Yosuke Tanigawa yk-tanigawa
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| print 'Hello world!'; |
yk-tanigawa
/ 0_reuse_code.js
Created
October 27, 2015 16:11
Here are some things you can do with Gists in GistBox.
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| // Use Gists to store code you would like to remember later on | |
| console.log(window); // log the "window" object to the console |
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| python -c "import site; print(site.getsitepackages())" | |
| export PYTHONPATH=/bio/lib/python2.7/site-packages:/bio/lib/site-python:$PYTHONPATH | |
| ~/bin/python -c "import site; print(site.getsitepackages())" | |
| export PYTHONPATH=/home/yt/lib/python2.7/site-packages:/home/yt/lib/site-python:$PYTHONPATH |
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| import sys; | |
| sys.path.append('/bio/lib/python2.7/site-packages'); | |
| sys.path.append('/bio/lib/site-python'); | |
| import numpy as np; |
yk-tanigawa
/ Main.scala
Created
October 28, 2015 16:22
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| object Main extends App{ | |
| // Here your code ! | |
| println("XXXXXXXX") | |
| } |
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 |
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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
/ 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 |
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
/ 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) |
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