たまにしかpythonを使わない人のためのメモ
int()で文字列を整数にできる
+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
Haruka Ozaki yuifu
yuifu
/ extract_specific_length_fastq.sh
Last active
October 30, 2015 14:10
Extract FASTQ entries with a specific sequence length
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| awk 'BEGIN{l=100}{if(NR%4==1){x=$0};if(length($0)==l){print x; print; getline; print; getline; print}}' foo.fastq |
yuifu
/ gtf_to_tsv.jl
Created
January 18, 2016 04:58
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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) |
yuifu
/ R one-liner for calculating seq lengths in FASTA
Created
February 24, 2016 11:14
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |
yuifu
/ example_join_by_dplyr.r
Last active
July 1, 2017 04:14
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # Installation | |
| # install.packages("dplyr") | |
| library(dplyr) | |
| df1 = data.frame( | |
| A=c("A1", "A2", "A3", "A4") | |
| ) | |
| df2 = data.frame( |
yuifu
/ 20170916_error_minialign
Created
September 16, 2017 14:06
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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. |
yuifu
/ gist:5976a59c16e5a2a7dc4c70b3fe675df9
Created
January 9, 2018 13:30
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| install.packages("tidyverse") | |
| install.packages("magrittr") | |
| source("https://bioconductor.org/biocLite.R") | |
| biocLite() |
yuifu
/ python_cheat_sheet.md
Last active
July 4, 2018 06:56
yuifu
/ count_number_of_files_in_channel.nf
Last active
June 18, 2019 05:42
I want to count the number of input and output files to check all files are properly processed. -> Solved!!
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| #!/usr/bin/env nextflow | |
| Channel.fromPath("*.txt") | |
| .map{[ | |
| file(it), | |
| file(it).baseName | |
| ]}.into{ | |
| input_files | |
| input_files_ | |
| input_files__ |
yuifu
/ gist:ad58bf1638450098979bf3d2210636a0
Created
March 19, 2020 14:12
EdgeR, strange case (too many DEGs)
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| ############### | |
| # 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) |
yuifu
/ gist:01d7f07ab165fcb3cb568d32636b4190
Created
April 20, 2020 07:44
Error massage while using Fire.jl
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| $ julia cli/run.jl relcov examples/data/RamDA_72h_A09.uniq.q40.bam examples/data/gencode.vM15.primary_assembly.annotation.protein_coding.head.bed zzz_experiments/_fire_test_relcov | |
| Start calculating relative gene body coverage... | |
| - bam: examples/data/RamDA_72h_A09.uniq.q40.bam | |
| - bed12: examples/data/gencode.vM15.primary_assembly.annotation.protein_coding.head.bed | |
| - output: zzz_experiments/_fire_test_relcov.geneBodyCoverage.txt | |
| zzz_experiments/_fire_test_relcov.geneBodyCoverage.pdf | |
| - transcript_length_cut: 100 | |
| - max_depth: 0 | |
| - N_bin: 100 |
OlderNewer