AlignmentParser
[source]¶Bases: object
Parser for manipulation of MSAs
Methods
a3mToTrimmed (alnFile, outFile) |
Convert an .a3m HH-suite file to a FASTA format |
align_sequences (seq1, seq2) |
Global pairwise alignment of two sequences |
read (alnFile, alnFormat) |
Read a multiple sequence alignment |
removeGaps (alnFile, outFile) |
Remove all gaps in a MSA |
resetA3M (alnFile, outFile) |
Reset a A3M alignment to FASTA sequences |
write (alignment, file, format) |
Write a MSA object to a file |
a3mToTrimmed
(alnFile, outFile)[source]¶Convert an .a3m HH-suite file to a FASTA format
AlnFile: | A3M format alignment file |
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OutFile: | MSA output file |
align_sequences
(seq1, seq2)[source]¶Global pairwise alignment of two sequences
Returns: | aligned sequences as tuple |
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read
(alnFile, alnFormat)[source]¶Read a multiple sequence alignment
AlnFile: | MSA file |
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AlnFormat: | MSA format |
Returns: | Biopython MSA generator |
removeGaps
(alnFile, outFile)[source]¶Remove all gaps in a MSA
AlnFile: | FASTA alignment file |
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OutFile: | FASTA sequence file |