presto.Sequence¶
Sequence processing functions
-
class
presto.Sequence.
AssemblyRecord
(seq=None)¶ Bases:
object
A class defining a paired-end assembly result
-
overlap
¶
-
-
class
presto.Sequence.
AssemblyStats
(n)¶ Bases:
object
Class containing p-value and z-score matrices for scoring assemblies
-
class
presto.Sequence.
PrimerAlignment
(seq=None)¶ Bases:
object
A class defining a primer alignment result
-
presto.Sequence.
alignAssembly
(head_seq, tail_seq, alpha=1e-05, max_error=0.3, min_len=8, max_len=1000, scan_reverse=False, assembly_stats=None, score_dict={('-', '-'): 0, ('-', '.'): 0, ('-', 'A'): 0, ('-', 'B'): 0, ('-', 'C'): 0, ('-', 'D'): 0, ('-', 'G'): 0, ('-', 'H'): 0, ('-', 'K'): 0, ('-', 'M'): 0, ('-', 'N'): 0, ('-', 'R'): 0, ('-', 'S'): 0, ('-', 'T'): 0, ('-', 'V'): 0, ('-', 'W'): 0, ('-', 'Y'): 0, ('.', '-'): 0, ('.', '.'): 0, ('.', 'A'): 0, ('.', 'B'): 0, ('.', 'C'): 0, ('.', 'D'): 0, ('.', 'G'): 0, ('.', 'H'): 0, ('.', 'K'): 0, ('.', 'M'): 0, ('.', 'N'): 0, ('.', 'R'): 0, ('.', 'S'): 0, ('.', 'T'): 0, ('.', 'V'): 0, ('.', 'W'): 0, ('.', 'Y'): 0, ('A', '-'): 0, ('A', '.'): 0, ('A', 'A'): 1, ('A', 'B'): 0, ('A', 'C'): 0, ('A', 'D'): 1, ('A', 'G'): 0, ('A', 'H'): 1, ('A', 'K'): 0, ('A', 'M'): 1, ('A', 'N'): 1, ('A', 'R'): 1, ('A', 'S'): 0, ('A', 'T'): 0, ('A', 'V'): 1, ('A', 'W'): 1, ('A', 'Y'): 0, ('B', '-'): 0, ('B', '.'): 0, ('B', 'A'): 0, ('B', 'B'): 1, ('B', 'C'): 1, ('B', 'D'): 1, ('B', 'G'): 1, ('B', 'H'): 1, ('B', 'K'): 1, ('B', 'M'): 1, ('B', 'N'): 1, ('B', 'R'): 1, ('B', 'S'): 1, ('B', 'T'): 1, ('B', 'V'): 1, ('B', 'W'): 1, ('B', 'Y'): 1, ('C', '-'): 0, ('C', '.'): 0, ('C', 'A'): 0, ('C', 'B'): 1, ('C', 'C'): 1, ('C', 'D'): 0, ('C', 'G'): 0, ('C', 'H'): 1, ('C', 'K'): 0, ('C', 'M'): 1, ('C', 'N'): 1, ('C', 'R'): 0, ('C', 'S'): 1, ('C', 'T'): 0, ('C', 'V'): 1, ('C', 'W'): 0, ('C', 'Y'): 1, ('D', '-'): 0, ('D', '.'): 0, ('D', 'A'): 1, ('D', 'B'): 1, ('D', 'C'): 0, ('D', 'D'): 1, ('D', 'G'): 1, ('D', 'H'): 1, ('D', 'K'): 1, ('D', 'M'): 1, ('D', 'N'): 1, ('D', 'R'): 1, ('D', 'S'): 1, ('D', 'T'): 1, ('D', 'V'): 1, ('D', 'W'): 1, ('D', 'Y'): 1, ('G', '-'): 0, ('G', '.'): 0, ('G', 'A'): 0, ('G', 'B'): 1, ('G', 'C'): 0, ('G', 'D'): 1, ('G', 'G'): 1, ('G', 'H'): 0, ('G', 'K'): 1, ('G', 'M'): 0, ('G', 'N'): 1, ('G', 'R'): 1, ('G', 'S'): 1, ('G', 'T'): 0, ('G', 'V'): 1, ('G', 'W'): 0, ('G', 'Y'): 0, ('H', '-'): 0, ('H', '.'): 0, ('H', 'A'): 1, ('H', 'B'): 1, ('H', 'C'): 1, ('H', 'D'): 1, ('H', 'G'): 0, ('H', 'H'): 1, ('H', 'K'): 1, ('H', 'M'): 1, ('H', 'N'): 1, ('H', 'R'): 1, ('H', 'S'): 1, ('H', 'T'): 1, ('H', 'V'): 1, ('H', 'W'): 1, ('H', 'Y'): 1, ('K', '-'): 0, ('K', '.'): 0, ('K', 'A'): 0, ('K', 'B'): 1, ('K', 'C'): 0, ('K', 'D'): 1, ('K', 'G'): 1, ('K', 'H'): 1, ('K', 'K'): 1, ('K', 'M'): 0, ('K', 'N'): 1, ('K', 'R'): 1, ('K', 'S'): 1, ('K', 'T'): 1, ('K', 'V'): 1, ('K', 'W'): 1, ('K', 'Y'): 1, ('M', '-'): 0, ('M', '.'): 0, ('M', 'A'): 1, ('M', 'B'): 1, ('M', 'C'): 1, ('M', 'D'): 1, ('M', 'G'): 0, ('M', 'H'): 1, ('M', 'K'): 0, ('M', 'M'): 1, ('M', 'N'): 1, ('M', 'R'): 1, ('M', 'S'): 1, ('M', 'T'): 0, ('M', 'V'): 1, ('M', 'W'): 1, ('M', 'Y'): 1, ('N', '-'): 1, ('N', '.'): 1, ('N', 'A'): 1, ('N', 'B'): 1, ('N', 'C'): 1, ('N', 'D'): 1, ('N', 'G'): 1, ('N', 'H'): 1, ('N', 'K'): 1, ('N', 'M'): 1, ('N', 'N'): 1, ('N', 'R'): 1, ('N', 'S'): 1, ('N', 'T'): 1, ('N', 'V'): 1, ('N', 'W'): 1, ('N', 'Y'): 1, ('R', '-'): 0, ('R', '.'): 0, ('R', 'A'): 1, ('R', 'B'): 1, ('R', 'C'): 0, ('R', 'D'): 1, ('R', 'G'): 1, ('R', 'H'): 1, ('R', 'K'): 1, ('R', 'M'): 1, ('R', 'N'): 1, ('R', 'R'): 1, ('R', 'S'): 1, ('R', 'T'): 0, ('R', 'V'): 1, ('R', 'W'): 1, ('R', 'Y'): 0, ('S', '-'): 0, ('S', '.'): 0, ('S', 'A'): 0, ('S', 'B'): 1, ('S', 'C'): 1, ('S', 'D'): 1, ('S', 'G'): 1, ('S', 'H'): 1, ('S', 'K'): 1, ('S', 'M'): 1, ('S', 'N'): 1, ('S', 'R'): 1, ('S', 'S'): 1, ('S', 'T'): 0, ('S', 'V'): 1, ('S', 'W'): 0, ('S', 'Y'): 1, ('T', '-'): 0, ('T', '.'): 0, ('T', 'A'): 0, ('T', 'B'): 1, ('T', 'C'): 0, ('T', 'D'): 1, ('T', 'G'): 0, ('T', 'H'): 1, ('T', 'K'): 1, ('T', 'M'): 0, ('T', 'N'): 1, ('T', 'R'): 0, ('T', 'S'): 0, ('T', 'T'): 1, ('T', 'V'): 0, ('T', 'W'): 1, ('T', 'Y'): 1, ('V', '-'): 0, ('V', '.'): 0, ('V', 'A'): 1, ('V', 'B'): 1, ('V', 'C'): 1, ('V', 'D'): 1, ('V', 'G'): 1, ('V', 'H'): 1, ('V', 'K'): 1, ('V', 'M'): 1, ('V', 'N'): 1, ('V', 'R'): 1, ('V', 'S'): 1, ('V', 'T'): 0, ('V', 'V'): 1, ('V', 'W'): 1, ('V', 'Y'): 1, ('W', '-'): 0, ('W', '.'): 0, ('W', 'A'): 1, ('W', 'B'): 1, ('W', 'C'): 0, ('W', 'D'): 1, ('W', 'G'): 0, ('W', 'H'): 1, ('W', 'K'): 1, ('W', 'M'): 1, ('W', 'N'): 1, ('W', 'R'): 1, ('W', 'S'): 0, ('W', 'T'): 1, ('W', 'V'): 1, ('W', 'W'): 1, ('W', 'Y'): 1, ('Y', '-'): 0, ('Y', '.'): 0, ('Y', 'A'): 0, ('Y', 'B'): 1, ('Y', 'C'): 1, ('Y', 'D'): 1, ('Y', 'G'): 0, ('Y', 'H'): 1, ('Y', 'K'): 1, ('Y', 'M'): 1, ('Y', 'N'): 1, ('Y', 'R'): 0, ('Y', 'S'): 1, ('Y', 'T'): 1, ('Y', 'V'): 1, ('Y', 'W'): 1, ('Y', 'Y'): 1})¶ Stitches two sequences together by aligning the ends
Parameters: - head_seq – the head SeqRecord.
- head_seq – the tail SeqRecord.
- alpha – the minimum p-value for a valid assembly.
- max_error – the maximum error rate for a valid assembly.
- min_len – minimum length of overlap to test.
- max_len – maximum length of overlap to test.
- scan_reverse – if True allow the head sequence to overhang the end of the tail sequence if False end alignment scan at end of tail sequence or start of head sequence.
- assembly_stats – optional successes by trials numpy.array of p-values.
- score_dict – optional dictionary of character scores in the . form {(char1, char2): score}.
Returns: assembled sequence object.
Return type:
-
presto.Sequence.
calculateDiversity
(seq_list, score_dict=getDNAScoreDict())¶ Determine the average pairwise error rate for a list of sequences
Parameters: - seq_list – List of SeqRecord objects to score
- score_dict – Optional dictionary of alignment scores as {(char1, char2): score}
Returns: Average pairwise error rate for the list of sequences
Return type:
-
presto.Sequence.
calculateSetError
(seq_list, ref_seq, ignore_chars=['n', 'N'], score_dict=getDNAScoreDict())¶ Counts the occurrence of nucleotide mismatches from a reference in a set of sequences
Parameters: - seq_list – list of SeqRecord objects with aligned sequences.
- ref_seq – SeqRecord object containing the reference sequence to match against.
- ignore_chars – list of characters to exclude from mismatch counts.
- score_dict – optional dictionary of alignment scores as {(char1, char2): score}.
Returns: error rate for the set.
Return type:
-
presto.Sequence.
checkSeqEqual
(seq1, seq2, ignore_chars={'-', '.', 'N', 'n'})¶ Determine if two sequences are equal, excluding missing positions
Parameters: - seq1 – SeqRecord object
- seq2 – SeqRecord object
- ignore_chars – Set of characters to ignore
Returns: True if the sequences are equal
Return type:
-
presto.Sequence.
compilePrimers
(primers)¶ Translates IUPAC Ambiguous Nucleotide characters to regular expressions and compiles them
Parameters: key – Dictionary of sequences to translate Returns: Dictionary of compiled regular expressions Return type: dict
-
presto.Sequence.
consensusUnify
(data, field, delimiter=('|', '=', ', '))¶ Reassigns all annotations to the consensus annotation in group
Parameters: - data – SeqData object contain sequences to process.
- field – field containing annotations to collapse.
- delimiter – a tuple of delimiters for (annotations, field/values, value lists).
Returns: modified sequences.
Return type:
-
presto.Sequence.
deleteSeqPositions
(seq, positions)¶ Deletes a list of positions from a SeqRecord
Parameters: - seq – SeqRecord objects
- positions – Set of positions (indices) to delete
Returns: Modified SeqRecord with the specified positions removed
Return type: SeqRecord
-
presto.Sequence.
deletionUnify
(data, field, delimiter=('|', '=', ', '))¶ Removes all sequences with differing annotations in a group
Parameters: - data – SeqData object contain sequences to process.
- field – field containing annotations to collapse.
- delimiter – a tuple of delimiters for (annotations, field/values, value lists).
Returns: modified sequences.
Return type:
-
presto.Sequence.
extractAlignment
(seq_record, start, length, rev_primer=False)¶ Extracts a subsequence from sequence
Parameters: - data – SeqRecord to process.
- start – position where subsequence starts.
- length – the length of the subsequence to extract.
- rev_primer – if True extract relative to the tail end of the sequence.
Returns: extraction results as an alignment object
Return type:
-
presto.Sequence.
filterLength
(data, min_length=250, inner=True, missing_chars='N-n.')¶ Filters sequences by length
Parameters: Returns: SeqResult object.
Return type:
-
presto.Sequence.
filterMissing
(data, max_missing=10, inner=True, missing_chars='N-n.')¶ Filters sequences by number of missing nucleotides
Parameters: Returns: SeqResult object.
Return type:
-
presto.Sequence.
filterQuality
(data, min_qual=0, inner=True, missing_chars='N-n.')¶ Filters sequences by quality score
Parameters: Returns: SeqResult object.
Return type:
-
presto.Sequence.
filterRepeats
(data, max_repeat=15, include_missing=False, inner=True, missing_chars='N-n.')¶ Filters sequences by fraction of ambiguous nucleotides
Parameters: - data (SeqData) – a SeqData object with a single SeqRecord to process.
- max_repeat (int) – the maximum number of allowed repeating characters.
- include_missing (int) – if True count ambiguous character repeats; if False do not consider ambiguous character repeats.
- inner (int) – if True exclude outer missing characters from calculation.
- missing_chars (str) – a string of missing character values.
Returns: SeqResult object.
Return type:
-
presto.Sequence.
findGapPositions
(seq_list, max_gap, gap_chars={'-', '.'})¶ Finds positions in a set of aligned sequences with a high number of gap characters.
Parameters: - seq_list – List of SeqRecord objects with aligned sequences
- max_gap – Float of the maximum gap frequency to consider a position as non-gapped
- gap_chars – Set of characters to consider as gaps
Returns: Positions (indices) with gap frequency greater than max_gap
Return type:
-
presto.Sequence.
frequencyConsensus
(seq_list, min_freq=0.6, ignore_chars={'-', '.', 'N', 'n'})¶ Builds a consensus sequence from a set of sequences
Parameters: - set_seq – List of SeqRecord objects
- min_freq – Frequency cutoff to assign a base
- ignore_chars – Set of characters to exclude when building a consensus sequence
Returns: Consensus SeqRecord object
Return type: SeqRecord
-
presto.Sequence.
getAAScoreDict
(mask_score=None, gap_score=None)¶ Generates a score dictionary
Parameters: - mask_score – Tuple of length two defining scores for all matches against an X character for (a, b), with the score for character (a) taking precedence; if None score symmetrically according to IUPAC character identity
- gap_score – Tuple of length two defining score for all matches against a [-, .] character for (a, b), with the score for character (a) taking precedence; if None score symmetrically according to IUPAC character identity
Returns: Score dictionary with keys (char1, char2) mapping to scores
Return type:
-
presto.Sequence.
getDNAScoreDict
(mask_score=None, gap_score=None)¶ Generates a score dictionary
Parameters: - mask_score – Tuple of length two defining scores for all matches against an N character for (a, b), with the score for character (a) taking precedence; if None score symmetrically according to IUPAC character identity
- gap_score – Tuple of length two defining score for all matches against a [-, .] character for (a, b), with the score for character (a) taking precedence; if None score symmetrically according to IUPAC character identity
Returns: Score dictionary with keys (char1, char2) mapping to scores
Return type:
-
presto.Sequence.
indexSeqSets
(seq_dict, field='BARCODE', delimiter=('|', '=', ', '))¶ Identifies sets of sequences with the same ID field
Parameters: - seq_dict – a dictionary index of sequences returned from SeqIO.index()
- field – the annotation field containing set IDs
- delimiter – a tuple of delimiters for (fields, values, value lists)
Returns: Dictionary mapping set name to a list of record names
Return type:
-
presto.Sequence.
joinAssembly
(head_seq, tail_seq, gap=0, insert_seq=None)¶ Concatenates two sequences
Parameters: - head_seq – the head SeqRecord.
- tail_seq – the tail SeqRecord.
- gap – number of gap characters to insert between head and tail ignored if insert_seq is not None.
- insert_seq – a string or Bio.Seq.Seq object, to insert between the head and tail; if None insert with N characters.
Returns: assembled sequence object.
