Last updated: 2019-04-10
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Knit directory: threeprimeseq/analysis/
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Modified: analysis/unexplainedeQTL_analysis.Rmd
Modified: code/Snakefile
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 70732bb | Briana Mittleman | 2019-04-10 | add scripts for new snake |
I need to make general scripts for the new processed snakefile:
filterBamBasedonWasp_general.py
def main(Bamin, out):
okRead={}
#pysam to read in bam allignments
bamfile = pysam.AlignmentFile(Bamin, "rb")
finalBam = pysam.AlignmentFile(out, "wb", template=bamfile)
n=0
k=0
#read name is the first col in each bam file
for read in bamfile.fetch():
#last piece is always the right piece
#vw=read.split(\t)[-1]
if read.has_tag('vW'):
x= read.get_tag('vW')
print(x)
if x == 1:
k+=1
finalBam.write(read)
else:
n+=1
continue
else:
finalBam.write(read)
print("with wv" + n)
print("pass filter" + k)
bamfile.close()
finalBam.close()
if __name__ == "__main__":
import sys, pysam
inBam=sys.argv[1]
outBam=sys.argv[2]
main(inBam, outBam)
Upstream10Bases_general.py
#python
def main(Fin, Fout):
outBed=open(Fout, "w")
chrom_lengths=open("/project2/gilad/briana/genome_anotation_data/chrom_lengths2.sort.bed","r")
#make a dictionary with chrom lengths
length_dic={}
for i in chrom_lengths:
chrom, start, end = i.split()
length_dic[str(chrom)]=int(end)
#write file
for ln in open(Fin):
chrom, start, end, name, score, strand = ln.split()
chrom=str(chrom)
if strand=="+":
start_new=int(start)-10
if start_new <= 1:
start_new = 0
end_new= int(start)
if end_new == 0:
end_new=1
outBed.write("%s\t%d\t%d\t%s\t%s\t%s\n"%(chrom, start_new, end_new, name, score, strand))
if strand == "-":
start_new=int(end)
end_new=int(end) + 10
if end_new >= length_dic[chrom]:
end_new = length_dic[chrom]
start_new=end_new-1
outBed.write("%s\t%d\t%d\t%s\t%s\t%s\n"%(chrom, start_new, end_new, name, score, strand))
outBed.close()
if __name__ == "__main__":
import sys
inFile = sys.argv[1]
outFile = sys.argv[2]
main(inFile, outFile)filterMissprimingInNuc10_gen.py
def main(Fin, Fout):
outBed=open(Fout, "w")
inBed=open(Fin, "r")
for ind, ln in enumerate(inBed):
if ind >=1:
chrom,start, end, name, score, strand, pctAT, pctGC, A, C, G, T, N, Other, Length, Sequence = ln.split()
Tperc= float(T) / float(Length)
if Tperc < .7:
if "TTTTTT" not in Sequence:
start_new=int(start)
end_new=int(end)
outBed.write("%s\t%d\t%d\t%s\t%s\t%s\n"%(chrom, start_new, end_new , name, score, strand))
outBed.close()
if __name__ == "__main__":
import sys
inFile = sys.argv[1]
outFile=sys.argv[2]
main(inFile, outFile)filterSortBedbyCleanedBed_gen.R
#!/bin/rscripts
# usage: Rscirpt --vanilla filterSortBedbyCleanedBed_gen.R bedfile cleannuc outfile
#this script takes in the sorted bed file and the clean reads, it will clean the bed file
library(dplyr)
library(tidyr)
library(data.table)
args = commandArgs(trailingOnly=TRUE)
bed=args[1]
clean= args[2]
output=args[3]
bedFile=fread(bed, col.names = c("Chrom", "start", "end", "name", "score", "strand"))
cleanFile=fread(clean, col.names = c("Chrom", "start", "end", "name", "score", "strand"))
intersection=bedFile %>% semi_join(cleanFile, by="name")
fwrite(intersection, file=output,quote = F, col.names = F, row.names = F, sep="\t")filterBamforMP.pysam2_gen.py
#!/usr/bin/env python
def main(Bin, Bamin, out):
okRead={}
for ln in open(Bin, "r"):
chrom, start_new , end_new , name, score, strand = ln.split()
okRead[name] = ""
#pysam to read in bam allignments
bamfile = pysam.AlignmentFile(Bamin, "rb")
finalBam = pysam.AlignmentFile(out, "wb", template=bamfile)
#read name is the first col in each bam file
n=0
for read in bamfile.fetch():
read_name=read.query_name
#if statement about name
if read_name in okRead.keys():
finalBam.write(read)
if n % 1000==0 : print(n)
n+=1
bamfile.close()
finalBam.close()
if __name__ == "__main__":
import sys, pysam
inBed= sys.argv[1]
inBam=sys.argv[2]
outBam=sys.argv[3]
main(inBed, inBam, outBam)
sessionInfo()R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS 10.14.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] workflowr_1.2.0 Rcpp_1.0.0 digest_0.6.18 rprojroot_1.3-2
[5] backports_1.1.3 git2r_0.24.0 magrittr_1.5 evaluate_0.13
[9] stringi_1.3.1 fs_1.2.6 whisker_0.3-2 rmarkdown_1.11
[13] tools_3.5.1 stringr_1.4.0 glue_1.3.0 xfun_0.5
[17] yaml_2.2.0 compiler_3.5.1 htmltools_0.3.6 knitr_1.21