Visualizing similarity of two sequences through a dot plot.
Usage:
python3 dotplotter.py --in1 <FILE> --in2 <FILE> --out <FILE>
or
python3 dotplotter.py --seq1 <STR> --seq2 <STR> --out <FILE>
Option1:
--in1 STR Input FASTA file1
--in2 STR Input FASTA file2
--out STR Figure output file
Option2:
--seq1 STR Sequence1
--seq2 STR Sequence2
--out STR Figure output file
Optional:
--kmer INT k-mer length[31]
--name1 STR Sequence1 name
--name2 STR Sequence2 name
--in1 specifies a FASTA file that contains the first nucleotide sequence. The sequence name from this file can be used as label if no other name is specified via --name1.
--in2 specifies a FASTA file that contains the second nucleotide sequence. The sequence name from this file can be used as label if no other name is specified via --name2.
--seq1 specifies the first input sequence. The characters will be turned into upper case characters to avoid mismatches due to case sensitivity.
--seq2 specifies the second input sequence. The characters will be turned into upper case characters to avoid mismatches due to case sensitivity.
--out specifies the figure output file. The file extension determines the type of figure file that is created. Only types supported by Python and the operating system are possible. Usually PNG, JPG, SVG, and PDF are supported.
--kmer specifies the size of k-mers to use for identification of similarities between both sequences. Smaller k-mer sizes will lead to more matches, but larger values will make the comparison more specific. Default: 31.
--name1 specifies the name of sequence 1 that will be displayed as axis label in the dotplot. This argument overwrites the sequence name that might have been retrieved from sequence file 1 if the sequence was provided as FASTA file.
--name2 specifies the name of sequence 2 that will be displayed as axis label in the dotplot. This argument overwrites the sequence name that might have been retrieved from sequence file 2 if the sequence was provided as FASTA file.
This repository.