trim.py

# Takes the output of extend_signal.py and extends the array further to match the length of the DNA array
import numpy as np

chrs = ['chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9','chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17','chr18','chr19','chr20','chr21','chr22']

# Inputs are extended_signal numpy arrays
chips = [
#'shsy5y.par.atmi.ppois.',
#'shsy5y.par.dmso.ppois.',
#'shsy5y.rchip.atmi.ppois.',
#'shsy5y.rchip.dmso.ppois.',
#'shsy5y.atac.SRR5819663_SRR5819664_treat_pileup.',
#'shsy5y.ctcf.SRR6334830.ppois.',
#'shsy5y.h3k27ac.SRR3363257.ppois.',
#'shsy5y.h3k27me3.SRR3363258.ppois.',
#'shsy5y.h3k4me1.SRR3363256.ppois.',
#'shsy5y.h3k4me3.SRR3363255.ppois.',
#'shsy5y.igg.SRR4291521_SRR4291522.ppois.',
'shsy5y.pol2.SRR6322542_SRR6322543.ppois.',
'shsy5y.s96.SRR4291525_SRR4291526.ppois.',
'shsy5y.rchip.atmi_nac.ppois.',
'shsy5y.rchip.dmso_nac.ppois.'
]

for chrom in chrs:
    dna_vec = np.load('/home1/05664/pwoolley/work/scripts/chip.smoothing/dna_vec/gc_vec/gc_vec.'+chrom+'.npy')
    max_len = len(dna_vec)

    # Adding zeros to the end of each array if needed
    for chip in chips:
        array = np.load('/scratch/05664/pwoolley/SHSY5Y_ChIP/chip.smoothing/extended_signal/'+chip+'extended_signal.'+chrom+'.npy')
        array = np.hstack((array,np.zeros(max_len-len(array))))
        np.save('/scratch/05664/pwoolley/SHSY5Y_ChIP/chip.smoothing/trimmed/'+chip+'trimmed.'+chrom+'.npy',array)