Alignment
Setup
Alignment
get_fasta
get_fasta (df, seq_col='kd_seq', id_col='kd_ID', path='out.fasta')
Generate fasta file from sequences.
get_fasta(kd,seq_col='kd_seq',id_col='kd_ID',path='raw/kinase_domains.fasta')To run clustalo alignment, can run either through terminal or the function
sudo apt-get update
sudo apt-get install clustalo
clustalo -i kinase_domains.fasta -o kinase_domains.aln --force --outfmt=clurun_clustalo
run_clustalo (input_fasta, output_aln, outfmt='clu')
Run Clustal Omega to perform multiple sequence alignment.
| Type | Default | Details | |
|---|---|---|---|
| input_fasta | .fasta fname | ||
| output_aln | .aln output fname | ||
| outfmt | str | clu |
run_clustalo("kinase_domains.fasta", "raw/kinase_domains.aln")aln2df
aln2df (fname)
df = aln2df("raw/kinase_domains.aln")get_aln_freq
get_aln_freq (df)
Get frequency of each amino acid across each position from the aln2df output.
freq_df = get_aln_freq(df)