SeqGroup(sequences=None, format='fasta', fix_duplicates=True, **kwargs)¶
SeqGroup class can be used to store a set of sequences (aligned or not).
- sequences – Path to the file containing the sequences or, alternatively, the text string containing the same information.
- format (fasta) – the format in which sequences are
encoded. Current supported formats are:
phylip(phylip sequencial) and
iphylip(phylip interleaved). Phylip format forces sequence names to a maximum of 10 chars. To avoid this effect, you can use the relaxed phylip format:
msf = ">seq1\nAAAAAAAAAAA\n>seq2\nTTTTTTTTTTTTT\n" seqs = SeqGroup(msf, format="fasta") print seqs.get_seq("seq1")
Returns the list of entries currently stored.
Returns the sequence associated to a given entry name.
Returns an iterator over all sequences in the collection. Each item is a tuple with the sequence name, sequence, and sequence comments
set_seq(name, seq, comments=None)¶
Updates or adds a sequence
Returns the text representation of the sequences in the supplied given format (default=FASTA). If “oufile” argument is used, the result is written into the given path.