star-allele-comp 0.2

Utility to compare star alleles

Star Alleles Comparator (star_allele_comp)

The comparator can compare HLA or KIR alleles between cohorts

Install

pip install git+https://github.com/linnil1/star_alleles_comparator

Usage

1. Using command line

star_allele_comp hla_result1.csv hla_result2.csv --family hla --save tmp --plot -v

The results will output to screen and save in .txt and .csv format.

The example output is the same as below (see next section).

The input CSV should adhere to the following format:

Columns

• id (required): The sample ID.
• method (optinal): The method. If not specified, filename will be used.
• allele* (required) Columns starting with allele will be used to store the allele for each id/sample with corresponding method. The value can be NULL, empty.

Format 1: Separate Columns for Alleles

For this format, each allele is represented in separate columns:

method,id,allele1,allele2,allele3,allele4
method1,id1,"A*01:02:03:04","A*01:02","B*01:01:01:01"
method1,id2,"A*01:02:03:04","A*01:02","B*01:01:01:01"
method1,id2,"C*03","C*03:03"
method2,id1,"A*01:02:03:04","A*01:02:03","B*01:02:02:01","B*04:01:02"
method2,id2,"A*01:02:03:04","A*01:02:03","B*01:02:02:01","B*04:01:02"
method2,id2,"C*03:03", "C*03:02"

Format 2: Using "alleles" Column with Underscore as Separator

In this format, the alleles column contains a single string with alleles separated by underscores:

method,id,alleles
method1,id3,"KIR2DL1*0010203_KIR2DL1*001_KIR2DS1*0010101"
method1,id4,"KIR2DL1*0010203_KIR2DL1*00102_KIR2DS1*00101"
method1,id3,"KIR2DL1*03105_KIR2DL1*03:03"
method2,id3,"KIR2DL1*001_KIR2DL1*0030203_KIR2DS1*0010208_KIR2DS1*0040102"
method2,id4,"KIR2DL1*0010203_KIR2DL1*0010203_KIR2DS1*0010202_KIR2DS1*0040302"
method2,id4,"KIR2DL1*00303_KIR2DL1*03002"

2. Using Python functions

Run comparison

from star_allele_comp import compare_method, print_all_summary, plot_summary
cohort = {
    "method1": { "sample_id1": [ "A*01:02:03:04", "A*01:02", "B*01:01:01:01", "B*03:01"] },
    "method2": { "sample_id1": [ "A*01:02:03:04", "A*01:02:03", "B*01:02:02:01", "B*04:01:02"] },
}
ground_truth_method = "method1"
result = compare_method(cohort, ground_truth_method, "hla")

Print result allele by allele

print(result)

# Method method2
# Sample sample_id1
# A*01:02:03:04    =4= A*01:02:03:04
# A*01:02          =2= A*01:02:03
# B*01:01:01:01    =1= B*01:02:02:01
# B*03:01          =0= B*04:01:02
# Note:
# Left hand side is the alleles in reference method/cohort
# Right hand side is the allele in another method/cohort

Print summary (i.e. Accuracy vs Resolution, Confusion Matrix)

# details are in star_allele_comp/summary.py:print_all_summary
df_cohort = result.to_dataframe()
print_all_summary(df_cohort)

Accuracy summary
           Accuracy                                num_match                     num_ref
Resolution        0     1    2    3    4   FP   FN         0  1  2  3  4  FP  FN       0  1  2  3  4  FP  FN
method
method1         1.0  1.00  1.0  1.0  1.0  0.0  0.0         4  4  4  2  2   0   0       4  4  4  2  2   0   0
method2         1.0  0.75  0.5  0.5  0.5  0.0  0.0         4  3  2  1  1   0   0       4  4  4  2  2   0   0

# Note In the accuracy summary table:
# * num_match represents the number of alleles that match the alleles in the ground truth method under the specific `Resolution`.
# * num_ref indicates the number of reference alleles with resolution >= `Resolution`
# * Accuracy is calculated as the ratio of num_match to num_ref.
# * Accuracy in FP is False Discovery Rate (FDR)
# * Accuracy in FN is False Negative Rate (FNR)


Confusion matrix (not the same sample)
            Count
 match_res      -1  0  1  2  3
 ref_res
-1              2  0  0  0  0
 1              1  1  0  0  0
 2              1  0  2  6  0
 3              0  0  0  0  1
 4              0  0  0  0  1

 # Note
 # -1 indicates FP or FN


Accuracy summary per resolution per gene
             Accuracy                               num_match                     num_ref
Resolution          0    1    2    3    4   FP   FN         0  1  2  3  4  FP  FN       0  1  2  3  4  FP  FN
method  gene
method1 A         1.0  1.0  1.0  1.0  1.0  0.0  0.0         2  2  2  1  1   0   0       2  2  2  1  1   0   0
        B         1.0  1.0  1.0  1.0  1.0  0.0  0.0         2  2  2  1  1   0   0       2  2  2  1  1   0   0

Plot summary (i.e. Accuracy vs Resolution, gene, methods)

figs = plot_summary(df_cohort)
# You can use Dash to show it
from dash import dcc, html, Dash
app = Dash(__name__)
app.layout = html.Div(children=[dcc.Graph(figure=fig) for fig in figs])
app.run(debug=True)

Develop

pip install pdoc
pdoc star_allele_comp --docformat google

Details