Handling of biological data¶
modpipe.sequence
– Handling of amino acid sequences¶
Handling of amino acid sequences and common file formats
- class modpipe.sequence.FASTAFile¶
Representation of a FASTA-format file
- class modpipe.sequence.PIRFile¶
Representation of a PIR-format file
- class modpipe.sequence.SPTRFile¶
Representation of a file containing UniProtKB/SwissProt or TrEMBL database entries
- class modpipe.sequence.Sequence¶
Representation of a single amino acid sequence
- clean(keep_char='')¶
Clean up the primary sequence
- get_id()¶
Return the ModPipe sequence identifier
- class modpipe.sequence.UniqueFile¶
Mapping file from alignment codes to ModPipe IDs
- add_sequence(modpipe_id, align_code)¶
Add a single mapping from an align code to a ModPipe ID
- file_name_from_seqfile(seqfile)¶
Given an input sequence file, return a suitable name for the unique file
- write(fh)¶
Write the code-ID mapping to a stream