constants module

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

mavis.constants.CALL_METHOD = MavisNamespace(CONTIG='contig', FLANK='flanking reads', INPUT='input', SPAN='spanning reads', SPLIT='split reads')

holds controlled vocabulary for allowed call methods

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

Type:MavisNamespace

mavis.constants.CIGAR = MavisNamespace(D=2, EQ=7, H=5, I=1, M=0, N=3, P=6, S=4, X=8)

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

Type:MavisNamespace

mavis.constants.CODON_SIZE = 3

the number of bases making up a codon

Type:int

mavis.constants.COLUMNS = MavisNamespace(annotation_figure='annotation_figure', annotation_figure_legend='annotation_figure_legend', annotation_id='annotation_id', assumed_untemplated='assumed_untemplated', break1_chromosome='break1_chromosome', break1_ewindow='break1_ewindow', break1_ewindow_count='break1_ewindow_count', break1_ewindow_practical_coverage='break1_ewindow_practical_coverage', break1_homologous_seq='break1_homologous_seq', break1_orientation='break1_orientation', break1_position_end='break1_position_end', break1_position_start='break1_position_start', break1_seq='break1_seq', break1_split_read_names='break1_split_read_names', break1_split_reads='break1_split_reads', break1_split_reads_forced='break1_split_reads_forced', break1_strand='break1_strand', break2_chromosome='break2_chromosome', break2_ewindow='break2_ewindow', break2_ewindow_count='break2_ewindow_count', break2_ewindow_practical_coverage='break2_ewindow_practical_coverage', break2_homologous_seq='break2_homologous_seq', break2_orientation='break2_orientation', break2_position_end='break2_position_end', break2_position_start='break2_position_start', break2_seq='break2_seq', break2_split_read_names='break2_split_read_names', break2_split_reads='break2_split_reads', break2_split_reads_forced='break2_split_reads_forced', break2_strand='break2_strand', call_method='call_method', call_sequence_complexity='call_sequence_complexity', cdna_synon='cdna_synon', cluster_id='cluster_id', cluster_size='cluster_size', contig_alignment_query_consumption='contig_alignment_query_consumption', contig_alignment_query_name='contig_alignment_query_name', contig_alignment_rank='contig_alignment_rank', contig_alignment_score='contig_alignment_score', contig_break1_read_depth='contig_break1_read_depth', contig_break2_read_depth='contig_break2_read_depth', contig_build_score='contig_build_score', contig_read_depth='contig_read_depth', contig_remap_coverage='contig_remap_coverage', contig_remap_score='contig_remap_score', contig_remapped_read_names='contig_remapped_read_names', contig_remapped_reads='contig_remapped_reads', contig_seq='contig_seq', contig_strand_specific='contig_strand_specific', contigs_assembled='contigs_assembled', disease_status='disease_status', event_type='event_type', exon_first_3prime='exon_first_3prime', exon_last_5prime='exon_last_5prime', filter_comment='filter_comment', flanking_median_fragment_size='flanking_median_fragment_size', flanking_pairs='flanking_pairs', flanking_pairs_compatible='flanking_pairs_compatible', flanking_pairs_compatible_read_names='flanking_pairs_compatible_read_names', flanking_pairs_read_names='flanking_pairs_read_names', flanking_stdev_fragment_size='flanking_stdev_fragment_size', fusion_cdna_coding_end='fusion_cdna_coding_end', fusion_cdna_coding_start='fusion_cdna_coding_start', fusion_mapped_domains='fusion_mapped_domains', fusion_protein_hgvs='fusion_protein_hgvs', fusion_sequence_fasta_file='fusion_sequence_fasta_file', fusion_sequence_fasta_id='fusion_sequence_fasta_id', fusion_splicing_pattern='fusion_splicing_pattern', gene1='gene1', gene1_aliases='gene1_aliases', gene1_direction='gene1_direction', gene2='gene2', gene2_aliases='gene2_aliases', gene2_direction='gene2_direction', gene_product_type='gene_product_type', genes_encompassed='genes_encompassed', genes_overlapping_break1='genes_overlapping_break1', genes_overlapping_break2='genes_overlapping_break2', genes_proximal_to_break1='genes_proximal_to_break1', genes_proximal_to_break2='genes_proximal_to_break2', inferred_pairing='inferred_pairing', library='library', linking_split_read_names='linking_split_read_names', linking_split_reads='linking_split_reads', net_size='net_size', opposing_strands='opposing_strands', pairing='pairing', product_id='product_id', protein_synon='protein_synon', protocol='protocol', raw_break1_half_mapped_reads='raw_break1_half_mapped_reads', raw_break1_split_reads='raw_break1_split_reads', raw_break2_half_mapped_reads='raw_break2_half_mapped_reads', raw_break2_split_reads='raw_break2_split_reads', raw_flanking_pairs='raw_flanking_pairs', raw_spanning_reads='raw_spanning_reads', repeat_count='repeat_count', spanning_read_names='spanning_read_names', spanning_reads='spanning_reads', stranded='stranded', supplementary_call='supplementary_call', tools='tools', tracking_id='tracking_id', transcript1='transcript1', transcript2='transcript2', untemplated_seq='untemplated_seq', validation_id='validation_id')

Column names for i/o files used throughout the pipeline

• annotation_figure_legend
• annotation_figure
• annotation_id
• break1_chromosome
• break1_ewindow_count
• break1_ewindow_practical_coverage
• break1_ewindow
• break1_homologous_seq
• break1_orientation
• break1_position_end
• break1_position_start
• break1_seq
• break1_split_reads_forced
• break1_split_reads
• break1_strand
• break2_chromosome
• break2_ewindow_count
• break2_ewindow_practical_coverage
• break2_ewindow
• break2_homologous_seq
• break2_orientation
• break2_position_end
• break2_position_start
• break2_seq
• break2_split_reads_forced
• break2_split_reads
• break2_strand
• call_method
• cdna_synon
• cluster_id
• cluster_size
• contig_alignment_cigar
• contig_alignment_query_name
• contig_alignment_reference_start
• contig_alignment_score
• contig_build_score
• contig_remap_coverage
• contig_remap_score
• contig_remapped_read_names
• contig_remapped_reads
• contig_seq
• contig_strand_specific
• contigs_assembled
• call_sequence_complexity
• event_type
• flanking_median_fragment_size
• flanking_pairs_compatible
• flanking_pairs
• flanking_stdev_fragment_size
• fusion_cdna_coding_end
• fusion_cdna_coding_end
• fusion_cdna_coding_start
• fusion_mapped_domains
• fusion_sequence_fasta_file
• fusion_sequence_fasta_id
• fusion_splicing_pattern
• fusion_protein_hgvs
• gene1_aliases
• gene1_direction
• gene1
• gene2_aliases
• gene2_direction
• gene2
• gene_product_type
• genes_encompassed
• genes_overlapping_break1
• genes_overlapping_break2
• genes_proximal_to_break1
• genes_proximal_to_break2
• inferred_pairing
• library
• linking_split_reads
• net_size
• opposing_strands
• pairing
• product_id
• protein_synon
• protocol
• raw_break1_split_reads
• raw_break2_split_reads
• raw_flanking_pairs
• raw_spanning_reads
• spanning_read_names
• spanning_reads
• stranded
• tools
• tracking_id
• transcript1
• transcript2
• supplementary_call
• untemplated_seq
• validation_id
• repeat_count
• assumed_untemplated

Type:MavisNamespace

mavis.constants.COMPLETE_STAMP = 'MAVIS.COMPLETE'

Filename for all complete stamp files

Type:str

mavis.constants.DISEASE_STATUS = MavisNamespace(DISEASED='diseased', NORMAL='normal')

holds controlled vocabulary for allowed disease status

• DISEASED: diseased
• NORMAL: normal

Type:MavisNamespace

mavis.constants.GENE_PRODUCT_TYPE = MavisNamespace(ANTI_SENSE='anti-sense', SENSE='sense')

controlled vocabulary for gene products

• SENSE: the gene product is a sense fusion
• ANTI_SENSE: the gene product is anti-sense

