Yosuke Tanigawa yk-tanigawa
yk-tanigawa
/ 20160303BiomartServer.ipynb
Created
March 4, 2016 07:19
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yk-tanigawa
/ file0.txt
Created
February 23, 2016 02:34
NCBI SRA (Short Read Archive) 形式から fastq 形式に変換する Makefile ref: http://qiita.com/yk-tanigawa/items/f78834d697daf23378b0
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| ## commands | |
| FASTQ-DUMP = /somewhere/fastq-dump | |
| ## files | |
| FASTQ1 = $(SRA:%.sra=%_1.fastq) | |
| FASTQ2 = $(SRA:%.sra=%_2.fastq) | |
| all: $(FASTQ1) $(FASTQ2) | |
| # obtain the paired-end fastq files from a given sra file |
yk-tanigawa
/ Makefile to obtain paired-end FASTQ file
Created
February 23, 2016 02:12
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| #usage: make SRA=XXXXX.sra | |
| ## commands | |
| FASTQ-DUMP = /somewhere/fastq-dump | |
| ## files | |
| FASTQ1 = $(SRA:%.sra=%_1.fastq) | |
| FASTQ2 = $(SRA:%.sra=%_2.fastq) | |
| all: $(FASTQ1) $(FASTQ2) |
yk-tanigawa
/ jupyter_notebook_config.py
Created
January 25, 2016 17:01
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| #------------------------------------------------------------------------------ | |
| # Configurable configuration | |
| #------------------------------------------------------------------------------ | |
| c = get_config() | |
| #c.NotebookApp.ip = '*' | |
| c.NotebookApp.password = u'sha1:xxxx' | |
| c.NotebookApp.open_browser = False | |
| #c.NotebookApp.port = 8899 |
yk-tanigawa
/ How to access to jupyter notebook at remote
Created
January 23, 2016 17:39
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| local$ ssh -L 8888:localhost:8888 remote | |
| remote$ jupyter notebook |
yk-tanigawa
/ file0.txt
Created
January 20, 2016 20:52
Scipyで標本分布を計算する(離散分布) ref: http://qiita.com/yk-tanigawa/items/0e4bd9480216c7a84106
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| from scipy import stats | |
| help(stats.rv_discrete) |
yk-tanigawa
/ revcomp.py
Created
December 28, 2015 16:03
Compute reverse complement nucleotide sequence with python
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| import string; | |
| def revcomp(sequence): | |
| return string.translate(sequence[::-1], string.maketrans("ACGT", "TGCA")) |
yk-tanigawa
/ Makefile
Created
December 20, 2015 04:01
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| CC = gcc | |
| LD = gcc | |
| CFLAGS = -Wall -Wextra -O2 | |
| LDFLAGS = #-lpthread -lm | |
| SRCS := $(wildcard *.c) | |
| OBJS = $(SRCS:.c=.o) | |
| DEPS = $(SRCS:.c=.dep) | |
| EXEC = $(SRCS:.c=) | |
| RM = rm -f |
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| $ ./chrom -f /data/yt/GRCh37.ch21.fasta -H /data/yt/GM12878_combined/ -o /work2/yt/scripts/20151105/out/ -k1 -r1000 -c21 -m10000 -M1000000 -n"KR" -e"KR" | |
| fasta file: /data/yt/GRCh37.ch21.fasta | |
| Hi-C data dir: /data/yt/GM12878_combined/ | |
| Output dir: /work2/yt/scripts/20151105/out/ | |
| k: 1 | |
| resolution: 1000 | |
| chromosome: 21 | |
| min distance: 10000 | |
| Max distance: 1000000 | |
| Normalization: KR |
yk-tanigawa
/ gist:93a2c0b855ff05a560c3
Last active
October 28, 2015 16:34
Scala install on mac book air
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| sudo port install scala2.11 scala2.11-docs | |
| sudo port select --set scala scala2.11 | |
| $scalac -version | |
| Scala compiler version 2.11.7 -- Copyright 2002-2013, LAMP/EPFL | |
| $ fsc -version | |
| Fast Scala compiler version 2.11.7 -- Copyright 2002-2013, LAMP/EPFL |