changeo.Gene
Gene annotations
- changeo.Gene.buildClonalGermline(receptors, references, seq_field='sequence_imgt', v_field='v_call', d_field='d_call', j_field='j_call', amino_acid=False)
Determine consensus clone sequence and create germline for clone
- Parameters:
receptors (changeo.Receptor.Receptor) – list of Receptor objects
references (dict) – dictionary of IMGT gapped germline sequences
seq_field (str) – Receptor attribute in which to look for sequence
v_field (str) – Receptor attributein which to look for V call
d_field (str) – Receptor attributein which to look for D call
j_field (str) – Receptor attributein which to look for J call
amino_acid (bool) – if True then use the amino acid positional fields, otherwise use the nucleotide fields.
- Returns:
- log dictionary, dictionary of {germline_type: germline_sequence},
dictionary of consensus {segment: gene call}
- Return type:
- changeo.Gene.buildGermline(receptor, references, seq_field='sequence_imgt', v_field='v_call', d_field='d_call', j_field='j_call', amino_acid=False)
Join gapped germline sequences aligned with sample sequences
- Parameters:
receptor (changeo.Receptor.Receptor) – Receptor object.
references (dict) – dictionary of IMGT gapped germline sequences.
seq_field (str) – Receptor attribute in which to look for sequence.
v_field (str) – Receptor attribute in which to look for V call.
d_field (str) – Receptor attribute in which to look for V call.
j_field (str) – Receptor attribute in which to look for V call.
amino_acid (bool) – if True then use the amino acid positional fields, otherwise use the nucleotide fields.
- Returns:
log dictionary, dictionary of {germline_type: germline_sequence}, dictionary of {segment: gene call}
- Return type:
- changeo.Gene.getAllele(gene, action='first')
Extract allele from gene call string
- changeo.Gene.getAlleleNumber(gene, action='first')
Extract allele number from gene call string
- changeo.Gene.getCAllele(gene, action='first')
Extract C-region allele gene call string
- changeo.Gene.getCGene(gene, action='first')
Extract C-region gene from gene call string
- changeo.Gene.getDAllele(gene, action='first')
Extract D allele gene from gene call string
- changeo.Gene.getDGermline(receptor, references, d_field='d_call', amino_acid=False)
Extract D allele and germline sequence
- Parameters:
receptor (changeo.Receptor.Receptor) – Receptor object
references (dict) – dictionary of germline sequences
d_field (str) – Receptor attribute containing the D allele assignment
amino_acid (bool) – if True then use the amino acid positional fields, otherwise use the nucleotide fields.
- Returns:
D allele name, D segment germline sequence
- Return type:
- changeo.Gene.getFamily(gene, action='first')
Extract family from gene call string
- changeo.Gene.getGene(gene, action='first')
Extract gene from gene call string
- changeo.Gene.getJAllele(gene, action='first')
Extract J allele gene from gene call string
- changeo.Gene.getJGermline(receptor, references, j_field='j_call', amino_acid=False)
Extract J allele and germline sequence
- Parameters:
receptor (changeo.Receptor.Receptor) – Receptor object
references (dict) – dictionary of germline sequences
j_field (str) – Receptor attribute containing the J allele assignment
amino_acid (bool) – if True then use the amino acid positional fields, otherwise use the nucleotide fields.
- Returns:
J allele name, J segment germline sequence
- Return type:
- changeo.Gene.getLocus(gene, action='first')
Extract locus from gene call string
- changeo.Gene.getVAllele(gene, action='first')
Extract V allele gene from gene call string
- changeo.Gene.getVGermline(receptor, references, v_field='v_call', amino_acid=False)
Extract V allele and germline sequence
- Parameters:
receptor (changeo.Receptor.Receptor) – Receptor object
references (dict) – dictionary of germline sequences
v_field (str) – Receptor attribute containing the V allele assignment
amino_acid (bool) – if True then use the amino acid positional fields, otherwise use the nucleotide fields.
- Returns:
V allele name, V segment germline sequence
- Return type:
- changeo.Gene.parseGeneCall(gene, regex, action='first')
Extract alleles from strings
- Parameters:
gene (str) – string with gene calls
regex (re.Pattern) – compiled regular expression for allele match
action (str) – action to perform for multiple alleles; one of (‘first’, ‘set’, ‘list’).
- Returns:
String of the allele when action is ‘first’; tuple: Tuple of allele calls for ‘set’ or ‘list’ actions.
- Return type:
- changeo.Gene.stitchRegions(receptor, v_seq, d_seq, j_seq, amino_acid=False)
Assemble full length region encoding
- Parameters:
receptor (changeo.Receptor.Receptor) – Receptor object
v_seq (str) – V segment germline sequence as a string
d_seq (str) – D segment germline sequence as a string
j_seq (str) – J segment germline sequence as a string
amino_acid (bool) – if True use amino acid positional fields, otherwise use nucleotide fields.
- Returns:
string defining germline regions
- Return type:
- changeo.Gene.stitchVDJ(receptor, v_seq, d_seq, j_seq, amino_acid=False)
Assemble full length germline sequence
- Parameters:
receptor (changeo.Receptor.Receptor) – Receptor object
v_seq (str) – V segment sequence as a string
d_seq (str) – D segment sequence as a string
j_seq (str) – J segment sequence as a string
amino_acid (bool) – if True use X for N/P regions and amino acid positional fields, otherwise use N and nucleotide fields.
- Returns:
full germline sequence
- Return type: