Provide utilities.
platform: | Unix |
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synopsis: | Give utility function for the analysis of TFFMs. |
Get the number of sequences, number of residues, and starting nucleotides.
Parameters: | seq_file (str) – File containing the sequences in fasta format |
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Returns: | The number of sequences, number of residues, and starting nucleotides occurrences |
Return type: | tuple of (int, int, dic of str->int) |
Parse a fasta file and return the list of SeqRecord items.
Parameters: | fasta_file (str) – Fasta file containing the sequences. |
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Returns: | The set of Bio.SeqRecord instances found in the fasta file. |
Return type: | list of Bio.SeqRecord |
Create a generator interlacing the iterables given in argument.
For example, roundrobin(‘ABC’, ‘D’, ‘EF’) –> A D E B F C
Parameters: | iterables – Pointer to the iterables. |
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Returns: | The generator over the intarlaced iterables. |
Return type: | Generator |
Give the same weight weight to all the sequences in sequences.
The sequences are constructed using the ghmm module and form a ghmm.SequenceSet.
Parameters: | sequences (ghmm.SequenceSet) – List of sequences to weight |
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Module author: Anthony Mathelier <amathelier@cmmt.ubc.ca>