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###############
# mat_count: 60668 x 28 matrix, gene expression levels
# mat_count_rmlow: 18186 x 28 matrix
# group: A vector of factor: factor(rep(1:7, each=4))
###############

### Remove low-count genes and round count
is_lowgenes = rowMeans(mat_count) < 5
mat_count_rmlow <- mat_count[!is_lowgenes,]
dim(mat_count_rmlow)

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#!/usr/bin/env nextflow

Channel.fromPath("*.txt")
.map{[
    file(it),
    file(it).baseName
    ]}.into{
        input_files
        input_files_
        input_files__

yuifu

この文章の目的

たまにしかpythonを使わない人のためのメモ

数値

• int()で文字列を整数にできる

文字列

• + で結合できる
• str() で数値を文字列にできる
• シングルクォーテーションとダブルクォーテーションが同じ意味

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install.packages("tidyverse")
install.packages("magrittr")

source("https://bioconductor.org/biocLite.R")
biocLite()

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minialign: malloc.c:2365: sysmalloc: Assertion `(old_top == (((mbinptr) (((char *) &((av)->bins[((1) - 1) * 2])) - __builtin_offsetof (struct malloc_chunk, fd)))) && old_size == 0) || ((unsigned long) (old_size) >= (unsigned long)((((__builtin_offsetof (struct malloc_chunk, fd_nextsize))+((2 * (sizeof(size_t))) - 1)) & ~((2 * (sizeof(size_t))) - 1))) && ((old_top)->size & 0x1) && ((unsigned long)old_end & pagemask) == 0)' failed.

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# Installation
# install.packages("dplyr")

library(dplyr)

df1 = data.frame(
	A=c("A1", "A2", "A3", "A4")
)

df2 = data.frame(

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R --slave -e 'library(Biostrings); seqs <- readDNAStringSet("test.fa"); write.table(data.frame(name=names(seqs), length=width(seqs)),stdout(), quote=F, row.names=F)' > hoge.txt

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path_gtf = "merged.asm/merged.gtf"
path_ofile = "merged.asm/merged.gtf.txt"


arr_attr = Array{Any,1}()
d_attr = Dict{Any,Any}()


# Extract all attributes
f = open(path_gtf)

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awk 'BEGIN{l=100}{if(NR%4==1){x=$0};if(length($0)==l){print x; print; getline; print; getline; print}}' foo.fastq