Make cleaning
This commit is contained in:
Eric Coissac
1
web_src/.gitignore
vendored
1
web_src/.gitignore
vendored
@@ -1,3 +1,4 @@
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/.quarto/
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**/*.quarto_ipynb
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Before Width: | Height: | Size: 12 KiB |
@@ -265,7 +265,7 @@ grep -B 2 root < /etc/passwd
|
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grep -B 2 root < /etc/passwd > result
|
||||
```
|
||||
|
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{width = 40%}
|
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{ width=20% }
|
||||
|
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## A basic `Unix` command: Piping a stream into another command
|
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|
||||
@@ -277,7 +277,7 @@ grep -B 2 root < /etc/passwd > result
|
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grep -B 2 root < /etc/passwd | less
|
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```
|
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|
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{width = 20%}
|
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{ width=20% }
|
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|
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## RTFM: Bash redirections
|
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|
||||
@@ -293,171 +293,3 @@ grep -B 2 root < /etc/passwd | less
|
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|
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|
||||
|
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# The `OBITools`
|
||||
|
||||
{width = 80%}
|
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|
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## RTFM !
|
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|
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The [documentation](http://obitools4.metabarcoding.org) is available online.
|
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|
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{width = 80%}
|
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|
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## An `OBITools` command
|
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|
||||
{width = 80%}
|
||||
|
||||
|
||||
## Decorated fasta sequences
|
||||
|
||||
Basic fasta sequence:
|
||||
|
||||
```
|
||||
>my_sequence this is my pretty sequence
|
||||
ACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT
|
||||
GTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT
|
||||
AACGACGTTGCAGTACGTTGCAGT
|
||||
```
|
||||
|
||||
*Decorated* fasta sequence:
|
||||
|
||||
```
|
||||
>my_sequence taxid=3456; direct=True; sample=A354; this is my pretty sequence
|
||||
ACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT
|
||||
GTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT
|
||||
AACGACGTTGCAGTACGTTGCAGT
|
||||
```
|
||||
*decoration* can be any set of `key=value;` couples
|
||||
|
||||
## Main OBITools commands (1/2)
|
||||
|
||||
|
||||
- Metabarcode design and quality assessment
|
||||
- `ecoPCR`: in silico PCR
|
||||
- `ecoPrimers`: new barcode markers and primers
|
||||
- `ecotaxstat`: getting the coverage of an ecoPCR output compared to the original ecoPCR database
|
||||
- `ecotaxspecificity`: Evaluates barcode resolution
|
||||
|
||||
- File format conversions
|
||||
- `obiconvert`: converts sequence files to different output formats
|
||||
- `obitab`: converts a sequence file to a tabular file
|
||||
|
||||
- Sequence annotations
|
||||
- `ecotag`: assigns sequences to taxa
|
||||
- `obiannotate`: adds/edits sequence record annotations
|
||||
|
||||
## Main OBITools commands (2/2)
|
||||
|
||||
- Computations on sequences
|
||||
- `illuminapairedend`: aligns paired-end Illumina reads
|
||||
- `ngsfilter`: Assigns sequence records to the corresponding experiment/sample based on DNA tags and primers
|
||||
- `obiclean`: tags a set of sequences for PCR/sequencing errors identification
|
||||
- `obiuniq`: groups and dereplicates sequences
|
||||
|
||||
- Sequence sampling and filtering
|
||||
- `obigrep`: filters sequence file
|
||||
- `obihead`: extracts the first sequence records
|
||||
|
||||
- Statistics over sequence file
|
||||
- `obicount`: counts the number of sequence records
|
||||
- `obistat`: computes basic statistics for attribute values
|
||||
|
||||
|
||||
## Regular expressions: Regex
|
||||
|
||||
> In computing, a regular expression is a specific pattern that provides concise and flexible means to "match" (specify and recognize) strings of text, such as particular characters, words, or patterns of characters.
|
||||
>
|
||||
> Common abbreviations for "regular expression" include regex and regexp.
|
||||
> - http://en.wikipedia.org/wiki/Regular_expression
|
||||
|
||||
## Graphical representation
|
||||
|
||||
A regular expression can be represented by an *automata*
|
||||
|
||||
{ width=50% }
|
||||
|
||||
## Occurrence of a regular pattern
|
||||
|
||||
If one can get to the final state, the text `match` the regular expression.
|
||||
|
||||
|
||||
{ width=50% }
|
||||
|
||||
> Tutu et **_toto_** sont sur un bateau. Toto tombe à l’eau.
