AlignmentParser[source]¶Bases: object
Parser for manipulation of MSAs
a3mToTrimmed(alnFile, outFile)[source]¶Convert an .a3m HH-suite file to a FASTA format
| AlnFile: | A3M format alignment file |
|---|---|
| OutFile: | MSA output file |
align_sequences(seq1, seq2)[source]¶Global pairwise alignment of two sequences
| Returns: | aligned sequences as tuple |
|---|
read(alnFile, alnFormat)[source]¶Read a multiple sequence alignment
| AlnFile: | MSA file |
|---|---|
| AlnFormat: | MSA format |
| Returns: | Biopython MSA generator |
removeGaps(alnFile, outFile)[source]¶Remove all gaps in a MSA
| AlnFile: | FASTA alignment file |
|---|---|
| OutFile: | FASTA sequence file |