modpipe.sequence – Handling of amino acid sequences
Handling of amino acid sequences and common file formats
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class modpipe.sequence.FASTAFile
Representation of a FASTA-format file
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read(fh)
Read sequences from the given stream in FASTA format. A list of
the sequences is returned, as Sequence objects.
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write(fh, seq, width=70)
Write a single Sequence object to the given stream in
FASTA format.
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class modpipe.sequence.PIRFile
Representation of a PIR-format file
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read(fh)
Read sequences from the given stream in PIR format. A list of
the sequences is returned, as Sequence objects.
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write(fh, seq, width=70)
Write a single Sequence object to the given stream in
PIR format.
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class modpipe.sequence.SPTRFile
Representation of a file containing UniProtKB/SwissProt or TrEMBL
database entries
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read(fh)
Read sequences from the given stream in SPTR format. A list of
the sequences is returned, as Sequence objects.
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class modpipe.sequence.Sequence
Representation of a single amino acid sequence
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clean()
Clean up the primary sequence
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get_id()
Return the ModPipe sequence identifier
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class modpipe.sequence.UniqueFile
Mapping file from alignment codes to ModPipe IDs
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add_sequence(modpipe_id, align_code)
Add a single mapping from an align code to a ModPipe ID
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file_name_from_seqfile(seqfile)
Given an input sequence file, return a suitable name for the
unique file
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write(fh)
Write the code-ID mapping to a stream