carushi

fc_gene <- enrichPathway(gene=unique(names(fc)), pvalueCutoff=0.1,  organism = "mouse", readable=T)
fc_gene
attributes(fc_gene)
index <- sapply(seq(1, length(fc_gene$Description)), function(x){return(which(fc_gene$Description == fc_gene$Description[x])[1] == x)})
attr(fc_gene, "result") <- attr(fc_gene, "result")[index,]
dotplot(fc_gene, showCategory=15)

carushi

fc_gene <- enrichPathway(gene=unique(names(fc)), pvalueCutoff=0.1,  organism = "mouse", readable=T)
fc_gene
attributes(fc_gene)
index <- sapply(seq(1, length(fc_gene$Description)), function(x){return(which(fc_gene$Description == fc_gene$Description[x])[1] == x)})
attr(fc_gene, "result") <- attr(fc_gene, "result")[index,]
dotplot(fc_gene, showCategory=15)

carushi

def list_length(L):
    if isinstance(L, (list, np.ndarray)):
        if len(L) > 0 and isinstance(L[0], (list, np.ndarray)):
            return [list_length(x) for x in L]
        else:
            return len(L)
    return 0

carushi

samtools view -f 16 temp.bam \
| awk 'BEGIN{OFS='\t'}{if(NF == 3 || length($10) >= 15) { print }}' \
| cut -f6,6 | sed -e 's/.*[^S]$/0/g' -e 's/.*[A-Z]\([0-9]*\)S$/\1/g' | sort -n \
| uniq -c > temp_rev.txt
samtools view -F 16 temp.bam \
| awk 'BEGIN{OFS='\t'}{if(NF == 3 || length($10) >= 15) { print }}' \
| cut -f6,6 | sed -e 's/^\([0-9]*\)S.*$/\1/g' -e 's/^.*[A-Z]$/0/g' | sort -n \
| uniq -c > temp.txt

carushi

seq 0 5 | xargs -I{} echo "samtools view -F 16 {}.bam | grep -v "XS:" | awk 'BEGIN{OFS='\t'}{if(length(\$10) >= 15) { print }}' | cut -f6,6 | grep \"^[0-9]*S\" | cut -f1,1 -d\"S\" | sort -n | uniq -c > {}_local.txt " | bash

seq 0 5 | xargs -I{} echo "samtools view -f 16 {}.bam | grep -v "XS:" | awk 'BEGIN{OFS='\t'}{if(length(\$10) >= 15) { print }}' | cut -f6,6 | grep \"[0-9]*S$\" | sed 's/.*[A-Z]\([0-9]*\)S\$/\1/g' | sort -n | uniq -c > {}_local_rev.txt "   | bash

carushi

#!/usr/bin/env python

""" Please apply this script to paired-end reads when you happen to see the bowtie error shown as below.
Error, fewer reads in file specified with -2 than in file specified with -1
terminate called after throwing an instance of 'int'
(ERR): bowtie2-align died with signal 6 (ABRT) (core dumped)

python read_truncate.py (1st fastq) (2nd fastq)
"""

carushi

ERRORLIST=("SRRXXXXXX") #SRR number
for NAME in "${ERRORLIST[@]}"
do
	echo $NAME
	cat ${NAME}.fastq | grep "^@SRR" -A 3 | grep -v "^\-\-$" > ${NAME}_trimmed.fastq
	python check_read.py ${NAME}_trimmed.fastq > ${NAME}_extracted.fastq
done

carushi

import sys

if __name__ == '__main__':
	file = sys.argv[1]
	list = []
	count = 0
	with open(file) as f:
		for line in f.readlines():
			if count%4 == 1:
				list.append(line)

carushi

for (time in c(10, 100, 1000, 10000, 100000, 100000)) {
  m <- c()
	for (r in 1:10000) {
		m <- c(m, max(rnorm(time)))
	}
	png(paste(time, ".png", sep=""))
	plot(hist(m), xlim=c(-2,6))
	dev.off()
}

carushi

from selenium import webdriver
from selenium.webdriver.common.action_chains import ActionChains
from selenium.webdriver.common.keys import Keys

driver = webdriver.Firefox()
driver.maximize_window()
driver.get("http://ksnctf.sweetduet.info/q/3/unya.html")
# driver.title
form = driver.find_element_by_xpath('//input[@type="text"]')
form.send_keys('c')