#!/dep/_conda/bin/python3
# coding: utf-8
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## Jasmine Amirzadegan
## 2022 APRIL 14
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## SNRQC.py:
## compute QC metrics specific to SSQuAWK v4 + workflows
## usage: python SNRQC.py intermediateSSQuAWKfile.txt
## python 3.7
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import pandas as pd
import sys

fn = sys.argv[1]
df = pd.read_csv(fn, sep = "\t", header = 0)



if (df['Sample'].str.contains('negativeControl')).any():
    m = df.loc[ (df['Sample'].str.contains('negativeControl')) ]
    noise = m['readsAlignPassFilt']
    SNR = []

    for i in df['readsAlignPassFilt']:
        SNR.append(i/noise.item())
        #[float(j) for j in SNR]
    df['SNR'] = SNR

else:
    df['SNR'] = "NA"

#print(df)
#fn1 = fn.split("/")[1]
#df.to_csv('test-data/snrqk_result' + fn1 + '.tsv', sep="\t")
df.to_csv('snrqk_result.tsv', sep='\t')