Type:MavisNamespace

mavis.constants.GIEMSA_STAIN = MavisNamespace(ACEN='acen', GNEG='gneg', GPOS100='gpos100', GPOS25='gpos25', GPOS33='gpos33', GPOS50='gpos50', GPOS66='gpos66', GPOS75='gpos75', GVAR='gvar', STALK='stalk')

holds controlled vocabulary relating to stains of chromosome bands

Type:MavisNamespace

class mavis.constants.MavisNamespace(*pos, **kwargs)

Bases: object

Namespace to hold module constants

Example

>>> nspace = MavisNamespace(thing=1, otherthing=2)
>>> nspace.thing
1
>>> nspace.otherthing
2

DELIM = '[;,\\s]+'

delimiter to use is parsing listable variables from the environment or config file

Type:str

add(attr, value, defn=None, cast_type=None, nullable=False, env_overwritable=False, listable=False)

Add an attribute to the name space

Parameters:

• attr (str) – name of the attribute being added
• value – the value of the attribute
• defn (str) – the definition, will be used in generating documentation and help menus
• cast_type (callable) – the function to use in casting the value
• nullable (bool) – True if this attribute can have a None value
• env_overwritable (bool) – True if this attribute will be overriden by its environment variable equivalent
• listable (bool) – True if this attribute can have multiple values

Example

>>> nspace = MavisNamespace()
>>> nspace.add('thing', 1, int, 'I am a thing')
>>> nspace = MavisNamespace()
>>> nspace.add('thing', 1, int)
>>> nspace = MavisNamespace()
>>> nspace.add('thing', 1)
>>> nspace = MavisNamespace()
>>> nspace.add('thing', value=1, cast_type=int, defn='I am a thing')

copy_from(source, attrs=None)

Copy variables from one namespace onto the current namespace

define(attr, *pos)

Get the definition of a given attribute or return a default (when given) if the attribute does not exist

Returns:definition for the attribute Return type:str Raises:KeyError – the attribute does not exist and a default was not given

Example

>>> nspace = MavisNamespace()
>>> nspace.add('thing', 1, defn='I am a thing')
>>> nspace.add('otherthing', 2)
>>> nspace.define('thing')
'I am a thing'
>>> nspace.define('otherthing')
Traceback (most recent call last):
....
>>> nspace.define('otherthing', 'I am some other thing')
'I am some other thing'

discard(attr)

Remove a variable if it exists

enforce(value)

checks that the current namespace has a given value

Returns:the input value Raises:KeyError – the value did not exist

Example

>>> nspace = MavisNamespace(thing=1, otherthing=2)
>>> nspace.enforce(1)
1
>>> nspace.enforce(3)
Traceback (most recent call last):
....

get(key, *pos)

get an attribute, return a default (if given) if the attribute does not exist

Example

>>> nspace = MavisNamespace(thing=1, otherthing=2)
>>> nspace.get('thing', 2)
1
>>> nspace.get('nonexistant_thing', 2)
2
>>> nspace.get('nonexistant_thing')
Traceback (most recent call last):
....

get_env_name(attr)

Get the name of the corresponding environment variable

Example

>>> nspace = MavisNamespace(a=1)
>>> nspace.get_env_name('a')
'MAVIS_A'

get_env_var(attr)

retrieve the environment variable definition of a given attribute

is_env_overwritable(attr)

Returns:True if the variable is overrided by specifying the environment variable equivalent Return type:bool

is_listable(attr)

Returns:True if the variable should be parsed as a list Return type:bool

is_nullable(attr)

Returns:True if the variable can be set to None Return type:bool

items()

Example

>>> MavisNamespace(thing=1, otherthing=2).items()
[('thing', 1), ('otherthing', 2)]

keys()

get the attribute keys as a list

Example

>>> MavisNamespace(thing=1, otherthing=2).keys()
['thing', 'otherthing']

classmethod parse_listable_string(string, cast_type=<class 'str'>, nullable=False)

