Karthik gkarthik

## tabulate_variants.py
import bjorn_support as bs
import mutations as bm
import pandas as pd


# FASTA must include reference NC_045512.2 (e.g. use cat to add the reference)
fasta_filepath = '2021-02-08_release.fa'
# specify name for output alignment
msa_filepath = 'msa.fa'
# run alignment (uses MAFFT but can be changed from bjorn_support.py)

## elasticsearch-restclient
# Using Emacs Restclient Mode to explore the Elasticsearch REST API
# http://www.elasticsearch.org/guide/en/elasticsearch/reference/

:es = http://127.0.0.1:9200

# Cluster Health

GET :es/_cat/health?v

# List of nodes

## bamfilter_oneliners.md

      
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                gkarthik
                / bamfilter_oneliners.md
            
            
              Created
              August 31, 2016 00:16
                — forked from davfre/bamfilter_oneliners.md
            
              
                SAM and BAM filtering oneliners
              
          
    SAM and BAM filtering one-liners
@author: David Fredman, david.fredmanAAAAAA@gmail.com (sans poly-A tail)

@dependencies: http://sourceforge.net/projects/bamtools/ and http://samtools.sourceforge.net/
Please comment or extend with additional/faster/better solutions.
BWA mapping (using piping for minimal disk I/O)

  
## angular-compile-dynamic-html.md

      
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                gkarthik
                / angular-compile-dynamic-html.md
            
            
              Created
              August 9, 2016 21:47
                — forked from umidjons/angular-compile-dynamic-html.md
            
              
                Compile dynamic template from outside of angular.
              
          
    Compile dynamic template from outside of angular

I want to load dynamic HTML content via AJAX, then compile it, because it contains
angular directives.
<!DOCTYPE html>
<html ng-app="app">
<head>
	import bjorn_support as bs
	import mutations as bm
	import pandas as pd


	# FASTA must include reference NC_045512.2 (e.g. use cat to add the reference)
	fasta_filepath = '2021-02-08_release.fa'
	# specify name for output alignment
	msa_filepath = 'msa.fa'
	# run alignment (uses MAFFT but can be changed from bjorn_support.py)
	# Using Emacs Restclient Mode to explore the Elasticsearch REST API
	# http://www.elasticsearch.org/guide/en/elasticsearch/reference/

	:es = http://127.0.0.1:9200

	# Cluster Health

	GET :es/_cat/health?v

	# List of nodes