<jupyter_start><jupyter_text>Idea1. load a blacklist-file1. expand bed1. check distribution1. get mean, mode, median, sd, mad  STE0072<jupyter_code>blackLisPath = "/Users/robinvanderweide/MEGA/Work/PhD/projects/rDNA/data/rDNA_bedfiles/STE0072/STE007212/STE007212_blacklist.sorted.bed"
RDNAalphaPath = "/Users/robinvanderweide/MEGA/Work/PhD/projects/rDNA/data/rDNA_bedfiles/STE0072/STE007212/STE007212_RDNAalpha.sorted.bed"
RD = getMedMad(RDNAalphaPath)
BL = getMedMad(blackLisPath)
[RD[0],BL[0],RD[0]/BL[0],np.log2(RD[0]/BL[0])]
blackLisPath = "/Users/robinvanderweide/MEGA/Work/PhD/projects/rDNA/data/rDNA_bedfiles/STE0072/BOXTELBLOOD0072/BOXTELBLOOD0072_blacklist.sorted.bed"
RDNAalphaPath = "/Users/robinvanderweide/MEGA/Work/PhD/projects/rDNA/data/rDNA_bedfiles/STE0072/BOXTELBLOOD0072/BOXTELBLOOD0072_RDNAalpha.sorted.bed"
RD = getMedMad(RDNAalphaPath)
BL = getMedMad(blackLisPath)
[RD[0],BL[0],RD[0]/BL[0],np.log2(RD[0]/BL[0])]
np.log2(94.21621621621621/103.30882352941177)<jupyter_output><empty_output><jupyter_text>STE0100<jupyter_code>blackLisPath = "/Users/robinvanderweide/MEGA/Work/PhD/projects/rDNA/data/rDNA_bedfiles/STE0100/STE100CLONE/STE100CLONE_blacklist.sorted.bed"
RDNAalphaPath = "/Users/robinvanderweide/MEGA/Work/PhD/projects/rDNA/data/rDNA_bedfiles/STE0100/STE100CLONE/STE100CLONE_RDNAalpha.sorted.bed"
RD = getMedMad(RDNAalphaPath)
BL = getMedMad(blackLisPath)
[RD[0],BL[0],RD[0]/BL[0],np.log2(RD[0]/BL[0])]
blackLisPath = "/Users/robinvanderweide/MEGA/Work/PhD/projects/rDNA/data/rDNA_bedfiles/STE0100/STE100BLOOD/STE100BLOOD_blacklist.sorted.bed"
RDNAalphaPath = "/Users/robinvanderweide/MEGA/Work/PhD/projects/rDNA/data/rDNA_bedfiles/STE0100/STE100BLOOD/STE100BLOOD_RDNAalpha.sorted.bed"
RD = getMedMad(RDNAalphaPath)
BL = getMedMad(blackLisPath)
[RD[0],BL[0],RD[0]/BL[0],np.log2(RD[0]/BL[0])]
np.log2(76.357142857142861/92.870967741935488)<jupyter_output><empty_output><jupyter_text>STE0106<jupyter_code>blackLisPath = "/Users/robinvanderweide/MEGA/Work/PhD/projects/rDNA/data/rDNA_bedfiles/STE0106/STE0106clone/STE0106clone_blacklist.sorted.bed"
RDNAalphaPath = "/Users/robinvanderweide/MEGA/Work/PhD/projects/rDNA/data/rDNA_bedfiles/STE0106/STE0106clone/STE0106clone_RDNAalpha.sorted.bed"
RD = getMedMad(RDNAalphaPath)
BL = getMedMad(blackLisPath)
[RD[0],BL[0],RD[0]/BL[0],np.log2(RD[0]/BL[0])]
blackLisPath = "/Users/robinvanderweide/MEGA/Work/PhD/projects/rDNA/data/rDNA_bedfiles/STE0106/STE0106blood/STE0106blood_blacklist.sorted.bed"
RDNAalphaPath = "/Users/robinvanderweide/MEGA/Work/PhD/projects/rDNA/data/rDNA_bedfiles/STE0106/STE0106blood/STE0106blood_RDNAalpha.sorted.bed"
RD = getMedMad(RDNAalphaPath)
BL = getMedMad(blackLisPath)
[RD[0],BL[0],RD[0]/BL[0],np.log2(RD[0]/BL[0])]
np.log2(117.34883720930233/116.78205128205128)<jupyter_output><empty_output><jupyter_text>STE0111<jupyter_code>blackLisPath = "/Users/robinvanderweide/MEGA/Work/PhD/projects/rDNA/data/rDNA_bedfiles/STE0111/STE0111EP4/STE0111EP4_blacklist_mapped.sorted.bed"
RDNAalphaPath = "/Users/robinvanderweide/MEGA/Work/PhD/projects/rDNA/data/rDNA_bedfiles/STE0111/STE0111EP4/STE0111EP4_RDNAalpha_mapped.sorted.bed"
RD = getMedMad(RDNAalphaPath)
BL = getMedMad(blackLisPath)
[RD[0],BL[0],RD[0]/BL[0],np.log2(RD[0]/BL[0])]
blackLisPath = "/Users/robinvanderweide/MEGA/Work/PhD/projects/rDNA/data/rDNA_bedfiles/STE0111/STE0111FP4/STE0111FP4_blacklist_mapped.sorted.bed"
RDNAalphaPath = "/Users/robinvanderweide/MEGA/Work/PhD/projects/rDNA/data/rDNA_bedfiles/STE0111/STE0111FP4/STE0111FP4_RDNAalpha_mapped.sorted.bed"
RD = getMedMad(RDNAalphaPath)
BL = getMedMad(blackLisPath)
[RD[0],BL[0],RD[0]/BL[0],np.log2(RD[0]/BL[0])]
blackLisPath = "/Users/robinvanderweide/MEGA/Work/PhD/projects/rDNA/data/rDNA_bedfiles/STE0111/STE0111BLOOD/STE0111BLOOD_blacklist_mapped.sorted.bed"
RDNAalphaPath = "/Users/robinvanderweide/MEGA/Work/PhD/projects/rDNA/data/rDNA_bedfiles/STE0111/STE0111BLOOD/STE0111BLOOD_RDNAalpha_mapped.sorted.bed"
RD = getMedMad(RDNAalphaPath)
BL = getMedMad(blackLisPath)
[RD[0],BL[0],RD[0]/BL[0],np.log2(RD[0]/BL[0])]
np.log2(130.38541666666666/133.38775510204081) #EP4
np.log2(157.13043478260869/133.38775510204081) #FP4<jupyter_output><empty_output>
{'fraction_non_alphanumeric': 0.15187140115163147, 'fraction_numerical': 0.11588291746641075, 'mean_word_length': 8.475, 'pattern_counts': {'":': 0, '<': 17, '<?xml version=': 0, '>': 17, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 1, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'chain_length': '4', 'dir': 'jupyter-structured-clean-dedup', 'id': '288502', 'license': 'AFL-1.1', 'n_tokens_mistral': 2224, 'n_tokens_neox': 1901, 'n_words': 99, 'path': 'covParser.ipynb', 'repo_name': 'robinweide/RETARD', 'size': '4168'}