simonthompson99

#-- convert pdf into single page png images with p01 numbering
for file in *.pdf; do
    echo 'converting $file'
    convert -density 400 -colorspace sRGB $file -scene 1 -alpha off ${file%.pdf}_p%02d.png;
done

simonthompson99

# rename repository
# change name on remote repo, copy ssh url from the clone button on main page
mv <old folder> <new folder>
git remote set-url origin git@github.com:genomicsengland/<new repo name>

# compare local copy of file to remote
git fetch origin
git diff origin/master -- <path to file>

# list all branches

simonthompson99

# open up current file (useful for opening markdowns in chrome)
:!open %

# search across folder tree for test
# From within buffer at top most level of folder tree to search
:grep '<searchstring>' **/*.<fileending to search> or grep -R <searchstring> . to recursievely search all files in project
:copen to open the quickfix list, and :ccl to close it
:cn to go to the next on the quickfix list
:cp to go to the previous
# OR

simonthompson99

-- pg dump of a specific schema from metrics db on index
pg_dump metrics -h 10.1.24.39 -p 5433 -U cdt_user -n <schema_name> > <out>.sql

-- select a random percentage of rows of table
select * from my_table tablesample bernoulli(<percentage in numbers, e.g. 10>)
-- or to select random rows in query
select * from query order by random() limit 100

-- useful aggregate functions to use with GROUP BY
string_agg(<field>, ';') /* equivalent to R's paste(<field>, collapse = ";") */

simonthompson99

# run three times a day (between 9am and 4pm), Mon - Fri
H H(9-16)/3 * * 1-5

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# batch renames files with hyphens to underscores
for i in `ls *-*`
do
NEW=`echo $i|tr '-' '_'`
git mv $i $NEW
done

# or do sed on the filename with multiple options
for i in `ls *.sql`
do

simonthompson99

# make white transparent
convert <in>.png -transparent white <out>.png

# change image to a4-sized pdf
convert -density 300 -page a4 <in>.png <out>.pdf

# remove large white backgrounds from multiple images
mogrify -trim +repage *.png

# make image grayscale

simonthompson99

# set up the SMTP server
# for qmul:
# host = smtp-mail.outlook.com
# port = 587
# username, password = full hh..@qmul.ac.uk email address
import smtplib
from os.path import basename
from email.mime.application import MIMEApplication
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText

simonthompson99

# Template objects allows you to add ${FIELD_NAME} tags into the file
# and then values can be substituted with
# template_object.substitute(FIELD_NAME = <field_value>)
def read_template(filename):
    """
    Returns a Template object comprising the contents of the 
    file specified by filename.
    """
    import Template
    with open(filename, 'r', encoding='utf-8') as template_file:

simonthompson99

#-- use the CDT Bot API token see https://cnfl.extge.co.uk/display/CDT/Generic+Login+Credentials+Information#GenericLoginCredentialsInformation-SlackCDTBotUser
#-- function to send df (d) to a specific channel with optional message, will break up if there are too many rows
send_df_to_slack_as_msg <- function(d, channel, api_token, msg = NA){
	require(knitr)
	require(slackr)
	slackr_setup(channel = channel, 
				api_token = api_token)
	d <- kable(d, format = 'rst')
	if(!is.na(msg)){
		slackr_msg(msg)