Mercurial > repos > jasmine_amir > snrqk2

comparison SNRQK2.py @ 0:2547394443a0

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"planemo upload commit 8b4c59e523d28c30368aebfa0416d9ff8e27d257"
author jasmine_amir
date Thu, 09 Jun 2022 19:29:02 -0400
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children 1ab67c0c0054
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1 #!/usr/bin/env python3
2 # coding: utf-8
3 ###########################################################
4 ###########################################################
5 ## Jasmine Amirzadegan
6 ## 2022 APRIL 14
7 ###########################################################
8 ## SNRQC.py:
9 ## compute QC metrics specific to SSQuAWK v4 + workflows
10 ## usage: python SNRQC.py intermediateSSQuAWKfile.txt
11 ## python 3.7
12 ###########################################################
13 import pandas as pd
14 import sys
15
16 fn = sys.argv[1]
17 df = pd.read_csv(fn, sep = "\t", header = 0)
18
19
20
21 if (df['Sample'].str.contains('negativeControl')).any():
22 m = df.loc[ (df['Sample'].str.contains('negativeControl')) ]
23 noise = m['readsAlignPassFilt']
24 SNR = []
25
26 for i in df['readsAlignPassFilt']:
27 SNR.append(i/noise.item())
28 #[float(j) for j in SNR]
29 df['SNR'] = SNR
30
31 else:
32 df['SNR'] = "NA"
33
34 #print(df)
35 #fn1 = fn.split("/")[1]
36 #df.to_csv('test-data/snrqk_result' + fn1 + '.tsv', sep="\t")
37 df.to_csv('snrqk_result.tsv', sep='\t')