KmerFreqCalc (KFC)

DATE:2020-1-24
version:0.2.1

Author Information:

Name: Liu Shuai
Department: Anhui University and the Institute of Zoology, Chinese Academy of Sciences jointly cultivation
E-mail: ls2659614061@126.com

Supervisor Information:

Name: Wu Qi
Department: Institute of Microbiology, Chinese Academy of Sciences
E-mail: wuq@im.ac.cn

General Procedure

• kmer frequency vector
  • 1.Read the sequences in the filement into a dictionary.
  • 2.Count the number of kmer in sequences.
  • 3.Make a summary statistic of all kmers' number of all subsequences.
  • 4.Calculate the frequencies of kmers.
  • 5.Make a cv.txt formated output.
    #example.cv.txt
    K
    Significant kmer number
    Inner product
    1 0.044418402253529
    2 -0.13694127815637536
    3 0.02302543931397616
    4 0.08209917560394331
    ......
• distance matrix
  • 1.Employee Cosine dissimilarity or Euclidean distance to calculate the difference among species
  • 2.Make a .meg format output opened up by MEGA.

Manual

kmer frequency vector

• python3 kmer_frequence_vector.py -K -fna.path -speciesname -CPU.NUM
  -K -num the length of kmer K>=1
  -fna.path -str the path of dna sequence as an input,whose suffix is fna,fa,ffn,or fasta
  -tag.name -str the name of sequence
  -CPU.NUM -num the number of CPU be used

distance matrix

• python3 distance_matrix.py cvtxt.directory CPU.NUM distance-type(COS or EUC)
  cvtxt.directory -str The path of cv.txt of species stored other suffix files must nonexistent
  CPU.NUM -num The number of CPU be used
  distance-type -str Euclidean distance or Cosine disimilarity