# --seq_pos_list is multi line, seprate by , 
python fastakit.py replace_base  --seq_pos_list seq_pos_list  --pos_count_from 1 \
	--seq_file assembly.fa --output assembly.new.fa --replace_base_with N

# or this just one pos
python fastakit.py replace_base  --seq_id 3 --pos_start 1 --pos_end 30 \
	--pos_count_from 1 --seq_file assembly.fa --output assembly.new.fa

biopython >= 1.72
fire >= 0.1.3
Python 3.6.1 :: Anaconda custom (64-bit)

# extract column or row or both by keywords, also support extrac sample name by group name
python fire_table.py extract --data Phylum.gt1percent.kruskal.test.txt.new3 --keywords A.S.14d,C.S.7d --extract_index 0 \
	--extract_column 1 	--prefix test4 --header 0 --index_col 0 --sample2group_fileds 0,1 --sample2group sample2group.txt \
	--sample2group_fileds "0,1" --same_outdir 1 --keep_metadata 1 --skip_not_exists 0

fire >= 0.1.3
pandas >= 0.23.4
Python 3.6.1 :: Anaconda custom (64-bit)

# heatmap homemade for category fragments data, you can defined the block freely by --value_segments !
python fire_sns.py heatmap-homemade --data Class.gt1.kruskal.test.txt.new2 --header 0 --index-col 0 --linewidths 0.2 --outdir . --prefix Class.gt1.kruskal.test.txt.new2.heatmap --oformat pdf --order_x LP.0d,LP.L.7d,LP.L.14d,LP.S.7d,LP.S.14d,OJ.0d,OJ.L.7d,OJ.L.14d,OJ.S.7d,OJ.S.14d --xlabel-rotation 90 --ylabel-rotation 0 --legend-ncol 1 --color-segments '#FAEBD7,#FFEBCD,#F5DEB3,#8B4513' --value_segments 0.5:1,1:2,2:5,5:15

# barplot
python fire_sns.py  barplot --outdir . --prefix  xx --data Species.all_relative_abundance.xls --oformats "pdf,png" barplot --fig_width_scale 0.35 --fig-height 10 --legend-locus bottom --ncol-leg 0

fire >= 0.1.3
matplotlib >= 3.0.0
palettable >= 3.1.1
pandas >= 0.23.4
seaborn >= 0.9.0
Python 3.6.1 :: Anaconda custom (64-bit)