mpa.ProfileFreq¶
Overview
ProfileFreq
is a program within the mpathic package which calculates the
fractional occurrence of each base or amino acid at each position.
Usage
>>> import mpathic as mpa
>>> pf = mpa.profile_freq_class
>>> pf.profile_freq_class()
Example Input and Output
Input tables must contain a position column (labeled ‘’pos’‘) and columns for each base or amino acid (labeled ct_A, ct_C…).
Example Input Table:
pos ct_A ct_C ct_G ct_T
0 10 20 40 30
...
Example Output Table:
pos freq_A freq_C freq_G freq_T
0 .1 .2 .4 .3
...
Class Details¶
-
class
mpathic.src.profile_freq.
ProfileFreq
(dataset_df=None, bin=None, start=0, end=None)¶ Profile Frequencies computes character frequencies (0.0 to 1.0) at each position
Parameters: - dataset_df: (pandas dataframe)
A dataframe containing a valid dataset.
- bin: (int)
A bin number specifying which counts to use
- start: (int)
An integer specifying the sequence start position
- end: (int)
An integer specifying the sequence end position
Returns: - freq_df: (pd.DataFrame)
A dataframe containing counts for each nucleotide/amino
acid character at each position.