This is a simple biology tool for extract all annotations you want from Genbank file(*.gb). Based on Biopython package.
basic usage:
python terminal.py -p/--program program_name [args]
arguments:
program list:
extract: extract all annotations you want to fasta files
statistic: statistic occurence times of annotations
muscle: run muscle alignment
macse: run macse alignment
extract, statistic and muscle args:
-i --infile input file
-c --contain contain annotations in this list only, separate using ',', do not use space
-e --except do not contain annotations in this list
combine args:
-i --infile input file folders list, separate using ',', do not use space
-m --mole_type molecular type, should be one of DNA, RNA, Protein
macse args:
-i --infile input file
-t --transl_table translation table (listed below)
1 The_Standard_Code
2 The_Vertebrate_Mitochondrial_Code
3 The_Yeast_Mitochondrial_Code
4 The_Mold_Protozoan_and_Coelenterate_Mitochondrial_Code_and_the_Mycoplasma_Spiroplasma_Code
5 The_Invertebrate_Mitochondrial_Code
6 The_Ciliate_Dasycladacean_and_Hexamita_Nuclear_Code
9 The_Echinoderm_and_Flatworm_Mitochondrial_Code
10 The_Euplotid_Nuclear_Code
11 The_Bacterial_Archaeal_and_Plant_Plastid_Code
12 The_Alternative_Yeast_Nuclear_Code
13 The_Ascidian_Mitochondrial_Code
14 The_Alternative_Flatworm_Mitochondrial_Code
15 Blepharisma_Nuclear_Code
16 Chlorophycean_Mitochondrial_Code
21 Trematode_Mitochondrial_Code
22 Scenedesmus_obliquus_mitochondrial_Code
23 Thraustochytrium_Mitochondrial_Code
extractor, extract annotations from input.gb, contain CDS, gene, rRNA, tRNA, except repeat_region and misc_feature:
python terminal.py -p extract -i input.gb -c CDS,gene,rRNA,tRNA -e repeat_region,misc_feature
macse alignment, translate table is 11:
python terminal.py -p macse -i \output\input-20xx-mm-dd_hh-mm-ss -t 11
combine all fasta files in CDS folder:
python terminal.py -p combine -i \CDS,\tRNA -m DNA
Most of untranslated Chinese comments are not important. Please don't care about it.