2_split_reads
int - Number of split reads before calling the breakpoint
raw_flanking_pairs
int - Number of flanking reads before calling the breakpoint. The count here is based on the number of unique query names
raw_spanning_reads
int - Number of spanning reads collected during evidence collection before calling the breakpoint
spanning_read_names
read query names of the spanning reads which support the current event
spanning_reads
int - the number of spanning reads which support the event
stranded
bool - Specifies if the sequencing protocol was strand specific or not. Expects a boolean
tools
The tools that called the event originally from the cluster step. Should be a semi-colon delimited list of <tool name>_<tool version>
transcript1
Transcript for the current annotation at the first breakpoint
transcript2
Transcript for the current annotation at the second breakpoint
untemplated_seq
str - The untemplated/novel sequence between the breakpoints
validation_id
Identifier for the validation step
mavis.constants.GENE_PRODUCT_TYPE = <vocab.vocab.Vocab object>

Vocab – controlled vocabulary for gene products

  • SENSE: the gene product is a sense fusion
  • ANTI_SENSE: the gene product is anti-sense
mavis.constants.GIESMA_STAIN = <vocab.vocab.Vocab object>

Vocab – holds controlled vocabulary relating to stains of chromosome bands

mavis.constants.NA_MAPPING_QUALITY = 255

int – mapping qaulity value to indicate mapping was not performed/calculated

mavis.constants.ORIENT = <vocab.vocab.Vocab object>

Vocab – holds controlled vocabulary for allowed orientation values

  • LEFT: left wrt to the positive/forward strand
  • RIGHT: right wrt to the positive/forward strand
  • NS: orientation is not specified
mavis.constants.PRIME = <vocab.vocab.Vocab object>

Vocab – holds controlled vocabulary

  • FIVE: five prime
  • THREE: three prime
mavis.constants.PROTOCOL = <vocab.vocab.Vocab object>

Vocab – holds controlled vocabulary for allowed protocol values

  • GENOME: genome
  • TRANS: transcriptome
mavis.constants.PYSAM_READ_FLAGS = <vocab.vocab.Vocab object>

Vocab – Enum-like. For readable PYSAM flag constants

  • MULTIMAP: template having multiple segments in sequencing
  • UNMAPPED: segment unmapped
  • MATE_UNMAPPED: next segment in the template unmapped
  • REVERSE: SEQ being reverse complemented
  • MATE_REVERSE: SEQ of the next segment in the template being reverse complemented
  • FIRST_IN_PAIR: the first segment in the template
  • LAST_IN_PAIR: the last segment in the template
  • SECONDARY: secondary alignment
  • SUPPLEMENTARY: supplementary alignment

note: descriptions are taken from the samfile documentation

mavis.constants.SPLICE_SITE_RADIUS = 2

int – number of bases away from an exon boundary considered to be part of the splice site such that if it were altered the splice site would be considered to be abrogated.

mavis.constants.SPLICE_TYPE = <vocab.vocab.Vocab object>

Vocab – holds controlled vocabulary for allowed splice type classification values

  • RETAIN: an intron was retained
  • SKIP: an exon was skipped
  • NORMAL: no exons were skipped and no introns were retained. the normal/expected splicing pattern was followed
  • MULTI_RETAIN: multiple introns were retained
  • MULTI_SKIP: multiple exons were skipped
  • COMPLEX: some combination of exon skipping and intron retention
mavis.constants.START_AA = 'M'

str – The amino acid expected to start translation

mavis.constants.STOP_AA = '*'

str – The amino acid expected to end translation

mavis.constants.STRAND = <vocab.vocab.Vocab object>

Vocab – holds controlled vocabulary for allowed strand values

  • POS: the positive/forward strand
  • NEG: the negative/reverse strand
  • NS: strand is not specified
mavis.constants.SVTYPE = <vocab.vocab.Vocab object>

Vocab – holds controlled vocabulary for acceptable structural variant classifications

  • DEL: deletion
  • TRANS: translocation
  • ITRANS: inverted translocation
  • INV: inversion
  • INS: insertion
  • DUP: duplication
mavis.constants.reverse_complement(s)[source]

wrapper for the Bio.Seq reverse_complement method

Parameters:s (str) – the input DNA sequence
Returns:the reverse complement of the input sequence
Return type:str

Warning

assumes the input is a DNA sequence

Example

>>> reverse_complement('ATCCGGT')
'ACCGGAT'
mavis.constants.sort_columns(input_columns)[source]
mavis.constants.translate(s, reading_frame=0)[source]

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

Parameters:
  • s (str) – the input DNA sequence
  • reading_frame (int) – where to start translating the sequence
Returns:

the amino acid sequence
Return type:

str