Perry samesense

SAM and BAM filtering one-liners

@author: David Fredman, [email protected] (sans poly-A tail)
@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/

Please extend with additional/faster/better solutions via a pull request!

BWA mapping (using piping for minimal disk I/O)

Go BigQuery tests

Reading and writing JSON with GO

Problem: I want to read and serve JSON, but the JSON structure differs by query. I solve this with an interface FleetVehicle, a base Vehicle struct, and additional specialized structs that allow for differetnail parsing. The Fleet struct holds raw json in RawVehicles, and parsed objects/structs in Vehicles. By writing MarsahJSON and UnmarshalJSON for the Fleet struct, and I control how each JSON block is parsed into a different type of struct/vehicle. To run: GOPATH=${PWD} go run helloVariant.go, and check http://localhost:8080/world. This loads multiple JSON files into one Fleet object allowing me to serve a concatenation of the JSON files. For now, each JSON block must use the data field to hold a list of vehicles.

helloVariant.go is the main file
src/varparse/varparse.go holds structs for variants in JSON
testVariant1.json and testVariant2.json are example files used by helloVariant.go
hello.go is my initial attempt
fleet.go, fleet_test.go, fleet_test_

Keybase proof

I hereby claim:

I am samesense on github.
I am samesense (https://keybase.io/samesense) on keybase.
I have a public key ASB-sPD-A8yIsdlWUcJNosvQ0yi326pqYwvZRVxkg3-LHQo

To claim this, I am signing this object:

vcf-snp-lookup

I hope you have some terminal/command line experience.

Navigate to your vcf.gz file in the terminal/command line.
Check your reference genome (install gzcat as needed):

gzcat {your_id}.filtered.snp.vcf.gz | head -100 | less

Look for something like -r /references/grch37

	#!/bin/bash

	# Create a temporary directory for storing intermediate files
	TMPDIR=${TMP:-/tmp}
	HEADER_FILE="$TMPDIR/header_$(date +%s%N).txt"
	NEW_HEAD_FILE="$TMPDIR/renamed0_$(date +%s%N).txt"
	RANDOM_FILE="$TMPDIR/renamed_$(date +%s%N).txt"
	INPUT_REST_FILE="$TMPDIR/input_rest_$(date +%s%N).txt"

	# Function to process input

	#!/usr/bin/env python3
	"""
	The idea here is to have one demo of each common argparse format
	type. This is useful for me to be able to copy/paste into a new
	script and have something to quickly edit and trim down to get
	the functionality I need.

	Example (in your terminal):

	$ python3 argparse-template.py "hello" 123 --enable

	import rule_maker

	one_out = 'out1'
	rule one:
	output:
	one_out
	shell:
	'touch {output}'

	# generate a snakefile file for the second rule

	def mk_rule(in_file, out_file, tmp_snake='tmp_snake.py'):
	'''input is single file
	output is single file
	'''
	with open(tmp_snake, 'w') as f:
	rule_str = f"""rule auto:
	input:
	'{in_file}'
	output:
	'{out_file}'

	''' Three rule ex '''

	rule one:
	output:
	'out1'
	shell:
	'touch {output}'

	rule two:
	input: