Wish list

BuddySuite Module Section

This is where new feature requests are queued up, and it is also a good place to store ToDo items. If proposing a new function, create a def block with the suggested function name. Include comments that explain what the function should do, any relevant references, and propose inputs and outputs if simple buddy objects are insufficient.

Example:

# ##################################################### WISH LIST #################################################### #
def predict_orfs():
    # Add all predicted open reading frames to seqrecord features list
    # http://www.ncbi.nlm.nih.gov/gorf/gorf.html
    return


def sim_ident(matrix):  
    # Return the pairwise similarity and identity scores among sequences
    # Input matrix will describe the relative scores for calculating similarity (eg. BLOSUM62)
    # Output should be a dictionary of values, easily parsable to create a table in the command line UI
    # http://imed.med.ucm.es/Tools/sias.html
    x = matrix
    return x


def delete_pattern():  
   # remove residues that match a given pattern from all records
    return

# - Allow batch calls. E.g., if 6 files are fed in as input, run the SeqBuddy command provided independently on each
# - Add support for selecting individual sequences to modify
# - Add FASTQ support... More generally, support letter annotation mods