OBITools4 Documentation on OBITools4 documentation

About

Mon, 01 Jan 0001 00:00:00 +0000

What are OBITools4? #

The development of OBITools began at LECA ( University of Grenoble) in the early 2000s, at the same time as the development of DNA metabarcoding methods in the same laboratory. The idea behind the OBITools project was to provide a set of UNIX command-line tools that mimic standard UNIX shell commands such as grep, uniq or wc, but which work on DNA sequence files. Unlike standard UNIX tools, where the processing unit is a line of text, with OBITools the processing unit is a sequence record. In addition, some commands implementing algorithms specific to the processing of DNA metabarcoding data have been added, making OBITools one of the sequence processing tools widely used on UNIX-like systems, suitable for the analysis of DNA metabarcoding data.

Regular Expressions

Mon, 01 Jan 0001 00:00:00 +0000

Regular Expressions #

Regular expressions are a powerful tool for describing patterns in text. They are used in several OBITools like obigrep , obiannotate or obiscript .

Single characters #

Pattern	Description
`.`	any character, possibly including newline (flag s=true)
`[xyz]`	character class
`[^xyz]`	negated character class
`[[:alpha:]]`	ASCII character class
`[[:^alpha:]]`	negated ASCII character class

Composites #

Pattern	Description
`xy`	x followed by y
`x\|y`	x or y (prefer x)

Repetitions #

Pattern	Description
`x*`	zero or more x, prefer more
`x+`	one or more x, prefer more
`x?`	zero or one x, prefer one
`x{n,m}`	n or n+1 or … or m x, prefer more
`x{n,}`	n or more x, prefer more
`x{n}`	exactly n x
`x*?`	zero or more x, prefer fewer
`x+?`	one or more x, prefer fewer
`x??`	zero or one x, prefer zero
`x{n,m}?`	n or n+1 or … or m x, prefer fewer
`x{n,}?`	n or more x, prefer fewer
`x{n}?`	exactly n x

Grouping #

Pattern	Description
`(re)`	numbered capturing group (submatch)
`(?P<name>re)`	named & numbered capturing group (submatch)
`(?<name>re)`	named & numbered capturing group (submatch)
`(?:re)`	non-capturing group
`(?flags)`	set flags within current group; non-capturing
`(?flags:re)`	set flags during re; non-capturing

Character classes #

Pattern	Description
`[\d]`	digits (== \d)
`[^\d]`	not digits (== \D)
`[\D]`	not digits (== \D)
`[^\D]`	not not digits (== \d)
`[[:name:]]`	named ASCII class inside character class (== [:name:])
`[^[:name:]]`	named ASCII class inside negated character class (== [:^name:])
`[\p{Name}]`	named Unicode property inside character class (== \p{Name})
`[^\p{Name}]`	named Unicode property inside negated character class (== \P{Name})

Named character classes #

Pattern	Description
`[[:alnum:]]`	alphanumeric (== `[0-9A-Za-z]`)
`[[:alpha:]]`	alphabetic (== `[A-Za-z]`)
`[[:ascii:]]`	ASCII (== `[\x00-\x7F]`)
`[[:blank:]]`	blank (== `[\t ]`)
`[[:cntrl:]]`	control (== `[\x00-\x1F\x7F]`)
`[[:digit:]]`	digits (== `[0-9]`)
`[[:graph:]]`	graphical (== `[!-~]` == [A-Za-z0-9!"#$%&'()*+,\-./:;<=>?@[\\\]^_`{\|}~])
`[[:lower:]]`	lower case (== `[a-z]`)
`[[:print:]]`	printable (== `[ -~]` == `[[:graph:]]`)
`[[:punct:]]`	punctuation (== [!-/:-@[-\`{-~])
`[[:space:]]`	whitespace (== `[\t\n\v\f\r ]`)
`[[:upper:]]`	upper case (== `[A-Z]`)
`[[:word:]]`	word characters (== `[0-9A-Za-z_]`)
`[[:xdigit:]]`	hex digit (== `[0-9A-Fa-f]`)

DNA Patterns

Mon, 01 Jan 0001 00:00:00 +0000

DNA Patterns #

DNA patterns are useful for describing short DNA sequences like oligonucleotides. They are used by several OBITools like obimultiplex , obipcr or obigrep . The advantage of using DNA patterns over classical regular expressions is that they can be matched with errors. Allowed errors can be simple mismatches, or mismatches and insertions/deletions.

Glossary of tags

Fri, 04 Oct 2024 17:16:03 +0200

Glossary of tags #

- D - #

definition :

text information about the sequence present in the original sequence file.
direction :

set to “forward” if the original sequence did not need to be reverse-complemented to be processed, set to “reverse” otherwise. ( obipcr)

- F - #

forward_error :

Number of mismatch between forward primer and priming site ( obipcr)
forward_match :

Forward primer priming site sequence ( obipcr)
forward_primer :

Forward primer sequence ( obipcr)