fakenewss / ocrdetector

OCRDetector

A novel bioinformatics pipeline named OCRDetector for detecting OCRs of the whole-genome based on cfDNA.

The original name is OCRDetector

email- [email protected]

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Usage:

python OCRDetectBycfDNA.py [-h usage] [-i input file] [-o OCRs output bed]

Options:

-h: usage

-i: bam file list of cfDNA

-o: output file of detected OCRs

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Example:

• python OCRDetectBycfDNA.py -i bamFileList.txt -o OCRs.bed or python OCRDetectBycfDNA.py -i bamFileList.txt -o OCRs.bed -c -1

  The above command can calculate the OCRs of the whole genome

  

• python OCRDetectBycfDNA.py -i bamFileList.txt -o OCRs.bed -c 1

  The above command can calculate the OCRs of chromosome 1

  

• python OCRDetectBycfDNA.py -h

  View the usage of the software

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Guidance：

Step1:

First, you need to modify the content of the bamFileList.txt file and replace it with the path of your cfDNA-seq data. The input cfDNA-seq data file is of bam type and has been indexed.

Step2:

python OCRDetectBycfDNA.py -i bamFileList.txt -o OCRs.bed

The above command can get the initial OCRs.

Step3:

Extract features and train machine learning models to filter false positives.

Step4:

Use bedtools to calculate the intersection of our OCRs and OCRs obtained from other data (ATAC-seq, Dnase-seq, TSS of Genes ).

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Waiting for subsequent updates

ocrdetector's Issues

reference GRCh37 required

I am unsure, but does OCRDetector require ensembl format build GRCh37?

python3 OCRDetectBycfDNA.py -i /home/ubuntu/data/bamFileList.txt -o OCRs.bed
begin
************************************* round : 0 -> 142602 *************************************
get bamfile done
Traceback (most recent call last):
File "OCRDetectBycfDNA.py", line 864, in
wpsList_Nor, lFdepth_Nor, sFdepth_Nor = callOneBed(bamfileList, contig, start, end, win=120)
File "OCRDetectBycfDNA.py", line 316, in callOneBed
for r in bamfile.fetch(contig, bed1, bed2):
File "pysam/libcalignmentfile.pyx", line 1081, in pysam.libcalignmentfile.AlignmentFile.fetch
File "pysam/libchtslib.pyx", line 685, in pysam.libchtslib.HTSFile.parse_region
ValueError: invalid contig 1

error in getPeakAveHeight - endPos bigger than startPos

Hi! I have encountered an error on getPeakAveHeight function while running OCRDetectBycfDNA.py.

I have added prints to the function to double check that wpsList is not empty. The problem seems to be that startPos is bigger than endPos. I'm not sure I understand how this is happening.

def getPeakAveHeight(wpsList, startPos, endPos):
    '''
    :param wpsList: 原始数据
    :param startPos: 起始位置
    :param endPos: 终止位置
    :return:
    '''
    if endPos > len(wpsList) or startPos == endPos:
        return 0

    print([startPos, endPos])
    print(wpsList)
    x = np.arange(startPos, endPos, 1)
    minNum = np.min(wpsList[startPos:endPos])
    minLine = np.array([minNum for i in range(endPos - startPos)])
    # lowLine = np.array([-0.5 for i in range(len(x))])
    return scipy.integrate.simps(np.subtract(np.array(wpsList)[startPos:endPos], minLine), x=x)

************************************  round :  786   ->   2841  *************************************
savgol filter done
scipy_signal_find_peaks done
[561, 587]
[0.34751679 0.34591636 0.34431592 ... 0.41062607 0.41341785 0.41620963]
[1064, 1263]
[0.34751679 0.34591636 0.34431592 ... 0.41062607 0.41341785 0.41620963]
[3526, 4162]
[0.34751679 0.34591636 0.34431592 ... 0.41062607 0.41341785 0.41620963]
[4313, 4800]
[0.34751679 0.34591636 0.34431592 ... 0.41062607 0.41341785 0.41620963]
[4900, 5141]
[0.34751679 0.34591636 0.34431592 ... 0.41062607 0.41341785 0.41620963]
[5436, 5572]
[0.34751679 0.34591636 0.34431592 ... 0.41062607 0.41341785 0.41620963]
[6121, 6342]
[0.34751679 0.34591636 0.34431592 ... 0.41062607 0.41341785 0.41620963]
[6616, 6514]
[0.34751679 0.34591636 0.34431592 ... 0.41062607 0.41341785 0.41620963]
Traceback (most recent call last):
  File "/home/julieta/Documents/github/OCRDetector/src/OCRDetectBycfDNA.py", line 881, in <module>
    ndrObjectList = findTssNDR(start, contig, peakObjectList, smoothWpsList_Nor, norm_lFdepth_Nor)
  File "/home/julieta/Documents/github/OCRDetector/src/OCRDetectBycfDNA.py", line 270, in findTssNDR
    aveHeight = getPeakAveHeight(smoothData, peakObjectList[i].endPos,
  File "/home/julieta/Documents/github/OCRDetector/src/OCRDetectBycfDNA.py", line 775, in getPeakAveHeight
    minNum = np.min(wpsList[startPos:endPos])
  File "/home/julieta/.local/lib/python3.10/site-packages/numpy/core/fromnumeric.py", line 2953, in min
    return _wrapreduction(a, np.minimum, 'min', axis, None, out,
  File "/home/julieta/.local/lib/python3.10/site-packages/numpy/core/fromnumeric.py", line 88, in _wrapreduction