redwood.py 文件源码

def fix_query_reflength(sequence_length, queries, doubled):
    """
    arguments:
     <sequence_length> This is the reference fasta length. It should be 2x the actual
               length of the reference since this program takes a sam file from
               a concatenated reference.
     <queries> This is a list of SQL-type query strings. This is generated
                from argparse.

    purpose:
     This function takes in a list of queries to use for read filtering
     for the redwood plot. It is often not advisable to plot all mapped reads
     since many of them are too small relative to the reference length. Also,
     the point of a death star plot is to show continuity of a circular
     reference, so short reads aren't very helpful there either.

     Currently, this function only recognizes the keyword argument 'reflength'.
    """
    if not doubled:
        sequence_length = int(sequence_length * 2)
    for i in range(len(queries)):
        if 'reflength' in queries[i].split():
            queries[i] = queries[i].replace('reflength', str(int(sequence_length/2)))