Return type:
-
presto.Sequence.
localAlignment
(seq_record, primers, primers_regex=None, max_error=0.3, max_len=1000, rev_primer=False, skip_rc=False, gap_penalty=(1, 1), score_dict={('-', '-'): 0, ('-', '.'): 0, ('-', 'A'): 0, ('-', 'B'): 0, ('-', 'C'): 0, ('-', 'D'): 0, ('-', 'G'): 0, ('-', 'H'): 0, ('-', 'K'): 0, ('-', 'M'): 0, ('-', 'N'): 0, ('-', 'R'): 0, ('-', 'S'): 0, ('-', 'T'): 0, ('-', 'V'): 0, ('-', 'W'): 0, ('-', 'Y'): 0, ('.', '-'): 0, ('.', '.'): 0, ('.', 'A'): 0, ('.', 'B'): 0, ('.', 'C'): 0, ('.', 'D'): 0, ('.', 'G'): 0, ('.', 'H'): 0, ('.', 'K'): 0, ('.', 'M'): 0, ('.', 'N'): 0, ('.', 'R'): 0, ('.', 'S'): 0, ('.', 'T'): 0, ('.', 'V'): 0, ('.', 'W'): 0, ('.', 'Y'): 0, ('A', '-'): 0, ('A', '.'): 0, ('A', 'A'): 1, ('A', 'B'): 0, ('A', 'C'): 0, ('A', 'D'): 1, ('A', 'G'): 0, ('A', 'H'): 1, ('A', 'K'): 0, ('A', 'M'): 1, ('A', 'N'): 1, ('A', 'R'): 1, ('A', 'S'): 0, ('A', 'T'): 0, ('A', 'V'): 1, ('A', 'W'): 1, ('A', 'Y'): 0, ('B', '-'): 0, ('B', '.'): 0, ('B', 'A'): 0, ('B', 'B'): 1, ('B', 'C'): 1, ('B', 'D'): 1, ('B', 'G'): 1, ('B', 'H'): 1, ('B', 'K'): 1, ('B', 'M'): 1, ('B', 'N'): 1, ('B', 'R'): 1, ('B', 'S'): 1, ('B', 'T'): 1, ('B', 'V'): 1, ('B', 'W'): 1, ('B', 'Y'): 1, ('C', '-'): 0, ('C', '.'): 0, ('C', 'A'): 0, ('C', 'B'): 1, ('C', 'C'): 1, ('C', 'D'): 0, ('C', 'G'): 0, ('C', 'H'): 1, ('C', 'K'): 0, ('C', 'M'): 1, ('C', 'N'): 1, ('C', 'R'): 0, ('C', 'S'): 1, ('C', 'T'): 0, ('C', 'V'): 1, ('C', 'W'): 0, ('C', 'Y'): 1, ('D', '-'): 0, ('D', '.'): 0, ('D', 'A'): 1, ('D', 'B'): 1, ('D', 'C'): 0, ('D', 'D'): 1, ('D', 'G'): 1, ('D', 'H'): 1, ('D', 'K'): 1, ('D', 'M'): 1, ('D', 'N'): 1, ('D', 'R'): 1, ('D', 'S'): 1, ('D', 'T'): 1, ('D', 'V'): 1, ('D', 'W'): 1, ('D', 'Y'): 1, ('G', '-'): 0, ('G', '.'): 0, ('G', 'A'): 0, ('G', 'B'): 1, ('G', 'C'): 0, ('G', 'D'): 1, ('G', 'G'): 1, ('G', 'H'): 0, ('G', 'K'): 1, ('G', 'M'): 0, ('G', 'N'): 1, ('G', 'R'): 1, ('G', 'S'): 1, ('G', 'T'): 0, ('G', 'V'): 1, ('G', 'W'): 0, ('G', 'Y'): 0, ('H', '-'): 0, ('H', '.'): 0, ('H', 'A'): 1, ('H', 'B'): 1, ('H', 'C'): 1, ('H', 'D'): 1, ('H', 'G'): 0, ('H', 'H'): 1, ('H', 'K'): 1, ('H', 'M'): 1, ('H', 'N'): 1, ('H', 'R'): 1, ('H', 'S'): 1, ('H', 'T'): 1, ('H', 'V'): 1, ('H', 'W'): 1, ('H', 'Y'): 1, ('K', '-'): 0, ('K', '.'): 0, ('K', 'A'): 0, ('K', 'B'): 1, ('K', 'C'): 0, ('K', 'D'): 1, ('K', 'G'): 1, ('K', 'H'): 1, ('K', 'K'): 1, ('K', 'M'): 0, ('K', 'N'): 1, ('K', 'R'): 1, ('K', 'S'): 1, ('K', 'T'): 1, ('K', 'V'): 1, ('K', 'W'): 1, ('K', 'Y'): 1, ('M', '-'): 0, ('M', '.'): 0, ('M', 'A'): 1, ('M', 'B'): 1, ('M', 'C'): 1, ('M', 'D'): 1, ('M', 'G'): 0, ('M', 'H'): 1, ('M', 'K'): 0, ('M', 'M'): 1, ('M', 'N'): 1, ('M', 'R'): 1, ('M', 'S'): 1, ('M', 'T'): 0, ('M', 'V'): 1, ('M', 'W'): 1, ('M', 'Y'): 1, ('N', '-'): 0, ('N', '.'): 0, ('N', 'A'): 0, ('N', 'B'): 0, ('N', 'C'): 0, ('N', 'D'): 0, ('N', 'G'): 0, ('N', 'H'): 0, ('N', 'K'): 0, ('N', 'M'): 0, ('N', 'N'): 0, ('N', 'R'): 0, ('N', 'S'): 0, ('N', 'T'): 0, ('N', 'V'): 0, ('N', 'W'): 0, ('N', 'Y'): 0, ('R', '-'): 0, ('R', '.'): 0, ('R', 'A'): 1, ('R', 'B'): 1, ('R', 'C'): 0, ('R', 'D'): 1, ('R', 'G'): 1, ('R', 'H'): 1, ('R', 'K'): 1, ('R', 'M'): 1, ('R', 'N'): 1, ('R', 'R'): 1, ('R', 'S'): 1, ('R', 'T'): 0, ('R', 'V'): 1, ('R', 'W'): 1, ('R', 'Y'): 0, ('S', '-'): 0, ('S', '.'): 0, ('S', 'A'): 0, ('S', 'B'): 1, ('S', 'C'): 1, ('S', 'D'): 1, ('S', 'G'): 1, ('S', 'H'): 1, ('S', 'K'): 1, ('S', 'M'): 1, ('S', 'N'): 1, ('S', 'R'): 1, ('S', 'S'): 1, ('S', 'T'): 0, ('S', 'V'): 1, ('S', 'W'): 0, ('S', 'Y'): 1, ('T', '-'): 0, ('T', '.'): 0, ('T', 'A'): 0, ('T', 'B'): 1, ('T', 'C'): 0, ('T', 'D'): 1, ('T', 'G'): 0, ('T', 'H'): 1, ('T', 'K'): 1, ('T', 'M'): 0, ('T', 'N'): 1, ('T', 'R'): 0, ('T', 'S'): 0, ('T', 'T'): 1, ('T', 'V'): 0, ('T', 'W'): 1, ('T', 'Y'): 1, ('V', '-'): 0, ('V', '.'): 0, ('V', 'A'): 1, ('V', 'B'): 1, ('V', 'C'): 1, ('V', 'D'): 1, ('V', 'G'): 1, ('V', 'H'): 1, ('V', 'K'): 1, ('V', 'M'): 1, ('V', 'N'): 1, ('V', 'R'): 1, ('V', 'S'): 1, ('V', 'T'): 0, ('V', 'V'): 1, ('V', 'W'): 1, ('V', 'Y'): 1, ('W', '-'): 0, ('W', '.'): 0, ('W', 'A'): 1, ('W', 'B'): 1, ('W', 'C'): 0, ('W', 'D'): 1, ('W', 'G'): 0, ('W', 'H'): 1, ('W', 'K'): 1, ('W', 'M'): 1, ('W', 'N'): 1, ('W', 'R'): 1, ('W', 'S'): 0, ('W', 'T'): 1, ('W', 'V'): 1, ('W', 'W'): 1, ('W', 'Y'): 1, ('Y', '-'): 0, ('Y', '.'): 0, ('Y', 'A'): 0, ('Y', 'B'): 1, ('Y', 'C'): 1, ('Y', 'D'): 1, ('Y', 'G'): 0, ('Y', 'H'): 1, ('Y', 'K'): 1, ('Y', 'M'): 1, ('Y', 'N'): 1, ('Y', 'R'): 0, ('Y', 'S'): 1, ('Y', 'T'): 1, ('Y', 'V'): 1, ('Y', 'W'): 1, ('Y', 'Y'): 1})¶ Performs pairwise local alignment of a list of short sequences against a long sequence
Parameters: - seq_record – a SeqRecord object to align primers against
- primers – dictionary of {names: short IUPAC ambiguous sequence strings}
- primers_regex – optional dictionary of {names: compiled primer regular expressions}
- max_error – maximum acceptable error rate before aligning reverse complement
- max_len – maximum length of sample sequence to align
- rev_primer – if True align with the tail end of the sequence
- skip_rc – if True do not check reverse complement sequences
- gap_penalty – a tuple of positive (gap open, gap extend) penalties
- score_dict – optional dictionary of alignment scores as {(char1, char2): score}
Returns: primer alignment result object
Return type:
-
presto.Sequence.
maskQuality
(data, min_qual=0)¶ Masks characters by in sequence by quality score
Parameters: Returns: SeqResult object.
Return type:
-
presto.Sequence.
maskSeq
(align, mode='mask', barcode=False, barcode_field='BARCODE', primer_field='PRIMER', delimiter=('|', '=', ', '))¶ Create an output sequence with primers masked or cut
Parameters: - align – a PrimerAlignment object.
- mode – defines the action taken; one of ‘cut’, ‘mask’, ‘tag’ or ‘trim’.
- barcode – if True add sequence preceding primer to description.
- barcode_field – name of the output barcode annotation.
- primer_field – name of the output primer annotation.
- delimiter – a tuple of delimiters for (annotations, field/values, value lists).
Returns: masked sequence.
Return type: Bio.SeqRecord.SeqRecord
-
presto.Sequence.
overlapConsensus
(head_seq, tail_seq, ignore_chars={'-', '.', 'N', 'n'})¶ Creates a consensus overlap sequences from two segments
Parameters: - head_seq – the overlap head SeqRecord.
- tail_seq – the overlap tail SeqRecord.
- ignore_chars – list of characters which do not contribute to consensus.
Returns: A SeqRecord object with consensus characters and quality scores.
Return type: SeqRecord
-
presto.Sequence.
qualityConsensus
(seq_list, min_qual=0, min_freq=0.6, dependent=False, ignore_chars={'-', '.', 'N', 'n'})¶ Builds a consensus sequence from a set of sequences
Parameters: - seq_list – List of SeqRecord objects
- min_qual – Quality cutoff to assign a base
- min_freq – Frequency cutoff to assign a base
- dependent – If False assume sequences are independent for quality calculation
- ignore_chars – Set of characters to exclude when building a consensus sequence
Returns: Consensus SeqRecord object
Return type: SeqRecord
-
presto.Sequence.
referenceAssembly
(head_seq, tail_seq, ref_dict, ref_db, min_ident=0.5, evalue=1e-05, max_hits=100, fill=False, aligner='usearch', aligner_exec='usearch', score_dict={('-', '-'): 0, ('-', '.'): 0, ('-', 'A'): 0, ('-', 'B'): 0, ('-', 'C'): 0, ('-', 'D'): 0, ('-', 'G'): 0, ('-', 'H'): 0, ('-', 'K'): 0, ('-', 'M'): 0, ('-', 'N'): 0, ('-', 'R'): 0, ('-', 'S'): 0, ('-', 'T'): 0, ('-', 'V'): 0, ('-', 'W'): 0, ('-', 'Y'): 0, ('.', '-'): 0, ('.', '.'): 0, ('.', 'A'): 0, ('.', 'B'): 0, ('.', 'C'): 0, ('.', 'D'): 0, ('.', 'G'): 0, ('.', 'H'): 0, ('.', 'K'): 0, ('.', 'M'): 0, ('.', 'N'): 0, ('.', 'R'): 0, ('.', 'S'): 0, ('.', 'T'): 0, ('.', 'V'): 0, ('.', 'W'): 0, ('.', 'Y'): 0, ('A', '-'): 0, ('A', '.'): 0, ('A', 'A'): 1, ('A', 'B'): 0, ('A', 'C'): 0, ('A', 'D'): 1, ('A', 'G'): 0, ('A', 'H'): 1, ('A', 'K'): 0, ('A', 'M'): 1, ('A', 'N'): 1, ('A', 'R'): 1, ('A', 'S'): 0, ('A', 'T'): 0, ('A', 'V'): 1, ('A', 'W'): 1, ('A', 'Y'): 0, ('B', '-'): 0, ('B', '.'): 0, ('B', 'A'): 0, ('B', 'B'): 1, ('B', 'C'): 1, ('B', 'D'): 1, ('B', 'G'): 1, ('B', 'H'): 1, ('B', 'K'): 1, ('B', 'M'): 1, ('B', 'N'): 1, ('B', 'R'): 1, ('B', 'S'): 1, ('B', 'T'): 1, ('B', 'V'): 1, ('B', 'W'): 1, ('B', 'Y'): 1, ('C', '-'): 0, ('C', '.'): 0, ('C', 'A'): 0, ('C', 'B'): 1, ('C', 'C'): 1, ('C', 'D'): 0, ('C', 'G'): 0, ('C', 'H'): 1, ('C', 'K'): 0, ('C', 'M'): 1, ('C', 'N'): 1, ('C', 'R'): 0, ('C', 'S'): 1, ('C', 'T'): 0, ('C', 'V'): 1, ('C', 'W'): 0, ('C', 'Y'): 1, ('D', '-'): 0, ('D', '.'): 0, ('D', 'A'): 1, ('D', 'B'): 1, ('D', 'C'): 0, ('D', 'D'): 1, ('D', 'G'): 1, ('D', 'H'): 1, ('D', 'K'): 1, ('D', 'M'): 1, ('D', 'N'): 1, ('D', 'R'): 1, ('D', 'S'): 1, ('D', 'T'): 1, ('D', 'V'): 1, ('D', 'W'): 1, ('D', 'Y'): 1, ('G', '-'): 0, ('G', '.'): 0, ('G', 'A'): 0, ('G', 'B'): 1, ('G', 'C'): 0, ('G', 'D'): 1, ('G', 'G'): 1, ('G', 'H'): 0, ('G', 'K'): 1, ('G', 'M'): 0, ('G', 'N'): 1, ('G', 'R'): 1, ('G', 'S'): 1, ('G', 'T'): 0, ('G', 'V'): 1, ('G', 'W'): 0, ('G', 'Y'): 0, ('H', '-'): 0, ('H', '.'): 0, ('H', 'A'): 1, ('H', 'B'): 1, ('H', 'C'): 1, ('H', 'D'): 1, ('H', 'G'): 0, ('H', 'H'): 1, ('H', 'K'): 1, ('H', 'M'): 1, ('H', 'N'): 1, ('H', 'R'): 1, ('H', 'S'): 1, ('H', 'T'): 1, ('H', 'V'): 1, ('H', 'W'): 1, ('H', 'Y'): 1, ('K', '-'): 0, ('K', '.'): 0, ('K', 'A'): 0, ('K', 'B'): 1, ('K', 'C'): 0, ('K', 'D'): 1, ('K', 'G'): 1, ('K', 'H'): 1, ('K', 'K'): 1, ('K', 'M'): 0, ('K', 'N'): 1, ('K', 'R'): 1, ('K', 'S'): 1, ('K', 'T'): 1, ('K', 'V'): 1, ('K', 'W'): 1, ('K', 'Y'): 1, ('M', '-'): 0, ('M', '.'): 0, ('M', 'A'): 1, ('M', 'B'): 1, ('M', 'C'): 1, ('M', 'D'): 1, ('M', 'G'): 0, ('M', 'H'): 1, ('M', 'K'): 0, ('M', 'M'): 1, ('M', 'N'): 1, ('M', 'R'): 1, ('M', 'S'): 1, ('M', 'T'): 0, ('M', 'V'): 1, ('M', 'W'): 1, ('M', 'Y'): 1, ('N', '-'): 1, ('N', '.'): 1, ('N', 'A'): 1, ('N', 'B'): 1, ('N', 'C'): 1, ('N', 'D'): 1, ('N', 'G'): 1, ('N', 'H'): 1, ('N', 'K'): 1, ('N', 'M'): 1, ('N', 'N'): 1, ('N', 'R'): 1, ('N', 'S'): 1, ('N', 'T'): 1, ('N', 'V'): 1, ('N', 'W'): 1, ('N', 'Y'): 1, ('R', '-'): 0, ('R', '.'): 0, ('R', 'A'): 1, ('R', 'B'): 1, ('R', 'C'): 0, ('R', 'D'): 1, ('R', 'G'): 1, ('R', 'H'): 1, ('R', 'K'): 1, ('R', 'M'): 1, ('R', 'N'): 1, ('R', 'R'): 1, ('R', 'S'): 1, ('R', 'T'): 0, ('R', 'V'): 1, ('R', 'W'): 1, ('R', 'Y'): 0, ('S', '-'): 0, ('S', '.'): 0, ('S', 'A'): 0, ('S', 'B'): 1, ('S', 'C'): 1, ('S', 'D'): 1, ('S', 'G'): 1, ('S', 'H'): 1, ('S', 'K'): 1, ('S', 'M'): 1, ('S', 'N'): 1, ('S', 'R'): 1, ('S', 'S'): 1, ('S', 'T'): 0, ('S', 'V'): 1, ('S', 'W'): 0, ('S', 'Y'): 1, ('T', '-'): 