yk-tanigawa

Ensembl BioMart

• Go to Ensembl portal and select BioMart
  • Human GRCh37: https://grch37.ensembl.org/
  • All others: http://ensembl.org/
• Select the following attributes:
  • Chromosome/scaffold name
  • Gene start (bp)
  • Gene end (bp)
• Gene stable ID

yk-tanigawa

Example usage of the figshare API

Yosuke Tanigawa

2020/5/22

To upload large files to figshare, one can use figshare API.

This notebook summarizes the basic usage of the figshare API.

yk-tanigawa

Save Kindle annotations to google drive

Electronic books (eBooks) are changing our way of reading books by providing us enhanced functionalities to interact with books. Amazon Kindle is one of the successful example of eBook servieces populated with millions of books. One of the notable functionality of Kindle is that readers can "highlight" the sentences in books and send the highlighted texts via email. While this enable users to easily export sections of the books, they need to manually organize their exported texts. Here I present a small Google Apps Script that automatically transfers the kindle annotations to Google drive. Given the search functionality of Google Drive, users can easily look up sections of books.

This Google Apps Script performs the following tasks: (1) checks your Gmail account; (2) identify email messages from Amazon Kindle service with your annotations (attachment files); and (3) save them to your google drive folder of your choice.

Note that some publishers has a maximum amoun

yk-tanigawa

%matplotlib inline

import numpy as np
import pandas as pd
import matplotlib, collections, itertools, os, re, textwrap, logging
import matplotlib.pyplot as plt
import matplotlib.gridspec as gridspec
import matplotlib.patches as mpatches
from functools import reduce

yk-tanigawa

#!/bin/bash

# parse args

if [ $# -lt 2 ] ; then
        echo "usage: $0 <target-server> <login-server> [local port (default: 18888)] [target port (default: 8888)] [login port (default: rand)]" >&2
        exit 1
fi

target=$1

yk-tanigawa

This script works as a wrapper for sbatch command.

Usage: sherlock-one-liner python --version

yk-tanigawa

yk-tanigawa

$ python pgen_write.py
2017-07-04 00:44:50,706 pgen_write   DEBUG    pgen write test script
2017-07-04 00:44:50,706 read_alleles_range DEBUG    reading alleles range 0:10 from ./pgen_in.pgen
2017-07-04 00:44:50,725 read_alleles_range DEBUG    The shape of the numpy nd-array is (10, 224676)
2017-07-04 00:44:50,725 pgen_write   DEBUG    shape of buffer is (10, 224676)
2017-07-04 00:44:50,727 pgen_write   DEBUG    writing SNP 0 of 10 ...
2017-07-04 00:44:50,728 pgen_write   DEBUG    writing SNP 1 of 10 ...
2017-07-04 00:44:50,730 pgen_write   DEBUG    writing SNP 2 of 10 ...
2017-07-04 00:44:50,731 pgen_write   DEBUG    writing SNP 3 of 10 ...
2017-07-04 00:44:50,733 pgen_write   DEBUG    writing SNP 4 of 10 ...

yk-tanigawa

np.array(
        Parallel(
            n_jobs=multiprocessing.cpu_count()
        )(delayed(pre_process_main)(read_3channel_file(lead_df, i))
          for i in range(batch_interval[0], batch_interval[1])),
        dtype = np.float64
    )

yk-tanigawa

#!/bin/sh

# (@) hello world

#SBATCH --job-name=hello
#SBATCH   --output=hello.%j.out
#SBATCH    --error=hello.%j.err
#SBATCH --time=0:01:00
#SBATCH --qos=normal
#SBATCH -p normal