Collections of my frequently used ID manipulation scripts in bioinformatic works.
idot <command> [<arguments>]
Command: find find id_file matched lines in target_file
diff find specific lines in id_file or target_file
replace replace id in the target_file according to the id_file
fasta fetch id_file match fasta sequences from all sequences
idot find [options] <id_file> <target_file>
Options: -d STR The delimiter character of fields, default <TAB>.
Valid delimiters: comma (","), space ("\s"), or <TAB> ("\t")
-f INT The field(s) that specified as ID column(s), default 1.
Use comma (",") to specify multiple fields. e.g. -f 1,2
-s STR The method used for ID sort. default: u.
Available methods: sn - strint number
s - string
n - number
u - unsorted (use id_file id order)
t - use target_file id order
r - reverse (in combination with others)
-h Help message
idot diff [options] <id_file> <target_file>
Options: -d STR The delimiter character of fields, default <TAB>.
Valid delimiters: comma (","), space ("\s"), or <TAB> ("\t")
-f INT The field(s) that specified as ID column(s), default 1.
Use comma (",") to specify multiple fields. e.g. -f 1,2
-p INT Print the specific ID of file: 1 - id_file (default)
2 - target_file
-h Help message
idot replace <id_file> <target_file>
idot fasta <id_file> <database_file>
Qinhu Wang ([email protected])
2017 (c) Qinhu Wang, Northwest A&F University
MIT