wub.mappers package¶
Submodules¶
wub.mappers.lastal module¶
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class
wub.mappers.lastal.
LastRecord
(score, r_name, r_start, r_aln_len, r_strand, r_len, r_aln, q_name, q_start, q_aln_len, q_strand, q_len, q_aln)¶ Bases:
tuple
Create new instance of LastRecord(score, r_name, r_start, r_aln_len, r_strand, r_len, r_aln, q_name, q_start, q_aln_len, q_strand, q_len, q_aln)
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q_aln
¶ Alias for field number 12
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q_aln_len
¶ Alias for field number 9
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q_len
¶ Alias for field number 11
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q_name
¶ Alias for field number 7
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q_start
¶ Alias for field number 8
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q_strand
¶ Alias for field number 10
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r_aln
¶ Alias for field number 6
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r_aln_len
¶ Alias for field number 3
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r_len
¶ Alias for field number 5
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r_name
¶ Alias for field number 1
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r_start
¶ Alias for field number 2
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r_strand
¶ Alias for field number 4
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score
¶ Alias for field number 0
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wub.mappers.lastal.
check_lastdb_files
(ref_dir, name)[source]¶ Check that all lastdb files with name label exist within directory
Parameters: - ref_dir – directory to check for lastdb files
- name – label to search for e.g. ‘a’ for a.prj
Returns: list of missing extensions, [] if none missing
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wub.mappers.lastal.
clean_lastdb_files
(ref_dir, name)[source]¶ Remove lastdb files having prefix name in ref_dir.
Parameters: - ref_dir – directory to check for lastdb files
- name – label to search for e.g. ‘a’ for a.prj
Returns: None
Return type: object
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wub.mappers.lastal.
compare_genomes_lastal
(ref_fasta, target_fasta, filter_alns=True, lastal_options=None, cleanup=True)[source]¶ Compare a refrence set of sequences to a target set os sequences using lastal alignment.
Parameters: - ref_fasta – Reference sequence set in fasta format.
- target_fasta – Target sequence set in fasta format.
- filter_alns – Filter alignments if True.
- lastal_options – Options passed to lastal in a dictionary.
- cleanup – If True then lastal database files will be deleted.
Returns: A pandas data frame with various per-alignment statistics.
Return type: DataFrame
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wub.mappers.lastal.
filter_top_per_query
(records)[source]¶ Filter lastal alignment records keeping the best scoring one per query.
Parameters: records – A collection of LastRecord named tuples. Returns: A list of LastRecord named tuples. Return type: list
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wub.mappers.lastal.
lastal_align
(database, query, executable='lastal', **kwargs)[source]¶ Runs lastal via subprocess.
Parameters: - database – database prefix
- query – filepath for the query file
- kwargs – -[args] wanted for lastal e.g. v=’’ for verbosity
Returns: alignment output
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wub.mappers.lastal.
lastdb
(ref_dir, ref_name, ref, executable='lastdb', **kwargs)[source]¶ Runs lastdb on ref within ref_dir using the label ref_name if any errors thrown during runtime, files are checked for existence if all files accounted for, successful=False but no errors thrown. Otherwise, IOError or CalledProcessError thrown.
Parameters: - ref_dir – directory you will find lastdb files in
- ref_name – name of the lastdb files e.g. a for a.prj..
- ref – filepath for reference file
- executable – path/executable for lastdb e.g. ont_lastdb
- kwargs – any -[arg] wanted see lastdb -h for details
Returns: True/False is successful with no errors and command run
Raises: IOError if files don’t exist
Raises: subprocess.CalledProcessError for errors during runtime