|
||||
|
||||
> Obama: «If daughters get tat**_too_**s, we will **_too_**»
|
||||
|
||||
## Exemples of regular expressions
|
||||
|
||||
Regular expressions defined on DNA → Σ={A,C,G,T}
|
||||
|
||||
| Regular expression | Automata |
|
||||
|-------------------------------|---------------------------------------------------------------------|
|
||||
| `ATG` (start codon) | { width=100% } |
|
||||
| `[ATG]TG` <br> `[^C]TG`(all start codons) | ![[ATG]TG](images/exp3.svg){ width=100% } |
|
||||
|
||||
## Exemples of regular expressions
|
||||
|
||||
Regular expressions defined on DNA → Σ={A,C,G,T}
|
||||
|
||||
| Regular expression | Automata |
|
||||
|-------------------------------|---------------------------------------------------------------------|
|
||||
| `.TG` <br> `[ACGT]TG` (all codons ending with TG) | { width=100% } |
|
||||
| `TTA+TT` <br> `TTAA*TT` (TT, at least one A, TT) | { width=100% } |
|
||||
|
||||
## Exemples of regular expressions
|
||||
|
||||
Regular expressions defined on DNA → Σ={A,C,G,T}
|
||||
|
||||
| Regular expression | Automata |
|
||||
|-------------------------------|---------------------------------------------------------------------|
|
||||
| `TAA`|`TAG`|`TGA` <br> `T(AA`|`AG`|`GA)` (All stop codons) | { width=100% } |
|
||||
|
||||
## Syntax of regular expressions
|
||||
|
||||
| Syntax | What it matches |
|
||||
|-------------------|--------------------------------------------------|
|
||||
| `^` | begining of the line |
|
||||
| `$` | end of the line |
|
||||
| `[]` | set of characters |
|
||||
| `[^]` | all characters but these ones (ex: `TTA{3,5}TT`) |
|
||||
| | | multiple choices |
|
||||
| `{}` | repetitions |
|
||||
| `*` | any number of times |
|
||||
| `+` | at least once |
|
||||
| `?` | none or once |
|
||||
| `\*` | the `*` character (same for `+`, `(`, `[`, ...) |
|
||||
|
||||
## Special characters: Regular expression extensions
|
||||
|
||||
| Special characters| What it matches |
|
||||
|-------------------|--------------------------------------------------|
|
||||
| `()` | used to define sub-expressions |
|
||||
| `\n` | used to reuse the text matched by the `n`th sub-expression |
|
||||
|
||||
## Syntax of extended regular expressions
|
||||
|
||||
Extended regular expressions defined on DNA → Σ={A,C,G,T}
|
||||
|
||||
| Regular expression | Automata |
|
||||
|-------------------------------|---------------------------------------------------------------------|
|
||||
| `([ACGT]{3})\1{9,}` (matching a stretch of at least the same codon 10 times) | As the langage described is not regular, no automaton can be used to represent the expression |
|
||||
|
||||
|
||||
[What is my regular expression engine capable of ?](https://en.wikipedia.org/wiki/Comparison_of_regular_expression_engines)
|
||||
|
||||
## Regular expressions and `obigrep`
|
||||
|
||||
Regular expressions can be used with `obigrep` to filter sequences with the appropriate options:
|
||||
|
||||
-s <REGULAR_PATTERN>, --sequence=<REGULAR_PATTERN>
|
||||
regular expression pattern used to select the
|
||||
sequence. The pattern is case insensitive
|
||||
-D <REGULAR_PATTERN>, --definition=<REGULAR_PATTERN>
|
||||
regular expression pattern matched against the
|
||||
definition of the sequence. The pattern is case
|
||||
sensitive
|
||||
-I <REGULAR_PATTERN>, --identifier=<REGULAR_PATTERN>
|
||||
regular expression pattern matched against the
|
||||
identifier of the sequence. The pattern is case
|
||||
sensitive
|
||||
|
||||
@@ -10,6 +10,7 @@ format:
|
||||
scrollable: true
|
||||
theme: beige
|
||||
html-math-method: mathjax
|
||||
embed-resources: true
|
||||
editor: visual
|
||||
---
|
||||
|
||||
@@ -347,9 +348,9 @@ knitr::include_graphics("figures/diversity.svg")
|
||||
- $\beta\text{-diversity}$ : $\beta = \frac{\gamma}{\alpha}$ ($sites/region$)
|
||||
:::
|
||||
|
||||
# $\alpha$-diversity
|
||||
# alpha-diversity
|
||||
|
||||
## Which is th most diverse environment ? {.flexbox .vcenter}
|
||||
## Which is the most diverse environment ? {.flexbox .vcenter}
|
||||
|
||||
```{r out.width = "400px"}
|
||||
knitr::include_graphics("figures/alpha_diversity.svg")
|
||||
@@ -1245,4 +1246,4 @@ boxplot(t(guiana.relfreq.final[,samples.type=="soil.Petit Plateau"]),log="y",
|
||||
names=qs,las=2,col=4,add=TRUE)
|
||||
```
|
||||
|
||||
## Bibliography
|
||||
## Bibliography
|
||||
|
||||
Reference in New Issue
Block a user