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Go BigQuery tests

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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_

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#!/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

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import rule_maker

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

# generate a snakefile file for the second rule 

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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}'

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''' Three rule ex '''

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

rule two:    
    input:

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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:

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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

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Exposing your clipboard over SSH

I frequently administer remote servers over SSH, and need to copy data to my clipboard. If the text I want to copy all fits on one screen, then I simply select it with my mouse and press CMD-C, which asks relies on m y terminal emulator (xterm2) to throw it to the clipboard.

This isn't practical for larger texts, like when I want to copy the whole contents of a file.

If I had been editing large-file.txt locally, I could easily copy its contents by using the pbcopy command:

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onsuccess:
    shell(
        "curl `singularity exec docker://vault:1.2.1 vault read -field=value secret/v1/users/evansj/twilio-a` -X POST --data-urlencode 'To=+12406819176' --data-urlencode 'From=+18174022818' -u `singularity exec docker://vault:1.2.1 vault read -field=value secret/v1/users/evansj/twilio-u` --data-urlencode 'Body=gatk done'"
        )
onerror:
    shell(
        "curl `singularity exec docker://vault:1.2.1 vault read -field=value secret/v1/users/evansj/twilio-a` -X POST --data-urlencode 'To=+12406819176' --data-urlencode 'From=+18174022818' -u `singularity exec docker://vault:1.2.1 vault read -field=value secret/v1/users/evansj/twilio-u` --data-urlencode 'Body=gatk fail'"
        )