pykits
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fastakit.py
If you upload genome to ncbi, and ncbi told your genome has some base is alignment to adapter, after you validate that and want to replace the region with N, you can: blast adapter.fa to your genome get m6 output, cat m6|awk '{print $2","$9","$10}' > adapter.to.assembly.m6.replace.list
# --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
python package dependence:
biopython >= 1.72
fire >= 0.1.3
Python 3.6.1 :: Anaconda custom (64-bit)
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fire_table.py
for metagenome/16s/vcf or other data process:
# 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
python package dependence:
fire >= 0.1.3
pandas >= 0.23.4
Python 3.6.1 :: Anaconda custom (64-bit)
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fire_sns.py
# 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
python package dependence:
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)