Seqgroup class¶
-
class
SeqGroup
(sequences=None, format='fasta', fix_duplicates=True, **kwargs)¶ Bases:
object
SeqGroup class can be used to store a set of sequences (aligned or not).
Parameters: - 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:
fasta
,phylip
(phylip sequencial) andiphylip
(phylip interleaved). Phylip format forces sequence names to a maximum of 10 chars. To avoid this effect, you can use the relaxed phylip format:phylip_relaxed
andiphylip_relaxed
.
msf = ">seq1\nAAAAAAAAAAA\n>seq2\nTTTTTTTTTTTTT\n" seqs = SeqGroup(msf, format="fasta") print seqs.get_seq("seq1")
-
get_entries
()¶ Returns the list of entries currently stored.
-
get_seq
(name)¶ Returns the sequence associated to a given entry name.
-
iter_entries
()¶ 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
-
write
(format='fasta', outfile=None)¶ 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.