sephraim

#!/bin/sh

# Convert a TSV (tab) file to a CSV (comma) file
#
# Please note that this will surround all values with
# double-quotes. All other double-quotes will be escaped.
#
# Example usage:
#   ./tab2csv.sh myfile.tsv > myfile.csv

sephraim

# Sorts a file by chromosomal position
# 
# Input file must have the following format:
# - Column 1: chromosome (e.g. chr1, chr10 *OR* 1, 10)
# - Column 2: start position (e.g. 4325484)
# - All other columns can be ordered in any way
#
# Input file sample:
#   chr17:5432542:G>A     .........
#   17:5432542:G>A        .........

sephraim

# Swaps the nucleotide sequence to the opposite strand
#
# This means if the sequence is on the forward strand,
# then the function will return the corresponding sequence
# on the reverse strand, and vice versa.
#
# For example:
#   Original: TCCAGACAC
#   Swapped:  GTGTCTGGA
#

sephraim

#!/bin/bash

# Split a file into N parts
#
# Each resulting file will have a .ptXX suffix
#
# Example - split file into 30 parts:
#   ./parts.sh myfile.txt 30

split -dl$((`wc -l < $1`/$2+1)) $1 $1.pt

sephraim

#!/bin/bash

##
# Remove Duplicates in a VCF
#
# A duplicate variant is when multiple records have the same
# CHROM, POS, REF, and ALT. This script will pick *one* of the
# duplicate variants and discard the rest. The record that is
# picked is the one that comes first in sorting order.
#

sephraim

#!/bin/bash

##
# Rename HGMD INFO tags
#
# Example usage:
#   ./rename_HGMD_INFO_tags.sh hgmd-hg19.vcf > hg19_HGMD_2015r4.MORL.vcf
##

tags=(

sephraim

// Use Gists to store code you would like to remember later on
console.log(window); // log the "window" object to the console

sephraim

/**
 * STEP 1: Write queries to import files into an SQLite database
 **/

/* Set file input mode */
.mode tabs

/* Import tables from TSV files */
.import file1.tsv table1
.import file2.tsv table2

sephraim

grep -wFf <(cut -f__COL1__-__COL2__ __FILE__ | sort | uniq -d) __FILE__

sephraim

ALTER TABLE  `__TABLE__`
  ADD  `__COL__`
  VARCHAR(255) NULL
  DEFAULT NULL
  COMMENT '__COMMENT__'
  AFTER `__ANOTHER_COL__` ;