Indraniel indraniel

## vcf-subpopulation-annotate.go
package main

/*
    Building & Usage
    ----------------

        go build -o foo subpopulation-annotate.go
       ./foo --in /path/to/input/test.vcf --sample-population-map /path/to/20120131-omni-2141-sample-superpopulation.dat --out /path/to/out.vcf.gz

    Where "20120131-omni-2141-sample-superpopulation.dat" is a tsv file like:

## vcf-filter.go
package main

import (
	"fmt"
	"log"
	"os"
	"os/signal"
	"strings"
	"syscall"

## vcf-display-populations-af.go
package main

import (
	"fmt"
	"log"
	"math"
	"os"
	"os/signal"
	"strconv"
	"strings"

## vcf-filter-by-maf.go
package main

import (
	"fmt"
	"log"
	"math"
	"os"
	"os/signal"
	"strconv"
	"strings"

## knit-latex.r
#!/usr/bin/env Rscript

args <- commandArgs(trailingOnly=TRUE)
file <- args[1]
cat(paste("Processing: ", file, "\n"))

library(knitr)
knit(file)

## analytics-project-layout.md

      
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                indraniel
                / analytics-project-layout.md
            
            
              Created
              September 29, 2015 17:16
            
              
                A WIP skeleton layout for analytics projects
              
          
    A useful starter skeleton layout for analytics project.
project-dir 
├── README.md
├── bin
├── data
│   ├── derived
│   ├── original
│   └── test

├── docs

  
## sff2fastq-main.c
/* N O T E S ******************************************************************/

/*
    substitute this file for the main.c in the sff2fastq project.  Upon
    recompliation you then try the following command:

        sff2fastq -n <sff-file>

    This will add an extra debugging line in the FASTQ output like:

## transpose.awk
#!/usr/bin/awk -f

# taken from: http://stackoverflow.com/questions/1729824/transpose-a-file-in-bash
{
    for (i=1; i<=NF; i++)  {
        a[NR,i] = $i
    }
}
NF>p { p = NF }
END {

## 1-fetch-na12878-pedigree-metadata.py
#!/usr/bin/env python

from __future__ import print_function, division
import sys, os, pprint
from glob import glob

import requests
from lxml import html
from toolz.curried import *

## Makefile
.PHONY: clean

PRJDIR := /path/to/project
DOCS := $(PRJDIR)/docs
RLIBS := /gscmnt/gc2801/analytics/idas/jira/BIO-1465/rpkgs
REPORTDIR := $(DOCS)/writeups
PDFLATEX := /home/archive/texlive-2015/2015/bin/x86_64-linux/pdflatex

writeup: $(REPORTDIR)/report.pdf
	package main

	/*
	Building & Usage
	----------------

	go build -o foo subpopulation-annotate.go
	./foo --in /path/to/input/test.vcf --sample-population-map /path/to/20120131-omni-2141-sample-superpopulation.dat --out /path/to/out.vcf.gz

	Where "20120131-omni-2141-sample-superpopulation.dat" is a tsv file like:
	package main

	import (
	"fmt"
	"log"
	"os"
	"os/signal"
	"strings"
	"syscall"
	#!/usr/bin/env Rscript

	args <- commandArgs(trailingOnly=TRUE)
	file <- args[1]
	cat(paste("Processing: ", file, "\n"))

	library(knitr)
	knit(file)
	/* N O T E S ******************************************************************/

	/*
	substitute this file for the main.c in the sff2fastq project. Upon
	recompliation you then try the following command:

	sff2fastq -n <sff-file>

	This will add an extra debugging line in the FASTQ output like:
	#!/usr/bin/awk -f

	# taken from: http://stackoverflow.com/questions/1729824/transpose-a-file-in-bash
	{
	for (i=1; i<=NF; i++) {
	a[NR,i] = $i
	}
	}
	NF>p { p = NF }
	END {
	#!/usr/bin/env python

	from __future__ import print_function, division
	import sys, os, pprint
	from glob import glob

	import requests
	from lxml import html
	from toolz.curried import *
	.PHONY: clean

	PRJDIR := /path/to/project
	DOCS := $(PRJDIR)/docs
	RLIBS := /gscmnt/gc2801/analytics/idas/jira/BIO-1465/rpkgs
	REPORTDIR := $(DOCS)/writeups
	PDFLATEX := /home/archive/texlive-2015/2015/bin/x86_64-linux/pdflatex

	writeup: $(REPORTDIR)/report.pdf