def vfind.find_variants(
fq_path: str,
adapters: tuple(str, str),
match_score: int = 3,
mismatch_score: int = -2,
gap_open_penalty: int = 5,
gap_extend_penalty: int = 2,
accept_prefix_alignment: float = 0.75,
accept_suffix_alignment: float = 0.75,
skip_translation: bool = False,
show_progress: bool = True,
n_threads: int = 3,
queue_len: int = 2,
)Find variable regions flanked by constant adapters.
fq_path: str [Required]: Path to fastq file.
adapters: tuple(str, str) [Required]: Constant adapter sequences flanking variable region.
match_score: int [Optional, Default = 3]: Match score used for alignment.
mismatch_score: int [Optional, Default = -2]: Mismatch score used for alignment.
gap_open_penalty: int [Optional, Default = 5]: Gap open penalty used for alignment. Note that this is given as a positive integer.
gap_extend_penalty: int [Optional, Default = 2]: Gap extension penalty used for alignment. Note that this is given as a positive integer.
accept_prefix_alignment: float (0, 1] [Optional, Default = 0.75]: Threshold for accepting alignments between read and 5' adapter (prefix) sequences. Set to 1 to skip alignment and only allow perfect matches of the prefix.
accept_suffix_alignment: float (0, 1] [Optional, Default = 0.75]: Threshold for accepting alignments between read and 3' adapter (suffix) sequences. Set to 1 to skip alignment and only allow perfect matches of the suffix.
skip_translation: bool [Optional, Default = False]: Whether to skip in-frame translation and return DNA sequences.
show_progress: bool [Optional, Default = True]: Whether to show visual progress bar.*
n_threads: int [Optional, Default = 3]: Number of threads to use for processing fastq.
queue_len: int [Optional, Default = 2]: Queue length used for processing fastq.
polars.DataFrame: Dataframe with sequence and count columns
corresponding to recovered sequences mapped to raw read counts.