chris-rands / mmprofiler Goto Github PK
View Code? Open in Web Editor NEWCreate mmseq2 profiles from (unaligned) protein families/clusters, under development
License: MIT License
Create mmseq2 profiles from (unaligned) protein families/clusters, under development
License: MIT License
@SilasK wasn't this working before- was it removed from conda? Thanks!
e.g.
$ conda install mmprofiler
Collecting package metadata: done
Solving environment: failed
PackagesNotFoundError: The following packages are not available from current channels:
- mmprofiler
Current channels:
- https://conda.anaconda.org/conda-forge/linux-64
- https://conda.anaconda.org/conda-forge/noarch
- https://conda.anaconda.org/bioconda/linux-64
- https://conda.anaconda.org/bioconda/noarch
- https://repo.anaconda.com/pkgs/main/linux-64
- https://repo.anaconda.com/pkgs/main/noarch
- https://repo.anaconda.com/pkgs/free/linux-64
- https://repo.anaconda.com/pkgs/free/noarch
- https://repo.anaconda.com/pkgs/r/linux-64
- https://repo.anaconda.com/pkgs/r/noarch
To search for alternate channels that may provide the conda package you're
looking for, navigate to
https://anaconda.org
and use the search bar at the top of the page.
trim all rims fasta header of OG clusters from xxxxx:yyyyy to xxxxx
Hey @chris-rands,
Could you add me as a contributor so I can directly push to your repo?
I suggest to try to conform to the guide for snakemake-workflows project, what do you think?
mmseqs msa2profile --help
prefilter options default description [value range]
--comp-bias-corr 1 correct for locally biased amino acid composition [0,1]
align options default description [value range]
--gap-open 11 Gap open cost
--gap-extend 1 Gap extension cost
profile options default description [value range]
--match-mode 0 0: Columns that have a residue in the first sequence are kept, 1: columns that have a residue in --match-ratio of all sequences are kept.
--match-ratio 0.500 columns that have a residue in this ratio of all sequences are kept
--pca 0.000 pseudo count admixture strength
--pcb 1.500 pseudo counts: Neff at half of maximum admixture (0.0,infinity)
--wg false use global sequence weighting for profile calculation
--filter-msa 1 filter msa: 0: do not filter, 1: filter
--cov 0.000 filter output MSAs using min. fraction of query residues covered by matched sequences [0.0,1.0]
--qid 0.000 reduce diversity of output MSAs using min.seq. identity with query sequences [0.0,1.0]
--qsc -20.000 reduce diversity of output MSAs using min. score per aligned residue with query sequences [-50.0,100.0]
--max-seq-id 0.900 reduce redundancy of output MSA using max. pairwise sequence identity [0.0,1.0]
--diff 1000 filter MSAs by selecting most diverse set of sequences, keeping at least this many seqs in each MSA block of length 50
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