Given some string, parse it into a list

Example

>>> MavisNamespace.parse_listable_string('1,2,3', int)
[1, 2, 3]
>>> MavisNamespace.parse_listable_string('1;2,None', int, True)
[1, 2, None]

reverse(value)

for a given value, return the associated key

Parameters:

value – the value to get the key/attribute name for

Raises:

• KeyError – the value is not unique
• KeyError – the value is not assigned

Example

>>> nspace = MavisNamespace(thing=1, otherthing=2)
>>> nspace.reverse(1)
'thing'

to_dict()

type(attr, *pos)

returns the type

Example

>>> nspace = MavisNamespace(thing=1, otherthing=2)
>>> nspace.type('thing')
<class 'int'>

values()

get the attribute values as a list

Example

>>> MavisNamespace(thing=1, otherthing=2).values()
[1, 2]

mavis.constants.NA_MAPPING_QUALITY = 255

mapping quality value to indicate mapping was not performed/calculated

Type:int

mavis.constants.ORIENT = MavisNamespace(LEFT='L', NS='?', RIGHT='R', compare=<function <lambda>>, expand=<function <lambda>>)

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

Type:MavisNamespace

mavis.constants.PRIME = MavisNamespace(FIVE=5, THREE=3)

holds controlled vocabulary

• FIVE: five prime
• THREE: three prime

Type:MavisNamespace

mavis.constants.PROTOCOL = MavisNamespace(GENOME='genome', TRANS='transcriptome')

holds controlled vocabulary for allowed protocol values

• GENOME: genome
• TRANS: transcriptome

Type:MavisNamespace

mavis.constants.PYSAM_READ_FLAGS = MavisNamespace(BLAT_ALIGNMENTS='ba', BLAT_PERCENT_IDENTITY='bi', BLAT_PMS='bp', BLAT_RANK='br', BLAT_SCORE='bs', FIRST_IN_PAIR=64, LAST_IN_PAIR=128, MATE_REVERSE=32, MATE_UNMAPPED=8, MULTIMAP=1, RECOMPUTED_CIGAR='rc', REVERSE=16, SECONDARY=256, SUPPLEMENTARY=2048, TARGETED_ALIGNMENT='ta', UNMAPPED=4)

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

Type:MavisNamespace

mavis.constants.START_AA = 'M'

The amino acid expected to start translation

Type:str

mavis.constants.STOP_AA = '*'

The amino acid expected to end translation

Type:str

mavis.constants.STRAND = MavisNamespace(NEG='-', NS='?', POS='+', compare=<function <lambda>>, expand=<function <lambda>>)

holds controlled vocabulary for allowed strand values

• POS: the positive/forward strand
• NEG: the negative/reverse strand
• NS: strand is not specified

Type:MavisNamespace

mavis.constants.SUBCOMMAND = MavisNamespace(ANNOTATE='annotate', CLUSTER='cluster', CONFIG='config', CONVERT='convert', OVERLAY='overlay', PAIR='pairing', SCHEDULE='schedule', SETUP='setup', SUMMARY='summary', VALIDATE='validate')

holds controlled vocabulary for allowed pipeline stage values

• annotate
• cluster
• config
• convert
• pairing
• pipeline
• schedule
• summary
• validate

Type:MavisNamespace

mavis.constants.SVTYPE = MavisNamespace(DEL='deletion', DUP='duplication', INS='insertion', INV='inversion', ITRANS='inverted translocation', TRANS='translocation')

holds controlled vocabulary for acceptable structural variant classifications

• DEL: deletion
• TRANS: translocation
• ITRANS: inverted translocation
• INV: inversion
• INS: insertion
• DUP: duplication

Type:MavisNamespace

mavis.constants.float_fraction(num)

cast input to a float

Parameters: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

mavis.constants.reverse_complement(s)

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)

mavis.constants.translate(s, reading_frame=0)

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