0, ('T', '.'): 0, ('T', 'A'): 0, ('T', 'B'): 1, ('T', 'C'): 0, ('T', 'D'): 1, ('T', 'G'): 0, ('T', 'H'): 1, ('T', 'K'): 1, ('T', 'M'): 0, ('T', 'N'): 1, ('T', 'R'): 0, ('T', 'S'): 0, ('T', 'T'): 1, ('T', 'V'): 0, ('T', 'W'): 1, ('T', 'Y'): 1, ('V', '-'): 0, ('V', '.'): 0, ('V', 'A'): 1, ('V', 'B'): 1, ('V', 'C'): 1, ('V', 'D'): 1, ('V', 'G'): 1, ('V', 'H'): 1, ('V', 'K'): 1, ('V', 'M'): 1, ('V', 'N'): 1, ('V', 'R'): 1, ('V', 'S'): 1, ('V', 'T'): 0, ('V', 'V'): 1, ('V', 'W'): 1, ('V', 'Y'): 1, ('W', '-'): 0, ('W', '.'): 0, ('W', 'A'): 1, ('W', 'B'): 1, ('W', 'C'): 0, ('W', 'D'): 1, ('W', 'G'): 0, ('W', 'H'): 1, ('W', 'K'): 1, ('W', 'M'): 1, ('W', 'N'): 1, ('W', 'R'): 1, ('W', 'S'): 0, ('W', 'T'): 1, ('W', 'V'): 1, ('W', 'W'): 1, ('W', 'Y'): 1, ('Y', '-'): 0, ('Y', '.'): 0, ('Y', 'A'): 0, ('Y', 'B'): 1, ('Y', 'C'): 1, ('Y', 'D'): 1, ('Y', 'G'): 0, ('Y', 'H'): 1, ('Y', 'K'): 1, ('Y', 'M'): 1, ('Y', 'N'): 1, ('Y', 'R'): 0, ('Y', 'S'): 1, ('Y', 'T'): 1, ('Y', 'V'): 1, ('Y', 'W'): 1, ('Y', 'Y'): 1})¶ Stitches two sequences together by aligning against a reference database
Parameters: - head_seq – the head SeqRecord.
- head_seq – the tail SeqRecord.
- ref_dict – a dictionary of reference SeqRecord objects.
- ref_db – the path and name of the reference database.
- min_ident – the minimum identity for a valid assembly.
- evalue – the E-value cut-off for ublast.
- max_hits – the maxhits output limit for ublast.
- fill – if False non-overlapping regions will be assigned Ns; if True non-overlapping regions will be filled with the reference sequence.
- aligner – the alignment tool; one of ‘blastn’ or ‘usearch’.
- aligner_exec – the path to the alignment tool executable.
- score_dict – optional dictionary of character scores in the form {(char1, char2): score}.
Returns: assembled sequence object.
Return type:
-
presto.Sequence.
reverseComplement
(seq)¶ Takes the reverse complement of a sequence
Parameters: seq – a SeqRecord object, Seq object or string to reverse complement Returns: Object of the same type as the input with the reverse complement sequence Return type: Seq
-
presto.Sequence.
scoreAA
(a, b, mask_score=None, gap_score=None)¶ Returns the score for a pair of IUPAC Extended Protein characters
Parameters: - a – First character
- b – Second character
- mask_score – Tuple of length two defining scores for all matches against an X character for (a, b), with the score for character (a) taking precedence; if None score symmetrically according to IUPAC character identity
- gap_score – Tuple of length two defining score for all matches against a gap (-, .) character for (a, b), with the score for character (a) taking precedence; if None score symmetrically according to IUPAC character identity
Returns: Score for the character pair
Return type:
-
presto.Sequence.
scoreAlignment
(seq_record, primers, start=0, rev_primer=False, score_dict={('-', '-'): 0, ('-', '.'): 0, ('-', 'A'): 0, ('-', 'B'): 0, ('-', 'C'): 0, ('-', 'D'): 0, ('-', 'G'): 0, ('-', 'H'): 0, ('-', 'K'): 0, ('-', 'M'): 0, ('-', 'N'): 0, ('-', 'R'): 0, ('-', 'S'): 0, ('-', 'T'): 0, ('-', 'V'): 0, ('-', 'W'): 0, ('-', 'Y'): 0, ('.', '-'): 0, ('.', '.'): 0, ('.', 'A'): 0, ('.', 'B'): 0, ('.', 'C'): 0, ('.', 'D'): 0, ('.', 'G'): 0, ('.', 'H'): 0, ('.', 'K'): 0, ('.', 'M'): 0, ('.', 'N'): 0, ('.', 'R'): 0, ('.', 'S'): 0, ('.', 'T'): 0, ('.', 'V'): 0, ('.', 'W'): 0, ('.', 'Y'): 0, ('A', '-'): 0, ('A', '.'): 0, ('A', 'A'): 1, ('A', 'B'): 0, ('A', 'C'): 0, ('A', 'D'): 1, ('A', 'G'): 0, ('A', 'H'): 1, ('A', 'K'): 0, ('A', 'M'): 1, ('A', 'N'): 1, ('A', 'R'): 1, ('A', 'S'): 0, ('A', 'T'): 0, ('A', 'V'): 1, ('A', 'W'): 1, ('A', 'Y'): 0, ('B', '-'): 0, ('B', '.'): 0, ('B', 'A'): 0, ('B', 'B'): 1, ('B', 'C'): 1, ('B', 'D'): 1, ('B', 'G'): 1, ('B', 'H'): 1, ('B', 'K'): 1, ('B', 'M'): 1, ('B', 'N'): 1, ('B', 'R'): 1, ('B', 'S'): 1, ('B', 'T'): 1, ('B', 'V'): 1, ('B', 'W'): 1, ('B', 'Y'): 1, ('C', '-'): 0, ('C', '.'): 0, ('C', 'A'): 0, ('C', 'B'): 1, ('C', 'C'): 1, ('C', 'D'): 0, ('C', 'G'): 0, ('C', 'H'): 1, ('C', 'K'): 0, ('C', 'M'): 1, ('C', 'N'): 1, ('C', 'R'): 0, ('C', 'S'): 1, ('C', 'T'): 0, ('C', 'V'): 1, ('C', 'W'): 0, ('C', 'Y'): 1, ('D', '-'): 0, ('D', '.'): 0, ('D', 'A'): 1, ('D', 'B'): 1, ('D', 'C'): 0, ('D', 'D'): 1, ('D', 'G'): 1, ('D', 'H'): 1, ('D', 'K'): 1, ('D', 'M'): 1, ('D', 'N'): 1, ('D', 'R'): 1, ('D', 'S'): 1, ('D', 'T'): 1, ('D', 'V'): 1, ('D', 'W'): 1, ('D', 'Y'): 1, ('G', '-'): 0, ('G', '.'): 0, ('G', 'A'): 0, ('G', 'B'): 1, ('G', 'C'): 0, ('G', 'D'): 1, ('G', 'G'): 1, ('G', 'H'): 0, ('G', 'K'): 1, ('G', 'M'): 0, ('G', 'N'): 1, ('G', 'R'): 1, ('G', 'S'): 1, ('G', 'T'): 0, ('G', 'V'): 1, ('G', 'W'): 0, ('G', 'Y'): 0, ('H', '-'): 0, ('H', '.'): 0, ('H', 'A'): 1, ('H', 'B'): 1, ('H', 'C'): 1, ('H', 'D'): 1, ('H', 'G'): 0, ('H', 'H'): 1, ('H', 'K'): 1, ('H', 'M'): 1, ('H', 'N'): 1, ('H', 'R'): 1, ('H', 'S'): 1, ('H', 'T'): 1, ('H', 'V'): 1, ('H', 'W'): 1, ('H', 'Y'): 1, ('K', '-'): 0, ('K', '.'): 0, ('K', 'A'): 0, ('K', 'B'): 1, ('K', 'C'): 0, ('K', 'D'): 1, ('K', 'G'): 1, ('K', 'H'): 1, ('K', 'K'): 1, ('K', 'M'): 0, ('K', 'N'): 1, ('K', 'R'): 1, ('K', 'S'): 1, ('K', 'T'): 1, ('K', 'V'): 1, ('K', 'W'): 1, ('K', 'Y'): 1, ('M', '-'): 0, ('M', '.'): 0, ('M', 'A'): 1, ('M', 'B'): 1, ('M', 'C'): 1, ('M', 'D'): 1, ('M', 'G'): 0, ('M', 'H'): 1, ('M', 'K'): 0, ('M', 'M'): 1, ('M', 'N'): 1, ('M', 'R'): 1, ('M', 'S'): 1, ('M', 'T'): 0, ('M', 'V'): 1, ('M', 'W'): 1, ('M', 'Y'): 1, ('N', '-'): 0, ('N', '.'): 0, ('N', 'A'): 0, ('N', 'B'): 0, ('N', 'C'): 0, ('N', 'D'): 0, ('N', 'G'): 0, ('N', 'H'): 0, ('N', 'K'): 0, ('N', 'M'): 0, ('N', 'N'): 0, ('N', 'R'): 0, ('N', 'S'): 0, ('N', 'T'): 0, ('N', 'V'): 0, ('N', 'W'): 0, ('N', 'Y'): 0, ('R', '-'): 0, ('R', '.'): 0, ('R', 'A'): 1, ('R', 'B'): 1, ('R', 'C'): 0, ('R', 'D'): 1, ('R', 'G'): 1, ('R', 'H'): 1, ('R', 'K'): 1, ('R', 'M'): 1, ('R', 'N'): 1, ('R', 'R'): 1, ('R', 'S'): 1, ('R', 'T'): 0, ('R', 'V'): 1, ('R', 'W'): 1, ('R', 'Y'): 0, ('S', '-'): 0, ('S', '.'): 0, ('S', 'A'): 0, ('S', 'B'): 1, ('S', 'C'): 1, ('S', 'D'): 1, ('S', 'G'): 1, ('S', 'H'): 1, ('S', 'K'): 1, ('S', 'M'): 1, ('S', 'N'): 1, ('S', 'R'): 1, ('S', 'S'): 1, ('S', 'T'): 0, ('S', 'V'): 1, ('S', 'W'): 0, ('S', 'Y'): 1, ('T', '-'): 0, ('T', '.'): 0, ('T', 'A'): 0, ('T', 'B'): 1, ('T', 'C'): 0, ('T', 'D'): 1, ('T', 'G'): 0, ('T', 'H'): 1, ('T', 'K'): 1, ('T', 'M'): 0, ('T', 'N'): 1, ('T', 'R'): 0, ('T', 'S'): 0, ('T', 'T'): 1, ('T', 'V'): 0, ('T', 'W'): 1, ('T', 'Y'): 1, ('V', '-'): 0, ('V', '.'): 0, ('V', 'A'): 1, ('V', 'B'): 1, ('V', 'C'): 1, ('V', 'D'): 1, ('V', 'G'): 1, ('V', 'H'): 1, ('V', 'K'): 1, ('V', 'M'): 1, ('V', 'N'): 1, ('V', 'R'): 1, ('V', 'S'): 1, ('V', 'T'): 0, ('V', 'V'): 1, ('V', 'W'): 1, ('V', 'Y'): 1, ('W', '-'): 0, ('W', '.'): 0, ('W', 'A'): 1, ('W', 'B'): 1, ('W', 'C'): 0, ('W', 'D'): 1, ('W', 'G'): 0, ('W', 'H'): 1, ('W', 'K'): 1, ('W', 'M'): 1, ('W', 'N'): 1, ('W', 'R'): 1, ('W', 'S'): 0, ('W', 'T'): 1, ('W', 'V'): 1, ('W', 'W'): 1, ('W', 'Y'): 1, ('Y', '-'): 0, ('Y', '.'): 0, ('Y', 'A'): 0, ('Y', 'B'): 1, ('Y', 'C'): 1, ('Y', 'D'): 1, ('Y', 'G'): 0, ('Y', 'H'): 1, ('Y', 'K'): 1, ('Y', 'M'): 1, ('Y', 'N'): 1, ('Y', 'R'): 0, ('Y', 'S'): 1, ('Y', 'T'): 1, ('Y', 'V'): 1, ('Y', 'W'): 1, ('Y', 'Y'): 1})¶ Performs a simple fixed position alignment of primers
Parameters: - seq_record – a SeqRecord object to align primers against
- primers – dictionary of {names: short IUPAC ambiguous sequence strings}
- start – position where primer alignment starts
- rev_primer – if True align with the tail end of the sequence
- score_dict – optional dictionary of {(char1, char2): score} alignment scores
Returns: primer alignment result object
Return type:
-
presto.Sequence.
scoreDNA
(a, b, mask_score=None, gap_score=None)¶ Returns the score for a pair of IUPAC Ambiguous Nucleotide characters
Parameters: - a – First characters
- b – Second character
- n_score – Tuple of length two defining scores for all matches against an N character for (a, b), with the score for character (a) taking precedence; if None score symmetrically according to IUPAC character identity
- gap_score – Tuple of length two defining score for all matches against a gap (-, .) character for (a, b), with the score for character (a) taking precedence; if None score symmetrically according to IUPAC character identity
Returns: Score for the character pair
Return type:
-
presto.Sequence.
scoreSeqPair
(seq1, seq2, ignore_chars={}, score_dict={('-', '-'): 1, ('-', '.'): 1, ('-', 'A'): 0, ('-', 'B'): 0, ('-', 'C'): 0, ('-', 'D'): 0, ('-', 'G'): 0, ('-', 'H'): 0, ('-', 'K'): 0, ('-', 'M'): 0, ('-', 'N'): 0, ('-', 'R'): 0, ('-', 'S'): 0, ('-', 'T'): 0, ('-', 'V'): 0, ('-', 'W'): 0, ('-', 'Y'): 0, ('.', '-'): 1, ('.', '.'): 1, ('.', 'A'): 0, ('.', 'B'): 0, ('.', 'C'): 0, ('.', 'D'): 0, ('.', 'G'): 0, ('.', 'H'): 0, ('.', 'K'): 0, ('.', 'M'): 0, ('.', 'N'): 0, ('.', 'R'): 0, ('.', 'S'): 0, ('.', 'T'): 0, ('.', 'V'): 0, ('.', 'W'): 0, ('.', 'Y'): 0, ('A', '-'): 0, ('A', '.'): 0, ('A', 'A'): 1, ('A', 'B'): 0, ('A', 'C'): 0, ('A', 'D'): 1, ('A', 'G'): 0, ('A', 'H'): 1, ('A', 'K'): 0, ('A', 'M'): 1, ('A', 'N'): 1, ('A', 'R'): 1, ('A', 'S'): 0, ('A', 'T'): 0, ('A', 'V'): 1, ('A', 'W'): 1, ('A', 'Y'): 0, ('B', '-'): 0, ('B', '.'): 0, ('B', 'A'): 0, ('B', 'B'): 1, ('B', 'C'): 1, ('B', 'D'): 1, ('B', 'G'): 1, ('B', 'H'): 1, ('B', 'K'): 1, ('B', 'M'): 1, ('B', 'N'): 1, ('B', 'R'): 1, ('B', 'S'): 1, ('B', 'T'): 1, ('B', 'V'): 1, ('B', 'W'): 1, ('B', 'Y'): 1, ('C', '-'): 0, ('C', '.'): 0, ('C', 'A'): 0, ('C', 'B'): 1, ('C', 'C'): 1, ('C', 'D'): 0, ('C', 'G'): 0, ('C', 'H'): 1, ('C', 'K'): 0, ('C', 'M'): 1, ('C', 'N'): 1, ('C', 'R'): 0, ('C', 'S'): 1, ('C', 'T'): 0, ('C', 'V'): 1, ('C', 'W'): 0, ('C', 'Y'): 1, ('D', '-'): 0, ('D', '.'): 0, ('D', 'A'): 1, ('D', 'B'): 1, ('D', 'C'): 0, ('D', 'D'): 1, ('D', 'G'): 1, ('D', 'H'): 1, ('D', 'K'): 1, ('D', 'M'): 1, ('D', 'N'): 1, ('D', 'R'): 1, ('D', 'S'): 1, ('D', 'T'): 1, ('D', 'V'): 1, ('D', 'W'): 1, ('D', 'Y'): 1, ('G', '-'): 0, ('G', '.'): 0, ('G', 'A'): 0, ('G', 'B'): 1, ('G', 'C'): 0, ('G', 'D'): 1, ('G', 'G'): 1, ('G', 'H'): 0, ('G', 'K'): 1, ('G', 'M'): 0, ('G', 'N'): 1, ('G', 'R'): 1, ('G', 'S'): 1, ('G', 'T'): 0, ('G', 'V'): 1, ('G', 'W'): 0, ('G', 'Y'): 0, ('H', '-'): 0, ('H', '.'): 0, ('H', 'A'): 1, ('H', 'B'): 1, ('H', 'C'): 1, ('H', 'D'): 1, ('H', 'G'): 0, ('H', 'H'): 1, ('H', 'K'): 1, ('H', 'M'): 1, ('H', 'N'): 1, ('H', 'R'): 1, ('H', 'S'): 1, ('H', 'T'): 1, ('H', 'V'): 1, ('H', 'W'): 1, ('H', 'Y'): 1, ('K', '-'): 0, ('K', '.'): 0, ('K', 'A'): 0, ('K', 'B'): 1, ('K', 'C'): 0, ('K', 'D'): 1, ('K', 'G'): 1, ('K', 'H'): 1, ('K', 'K'): 1, ('K', 'M'): 0, ('K', 'N'): 1, ('K', 'R'): 1, ('K', 'S'): 1, ('K', 'T'): 1, ('K', 'V'): 1, ('K', 'W'): 1, ('K', 'Y'): 1, ('M', '-'): 0, ('M', '.'): 0, ('M', 'A'): 1, ('M', 'B'): 1, ('M', 'C'): 1, ('M', 'D'): 1, ('M', 'G'): 0, ('M', 'H'): 1, ('M', 'K'): 0, ('M', 'M'): 1, ('M', 'N'): 1, ('M', 'R'): 1, ('M', 'S'): 1, ('M', 'T'): 0, ('M', 'V'): 1, ('M', 'W'): 1, ('M', 'Y'): 1, ('N', '-'): 0, ('N', '.'): 0, ('N', 'A'): 1, ('N', 'B'): 1, ('N', 'C'): 1, ('N', 'D'): 1, ('N', 'G'): 1, ('N', 'H'): 1, ('N', 'K'): 1, ('N', 'M'): 1, ('N', 'N'): 1, ('N', 'R'): 1, ('N', 'S'): 1, ('N', 'T'): 1, ('N', 'V'): 1, ('N', 'W'): 1, ('N', 'Y'): 1, ('R', '-'): 0, ('R', '.'): 0, ('R', 'A'): 1, ('R', 'B'): 1, ('R', 'C'): 0, ('R', 'D'): 1, ('R', 'G'): 1, ('R', 'H'): 1, ('R', 'K'): 1, ('R', 'M'): 1, ('R', 'N'): 1, ('R', 'R'): 1, ('R', 'S'): 1, ('R', 'T'): 0, ('R', 'V'): 1, ('R', 'W'): 1, ('R', 'Y'): 0, ('S', '-'): 0, ('S', '.'): 0, ('S', 'A'): 0, ('S', 'B'): 1, ('S', 'C'): 1, ('S', 'D'): 1, ('S', 'G'): 1, ('S', 'H'): 1, ('S', 'K'): 1, ('S', 'M'): 1, ('S', 'N'): 1, ('S', 'R'): 1, ('S', 'S'): 1, ('S', 'T'): 0, ('S', 'V'): 1, ('S', 'W'): 0, ('S', 'Y'): 1, ('T', '-'): 0, ('T', '.'): 0, ('T', 'A'): 0, ('T', 'B'): 1, ('T', 'C'): 0, ('T', 'D'): 1, ('T', 'G'): 0, ('T', 'H'): 1, ('T', 'K'): 1, ('T', 'M'): 0, ('T', 'N'): 1, ('T', 'R'): 0, ('T', 'S'): 0, ('T', 'T'): 1, ('T', 'V'): 0, ('T', 'W'): 1, ('T', 'Y'): 1, ('V', '-'): 0, ('V', '.'): 0, ('V', 'A'): 1, ('V', 'B'): 1, ('V', 'C'): 1, ('V', 'D'): 1, ('V', 'G'): 1, ('V', 'H'): 1, ('V', 'K'): 1, ('V', 'M'): 1, ('V', 'N'): 1, ('V', 'R'): 1, ('V', 'S'): 1, ('V', 'T'): 0, ('V', 'V'): 1, ('V', 'W'): 1, ('V', 'Y'): 1, ('W', '-'): 0, ('W', '.'): 0, ('W', 'A'): 1, ('W', 'B'): 1, ('W', 'C'): 0, ('W', 'D'): 1, ('W', 'G'): 0, ('W', 'H'): 1, ('W', 'K'): 1, ('W', 'M'): 1, ('W', 'N'): 1, ('W', 'R'): 1, ('W', 'S'): 0, ('W', 'T'): 1, ('W', 'V'): 1, ('W', 'W'): 1, ('W', 'Y'): 1, ('Y', '-'): 0, ('Y', '.'): 0, ('Y', 'A'): 0, ('Y', 'B'): 1, ('Y', 'C'): 1, ('Y', 'D'): 1, ('Y', 'G'): 0, ('Y', 'H'): 1, ('Y', 'K'): 1, ('Y', 'M'): 1, ('Y', 'N'): 1, ('Y', 'R'): 0, ('Y', 'S'): 1, ('Y', 'T'): 1, ('Y', 'V'): 1, ('Y', 'W'): 1, ('Y', 'Y'): 1})¶ Determine the error rate for a pair of sequences
Parameters: - seq1 – SeqRecord object
- seq2 – SeqRecord object
- ignore_chars – Set of characters to ignore when scoring and counting the weight
- score_dict – Optional dictionary of alignment scores
Returns: Tuple of the (score, minimum weight, error rate) for the pair of sequences
Return type: Tuple
-
presto.Sequence.
sequentialAssembly
(head_seq, tail_seq, ref_dict, ref_db, alpha=1e-05, max_error=0.3, min_len=8, max_len=1000, scan_reverse=False, min_ident=0.5, evalue=1e-05, max_hits=100, fill=False, aligner='usearch', aligner_exec='usearch', assembly_stats=None, score_dict={('-', '-'): 0, ('-', '.'): 0, ('-', 'A'): 0, ('-', 'B'): 0, ('-', 'C'): 0, ('-', 'D'): 0, ('-', 'G'): 0, ('-', 'H'): 0, ('-', 'K'): 0, ('-', 'M'): 0, ('-', 'N'): 0, ('-', 'R'): 0, ('-', 'S'): 0, ('-', 'T'): 0, ('-', 'V'): 0, ('-', 'W'): 0, ('-', 'Y'): 0, ('.', '-'): 0, ('.', '.'): 0, ('.', 'A'): 0, ('.', 'B'): 0, ('.', 'C'): 0, ('.', 'D'): 0, ('.', 'G'): 0, ('.', 'H'): 0, ('.', 'K'): 0, ('.', 'M'): 0, ('.', 'N'): 0, ('.', 'R'): 0, ('.', 'S'): 0, ('.', 'T'): 0, ('.', 'V'): 0, ('.', 'W'): 0, ('.', 'Y'): 0, ('A', '-'): 0, ('A', '.'): 0, ('A', 'A'): 1, ('A', 'B'): 0, ('A', 'C'): 0, ('A', 'D'): 1, ('A', 'G'): 0, ('A', 'H'): 1, ('A', 'K'): 0, ('A', 'M'): 1, ('A', 'N'): 1, ('A', 'R'): 1, ('A', 'S'): 0, ('A', 'T'): 0, ('A', 'V'): 1, ('A', 'W'): 1, ('A', 'Y'): 0, ('B', '-'): 0, ('B', '.'): 0, ('B', 'A'): 0, ('B', 'B'): 1, ('B', 'C'): 1, ('B', 'D'): 1, ('B', 'G'): 1, ('B', 'H'): 1, ('B', 'K'): 1, ('B', 'M'): 1, ('B', 'N'): 1, ('B', 'R'): 1, ('B', 'S'): 1, ('B', 'T'): 1, ('B', 'V'): 1, ('B', 'W'): 1, ('B', 'Y'): 1, ('C', '-'): 0, ('C', '.'): 0, ('C', 'A'): 0, ('C', 'B'): 1, ('C', 'C'): 1, ('C', 'D'): 0, ('C', 'G'): 0, ('C', 'H'): 1, ('C', 'K'): 0, ('C', 'M'): 1, ('C', 'N'): 1, ('C', 'R'): 0, ('C', 'S'): 1, ('C', 'T'): 0, ('C', 'V'): 1, ('C', 'W'): 0, ('C', 'Y'): 1, ('D', '-'): 0, ('D', '.'): 0, ('D', 'A'): 1, ('D', 'B'): 1, ('D', 'C'): 0, ('D', 'D'): 1, ('D', 'G'): 1, ('D', 'H'): 1, ('D', 'K'): 1, ('D', 'M'): 1, ('D', 'N'): 1, ('D', 'R'): 1, ('D', 'S'): 1, ('D', 'T'): 1, ('D', 'V'): 1, ('D', 'W'): 1, ('D', 'Y'): 1, ('G', '-'): 0, ('G', '.'): 0, ('G', 'A'): 0, ('G', 'B'): 1, ('G', 'C'): 0, ('G', 'D'): 1, ('G', 'G'): 1, ('G', 'H'): 0, ('G', 'K'): 1, ('G', 'M'): 0, ('G', 'N'): 1, ('G', 'R'): 1, ('G', 'S'): 1, ('G', 'T'): 0, ('G', 'V'): 1, ('G', 'W'): 0, ('G', 'Y'): 0, ('H', '-'): 0, ('H', '.'): 0, ('H', 'A'): 1, ('H', 'B'): 1, ('H', 'C'): 1, ('H', 'D'): 1, ('H', 'G'): 0, ('H', 'H'): 1, ('H', 'K'): 1, ('H', 'M'): 1, ('H', 'N'): 1, ('H', 'R'): 1, ('H', 'S'): 1, ('H', 'T'): 1, ('H', 'V'): 1, ('H', 'W'): 1, ('H', 'Y'): 1, ('K', '-'): 0, ('K', '.'): 0, ('K', 'A'): 0, ('K', 'B'): 1, ('K', 'C'): 0, ('K', 'D'): 1, ('K', 'G'): 1, ('K', 'H'): 1, ('K', 'K'): 1, ('K', 'M'): 0, ('K', 'N'): 1, ('K', 'R'): 1, ('K', 'S'): 1, ('K', 'T'): 1, ('K', 'V'): 1, ('K', 'W'): 1, ('K', 'Y'): 1, ('M', '-'): 0, ('M', '.'): 0, ('M', 'A'): 1, ('M', 'B'): 1, ('M', 'C'): 1, ('M', 'D'): 1, ('M', 'G'): 0, ('M', 'H'): 1, ('M', 'K'): 0, ('M', 'M'): 1, ('M', 'N'): 1, ('M', 'R'): 1, ('M', 'S'): 1, ('M', 'T'): 0, ('M', 'V'): 1, ('M', 'W'): 1, ('M', 'Y'): 1, ('N', '-'): 1, ('N', '.'): 1, ('N', 'A'): 1, ('N', 'B'): 1, ('N', 'C'): 1, ('N', 'D'): 1, ('N', 'G'): 1, ('N', 'H'): 1, ('N', 'K'): 1, ('N', 'M'): 1, ('N', 'N'): 1, ('N', 'R'): 1, ('N', 'S'): 1, ('N', 'T'): 1, ('N', 'V'): 1, ('N', 'W'): 1, ('N', 'Y'): 1, ('R', '-'): 0, ('R', '.'): 0, ('R', 'A'): 1, ('R', 'B'): 1, ('R', 'C'): 0, ('R', 'D'): 1, ('R', 'G'): 1, ('R', 'H'): 1, ('R', 'K'): 1, ('R', 'M'): 1, ('R', 'N'): 1, ('R', 'R'): 1, ('R', 'S'): 1, ('R', 'T'): 0, ('R', 'V'): 1, ('R', 'W'): 1, ('R', 'Y'): 0, ('S', '-'): 0, ('S', '.'): 0, ('S', 'A'): 0, ('S', 'B'): 1, ('S', 'C'): 1, ('S', 'D'): 1, ('S', 'G'): 1, ('S', 'H'): 1, ('S', 'K'): 1, ('S', 'M'): 1, ('S', 'N'): 1, ('S', 'R'): 1, ('S', 'S'): 1, ('S', 'T'): 0, ('S', 'V'): 1, ('S', 'W'): 0, ('S', 'Y'): 1, ('T', '-'): 0, ('T', '.'): 0, ('T', 'A'): 0, ('T', 'B'): 1, ('T', 'C'): 0, ('T', 'D'): 1, ('T', 'G'): 0, ('T', 'H'): 1, ('T', 'K'): 1, ('T', 'M'): 0, ('T', 'N'): 1, ('T', 'R'): 0, ('T', 'S'): 0, ('T', 'T'): 1, ('T', 'V'): 0, ('T', 'W'): 1, ('T', 'Y'): 1, ('V', '-'): 0, ('V', '.'): 0, ('V', 'A'): 1, ('V', 'B'): 1, ('V', 'C'): 1, ('V', 'D'): 1, ('V', 'G'): 1, ('V', 'H'): 1, ('V', 'K'): 1, ('V', 'M'): 1, ('V', 'N'): 1, ('V', 'R'): 1, ('V', 'S'): 1, ('V', 'T'): 0, ('V', 'V'): 1, ('V', 'W'): 1, ('V', 'Y'): 1, ('W', '-'): 0, ('W', '.'): 0, ('W', 'A'): 1, ('W', 'B'): 1, ('W', 'C'): 0, ('W', 'D'): 1, ('W', 'G'): 0, ('W', 'H'): 1, ('W', 'K'): 1, ('W', 'M'): 1, ('W', 'N'): 1, ('W', 'R'): 1, ('W', 'S'): 0, ('W', 'T'): 1, ('W', 'V'): 1, ('W', 'W'): 1, ('W', 'Y'): 1, ('Y', '-'): 0, ('Y', '.'): 0, ('Y', 'A'): 0, ('Y', 'B'): 1, ('Y', 'C'): 1, ('Y', 'D'): 1, ('Y', 'G'): 0, ('Y', 'H'): 1, ('Y', 'K'): 1, ('Y', 'M'): 1, ('Y', 'N'): 1, ('Y', 'R'): 0, ('Y', 'S'): 1, ('Y', 'T'): 1, ('Y', 'V'): 1, ('Y', 'W'): 1, ('Y', 'Y'): 1})¶ Stitches sequences together by first attempting de novo assembly then falling back to reference guided assembly
Parameters: - head_seq – the head SeqRecord
- head_seq – the tail SeqRecord
- ref_dict – a dictionary of reference SeqRecord objects
- ref_db – the path and name of the reference database
- alpha – the minimum p-value for a valid de novo assembly
- max_error – the maximum error rate for a valid de novo assembly
- min_len – minimum length of overlap to test for de novo assembly
- max_len – maximum length of overlap to test for de novo assembly
- scan_reverse – if True allow the head sequence to overhang the end of the tail sequence in de novo assembly if False end alignment scan at end of tail sequence or start of head sequence
- min_ident – the minimum identity for a valid reference guided assembly
- evalue – the E-value cut-off for reference guided assembly
- max_hits – the maxhits output limit for reference guided assembly
- fill – if False non-overlapping regions will be assigned Ns in reference guided assembly; if True non-overlapping regions will be filled with the reference sequence.
- aligner – the alignment tool; one of ‘blastn’ or ‘usearch’
- aligner_exec – the path to the alignment tool executable
- assembly_stats – optional successes by trials numpy.array of p-values
- score_dict – optional dictionary of character scores in the form {(char1, char2): score}.
Returns: assembled sequence object.
Return type:
-
presto.Sequence.
subsetSeqIndex
(seq_dict, field, values, delimiter=('|', '=', ', '))¶ Subsets a sequence set by annotation value
Parameters: - seq_dict – Dictionary index of sequences returned from SeqIO.index()
- field – Annotation field to select keys by
- values – List of annotation values that define the retained keys
- delimiter – Tuple of delimiters for (annotations, field/values, value lists)
Returns: List of keys
Return type:
-
presto.Sequence.
subsetSeqSet
(seq_iter, field, values, delimiter=('|', '=', ', '))¶ Subsets a sequence set by annotation value
Parameters: - seq_iter – Iterator or list of SeqRecord objects
- field – Annotation field to select by
- values – List of annotation values that define the retained sequences
- delimiter – Tuple of delimiters for (annotations, field/values, value lists)
Returns: Modified list of SeqRecord objects
Return type:
-
presto.Sequence.
translateAmbigDNA
(key)¶ Translates IUPAC Ambiguous Nucleotide characters to or from character sets
Parameters: key – String or re.search object containing the character set to translate Returns: Character translation Return type: str
-
presto.Sequence.
trimQuality
(data, min_qual=0, window=10, reverse=False)¶ Cuts sequences using a moving mean quality score
Parameters: Returns: SeqResult object.
Return type: