mgkit.io.fasta module¶
Simple fasta parser and a few utility functions
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mgkit.io.fasta.
load_fasta
(file_handle)¶ Changed in version 0.1.13: now returns uppercase sequences
Loads a fasta file and returns a generator of tuples in which the first element is the name of the sequence and the second the sequence
Parameters: file_handle (str, file) – fasta file to open; a file name or a file handle is expected Yields: tuple – first element is the sequence name/header, the second element is the sequence
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mgkit.io.fasta.
load_fasta_files
(files)¶ New in version 0.3.4.
Loads all fasta files from a list or iterable
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mgkit.io.fasta.
load_fasta_prodigal
(file_handle)¶ New in version 0.3.1.
Reads a Prodigal aminoacid fasta file and yields a dictionary with basic information about the sequences.
Parameters: file_handle (str, file) – passed to load_fasta()
Yields: dict – dictionary with the information contained in the header, the last of the attributes put into key attr, while the rest are transformed to other keys: seq_id, seq, start, end (genomic), strand, ordinal of
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mgkit.io.fasta.
load_fasta_rename
(file_handle, name_func=None)¶ New in version 0.3.1.
Renames the header of the sequences using name_func, which is called on each header. By default, the behaviour is to keep the header to the left of the first space (BLAST behaviour).
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mgkit.io.fasta.
split_fasta_file
(file_handle, name_mask, num_files)¶ New in version 0.1.13.
Splits a fasta file into a series of smaller files.
Parameters:
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mgkit.io.fasta.
write_fasta_sequence
(file_handle, name, seq, wrap=60, write_mode='a')¶ Write a fasta sequence to file. If the file_handle is a string, the file will be opened using write_mode.
Parameters: