jameslz/snippets

code snippets

snippets：code snippets

1. aitchison distance matrix

compile

cd aitchison
cc -g -Wall -Wno-unused-function -Wc++-compat -O2   aitchison.c  -o  aitchison  kstring.c  -lz -lm

example

 ./aitchison zotu_table.txt

2. otutab_rare: implemetation uisng fastrand.

fastrand

** compile **

cc -g -Wall -Wno-unused-function -Wc++-compat -O2   otutab_rare.c  -o  otutab_rare  kstring.c fastrand.c  -lz

example

usearch -otutab_rare zotu_table.txt  -randseed 11  -sample_size  30000  -output otutab_usearch.txt
otutab_rare  -s 11  zotu_table.txt  30000   >otutab_fastrand.txt
tsv-utils  agg  fastrand:otutab_fastrand.txt  usearch:otutab_usearch.txt  >otutab.norm.txt

3. Cumulative sum scaling (css) normalization

DO NOT USE IT

normalization constant： 1000 lth quantile： 0.5

** compile **

cc -g -Wall -Wno-unused-function -Wc++-compat -O2  css.c  -o  css  kstring.c -lm  -lz

interface

Usage: css <otutab>

Options:
  -l   logarithmic transform to normalized count. [NONE].
  -f   fixed constant normalized factor 1000. [NONE].

example

./css  -l  zotu_table.txt