SQD

executing unix commands with multi processes

installation

$ npm install -g sqd

usage

$ sqd -c command [--debug] [--exit] [-p nProcess] [-s separator_command] <input file> [output file]

grep with 8 processes

sqd -c "grep -e something" -p 8 input.txt

results are on STDOUT.

sed with 4 processes (default), results to output.txt

sqd -c "sed -e y/ATCG/atcg/" input.txt output.txt

with separator option, we can also handle binary files

sqd -c "samtools view -" -s bam input.bam

reducing

sqd -c "node foobar.js" sample.txt --reduce

in foobar.js

if (process.env.sqd_map) {
  process.stdin.on("data", function(data) {
    // do something, separated into multi processes
  });
}
else if (process.env.sqd_reduce) {
  process.stdin.on("data", function(data) {
    // do somothing which reduces the results
  });
}
process.stdin.resume()

options

• -p: the number of processes
• --debug: debug mode (showing time, temporary files)
• --exit: exits when child processes emit an error or emit to stderr
• -s: (see separator section)
• --reduce: reducing the results with the same command, which is given an environmental variable named sqd_reduce with value "1"

additional environment variables in child processes

Be careful that all values are parsed as string.

• sqd_n: process number named by sqd, differs among child processes
• sqd_start: start position of the file passed to the child process
• sqd_end: end position of the file passed to the child process
• sqd_command: command string (common)
• sqd_input: input file name (common)
• sqd_tmpfile: path to the tmpfile used in the child process
• sqd_debug: debug mode or not. '1' or '0' (common)
• sqd_hStart:: start position of the header (common)
• sqd_map:: "1", unless it is spawned for reducing. undefined, otherwise
• sqd_reduce:: "1", if it is spawned for reducing. undefined, otherwise

separator

sqd requires a separator which separates a given input file into multiple chunks. separator offers the way how sqd separates the file by JSON format.

the JSON keys are

• positions: start positions of each chunks in the file

"positions": [133, 271, 461, 631]

• header: range of the header section of the file, null when there is no header section

"header": [0, 133]

• size: file size (optional)

"size": 34503

available separators

• -s line: default. separate by line
• -s bam: see SAM/BAM format specification
• -s fastq: see fastq format

sqdm --much more memory

$ sqdm [memory=4000MB] -c command [--debug] [--exit] [-p nProcess] [-s separator_command] <input file> [output file]

sqd with 8000MB(≒8GB) memory

sqdm 8000 -c "cat" sample.txt