Mmseq
Implementation of the MMSeq2 clustering algorithm. https://github.com/soedinglab/MMseqs2
mmseqs_cluster(query_fasta, reference_fasta=None, cluster_threshold=0.9, sort=True, coverage_mode=0, sensitivity=7.0, outfile_name_suffix='clusters', tmp_dir='/tmp', cluster_mode=0, self_match=True)
¶
Cluster sequences using MMSeqs2 https://mmseqs.com/latest/userguide.pdf
| PARAMETER | DESCRIPTION |
|---|---|
query_fasta
|
Path to the query FASTA file.
|
reference_fasta
|
Path to the reference FASTA file. Default is None.
|
cluster_threshold
|
Cluster threshold. Default is 0.9.
|
sort
|
Sort the output. Default is True.
|
coverage_mode
|
Coverage mode. Default is 0. See MMSeqs2 documentation for more details.
|
sensitivity
|
Sensitivity. Default is 7.0.
|
outfile_name_suffix
|
Suffix for the output file and path. Default is "clusters" saved in the current working directory.
|
tmp_dir
|
Temporary directory. Default is
|
cluster_mode
|
Cluster mode. Default is 0. See MMSeqs2 documentation for more details.
|
self_match
|
Include self-matches. Default is True.
|
mmseqs_parser(tsv_filename, save=False, save_filename=None)
¶
Parse MMSeq2 output TSV file.
| PARAMETER | DESCRIPTION |
|---|---|
tsv_filename
|
Path to the MMSeq2 output TSV file.
|
save
|
Save the parsed clusters to a file. Default is False.
|
save_filename
|
File Path to save the parsed clusters. Default is None.
|
| RETURNS | DESCRIPTION |
|---|---|
DataFrame
|
DataFrame containing the parsed MMSeq2 output. |