fix rst syntax

remove hieroglyph specific class transform in classical sphinx

fix rst syntax
762bdd0a · Bertrand NÉRON · ce5b8ed5 · 762bdd0a · 762bdd0a · 762bdd0a
Commit 762bdd0a authored 2 years ago by Bertrand NÉRON
--- a/source/Installation/linux_admin.rst
+++ b/source/Installation/linux_admin.rst
@@ -90,6 +90,16 @@ man vs info vs help
 set the date and time
 =====================
+Having a right time is important, lot of tools used time to know if they have to do something ...
+We will set time of the machine to the UTC time
+Then the correction to the localtime will be perform by Linux
+To set the time
+#. restart your PC and press escape key during boot phase
+#. select enter set up
+#. set the time
+#. save and exit
 sudoers
@@ -119,6 +129,7 @@ create new user
 only root can perform this command
 create new group
 ================

--- a/source/Unix/chain_commands.rst
+++ b/source/Unix/chain_commands.rst
@@ -125,10 +125,11 @@ Redirecting Standard Error
 * how to redirect stdout and stderr in same file?
-.. rst-class:: build
+    ``squizz -c FASTA qn1.gb > qn1.fa 2>&1``
-   * ``squizz -c FASTA qn1.gb > qn1.fa 2>&1``
+.. warning::
-   * .. warning:: 2>&1 there is no spaces between >and &1 
+    2>&1 there is no spaces between >and &1
 The chain command
 =================
@@ -164,14 +165,14 @@ How do I run several commands in Sequence or all at once?
 | and store the result in ``QR1.FA`` file
 | all in one command line
-.. rst-class:: build
-   * squizz -c FASTA ~/DataBio/Sequences/Nucleique/qr1.gde > qr1.fa ; tr 'acgt' 'ACGT' < qr1.fa > QR1.FA
+    ``squizz -c FASTA ~/DataBio/Sequences/Nucleique/qr1.gde > qr1.fa ; tr 'acgt' 'ACGT' < qr1.fa > QR1.FA``
 limitation
 ==========
-squizz -c FASTA qr1.gd > qr1.fa ; tr 'acgt' 'ACGT' < qr1.fa > QR1.FA
+    ``squizz -c FASTA qr1.gd > qr1.fa ; tr 'acgt' 'ACGT' < qr1.fa > QR1.FA``
 | Here there is no consequences.
 | But if my command is more complex like ``squizz -c FASTA qr1.gd > qr1.fa ; blastall -p blastp -d sp -i qr1.fa``
@@ -204,3 +205,36 @@ command2 will be executed if and only if command1 returned zero exit status.
   The exit status depends how the developer implement programs.
   Sometimes the developer does not follow the convention.
   So it's not possible to chain correctly those programs.
+xargs
+=====
+build and execute command lines from standard input
+xargs executes the command with any initial-arguments
+followed by items read from standard input.
+Do not forget to add -l to process standard input line by line
+::
+   find . -name '*.fasta' | xargs grep ">"
+* **-I** allows you to insert the line from the standard input
+  somewhere else than in the end of the command
+::
+   find . -name '*.fasta' | xargs -I fic cat fic >>allmysequences
+tee
+===
+* tee copies its input stream to the standard output and the files
+  specified in argument
+.. figure:: ../_static/unix/images/688px-Tee.png
+   :class: align-center
+   :width: 500px
+   http://en.wikipedia.org/wiki/Tee_%28command%29#mediaviewer/File:Tee.svg
--- a/source/Unix/file_system.rst
+++ b/source/Unix/file_system.rst
@@ -15,14 +15,6 @@ File system
 * who am I ?
 * where am I ?
-.. rst-class:: build
-   * who am I ? 
-      * | We will see this later on this course.
-        | For now you are the user "unix"
-   * where am I ?
  * somewhere on the file system !
@@ -38,8 +30,6 @@ what is a "tree structure"?
 do you already know a tree structure in biology?
-.. rst-class:: build
 .. figure:: ../_static/unix/images/F1_large.jpg
  :class: align-center
  :width: 500px
@@ -56,27 +46,24 @@ file sytem tree structure
 * ancestors are replaced by directories and species by files.
 * so it contains directories that contains other directories and/or files.
-* where am I?
+where am I?
-.. rst-class:: build
-      * in a directory.
+in a directory.
 what directory ?
 ================
-* ``pwd`` (for **p**\ rint **w**\ orking **d**\ irectory)
+``pwd`` (for **p**\ rint **w**\ orking **d**\ irectory)
-.. rst-class:: build
-   * /home/unix
+/home/unix
-   * This the coordinates of your current position.
+| This the coordinates of your current position.
-   * But what does it mean?
+| But what does it mean?
-   * To navigate, coordinates are not enough.
+| To navigate, coordinates are not enough.
-   * You need a map!
+| You need a map!
 where am I on the map?
@@ -88,17 +75,16 @@ This is my map!
      :class: align-center
      :width: 600px
-* So now, I know where I'am.
+| So now, I know where I'am.
-* But now, I'd like to explore the map.
+| But now, I'd like to explore the map.
 let's go for exploration
 ========================
-* I need to know how to move.
+| I need to know how to move.
-* I need know how to specify my destination.
+| I need know how to specify my destination.
-.. rst-class:: build
 * how to move?
@@ -154,9 +140,8 @@ Exploration
 what are there in a this directory?
-.. rst-class:: build
-   * ``ls`` (list directory contents)
+| ``ls`` (list directory contents)
 ls
 ==
@@ -206,7 +191,7 @@ how to get the listing of all files like abcd2_mouse.fa or abcd3_human.sp but **
 abcd_result.txt?
-create direcotries
+create directories
 ==================
 * **mkdir path** create a directory. 
@@ -304,222 +289,3 @@ The command establishing this link is: ::
 * ln -s source_file  link_name
 We can create a link toward a directory
-Permissions
-===========
-* Unix is a multi-users system. So some users have some rights to do something and some other not.
-* The system allow to protect your data form an other user.
-* The system allow some users to work in groups.
-all this features are managed  by the **permissions** (or right access)
-3 classes of permissions
-========================
-::
-   $ ls -l
-   total 1176
-   drwxr-xr-x 4 bneron CIB   4096 Mar  4  2014 Alignment
-   -rw-r--r-- 1 bneron CIB 220196 Mar  4  2014 CIP-55-138_A.b_A06_037.ab1
-   drwxr-xr-x 3 bneron bneron   4096 Jun  4 14:51 HMM
-.. figure:: ../_static/unix/images/permissions.png
-   :class: align-center
-   :width: 650px
-| **U**: user 
-| **G**: group
-| **O**: others
-| **r**: read      (4)
-| **w**: write     (2)
-| **x**: execute   (1)
-rwx what does it really mean?
-=============================
-+---+---+------------------------+-------------------------------------------------+
-|   |   | file                   | directory                                       |
-+===+===+========================+=================================================+
-| r | 4 | read                   | allow to list                                   |
-+---+---+------------------------+-------------------------------------------------+
-| w | 2 | write                  | allow to create and delete file and directories |
-+---+---+------------------------+-------------------------------------------------+
-| x | 1 | the file is executable | allow to enter and pass trhough the directory   |
-+---+---+------------------------+-------------------------------------------------+
-who am I?
-=========
-Permisions are based on your identity and the groups to wich you belong.
-* **whoami** => give you the login you logged with
-* **id  <login>** => give the id and the groups to which the login blong (login is optional) ::
-   bneron@bic-t2a:~$id
-   uid=2896(bneron) gid=3044(CIB) groups=3044(CIB),87(biok),110(sis),547(mobyle),990(gensoft),3160(vpn-ssl-users),20000(bioweb)
-* uid is my login
-* gid is my primary group
-* groups is the list of all groups to which I belongs (max 16 groups).
-change permisions
-=================
-**chmod [ugo] [+-] [rwx] <target>**
-::
-   chmod [ugo] [+-] [rwx] <target>
-   drwxr-xr-x 4 bneron CIB   4096 Mar  4  2014 Alignment
-   chmod g+w Alignment
-   drwxrwxr-x 4 bneron CIB   4096 Mar  4  2014 Alignment
-   chmod o-rx  Alignment
-   drwxrwx--- 4 bneron CIB   4096 Mar  4  2014 Alignment
-   chmod g-wo+x Alignment
-   chmod: invalid mode: 'g-wo+x'
-   chmod go +rx Alignment
-   drwxrwxr-x 4 bneron CIB   4096 Mar  4  2014 Alignment
-you can use -R option to apply permision to a directory and recursively to its contents.
-change permisions syntax 2
-==========================
-**chmod num_value <target>**
-| num value is composed of 3 digits respectively for
-| user, group, other
-| each value is the sum of the octal symbols
-| for instance for w => 4, read rw => 4+2 = 6 ...  
-::
-   -rw-r--r-- 1 bneron sis 0 Oct 16 13:59 file1
-   chmod 755 file1
-   -rwxr-xr-x 1 bneron sis 0 Oct 16 13:59 file1
-   chmod 640 file1
-   -rw-r----- 1 bneron sis 0 Oct 16 13:59 file1
-octal notation
-==============
-+----------------------+----------+-----------------------+
-| Symbolic             | Octal    | English               |
-| Notation             | Notation |                       |
-+======================+==========+=======================+
-| \-\-\-\-\-\-\-\-\-\- | 000      | no permissions        |
-+----------------------+----------+-----------------------+
-| ---x--x--x           | 111      | execute               |
-+----------------------+----------+-----------------------+
-| --w--w--w-           | 222      | write                 |
-+----------------------+----------+-----------------------+
-| --wx-wx-wx           | 333      | write & execute       |
-+----------------------+----------+-----------------------+
-| -r--r--r--           | 444      | read                  |
-+----------------------+----------+-----------------------+
-| -r-xr-xr-x           | 555      | read & execute        |
-+----------------------+----------+-----------------------+
-| -rw-rw-rw-           | 666      | read & write          |
-+----------------------+----------+-----------------------+
-| -rwxrwxrwx           | 777      | read, write & execute |
-+----------------------+----------+-----------------------+
-**exercises:**
-| create files and directories, 
-| change their permisions.
-permissions by default
-======================
-To controls the file/dir's permissions at their creation.
-* **umask** display the mask in octal notation: 0022 
-* **umask -S** display the mask in symbolic notation: u=rwx,g=rx,o=rx
-| umask is the complement to 7 to the permissions applied
-| umask = 0022 
-| **directories**: permissions are 777
-| 7-0=\ **7**, 7-0=\ **7**, 7-2=\ **5**, 7-2=\ **5** 
-| directories will be created with 755 rights (rwxr-xr-x)
-| **files** is same as dir except, never **x** by default
-| 7-0=\ **7**, 7-0=\ **7**, 7-2=\ **5**, 7-2=\ **5** then remove **x** if necessary 
-| files will be created with 644 rights (rw-r--r--)
-octal codes meaning
-===================
-+----------------+---------------------+----------------+
-| Octal digit in |                     |                |
-| umask command  | Allows on directory | allows on file |
-+================+=====================+================+
-| 0              | read, write,execute | read, write    |
-+----------------+---------------------+----------------+
-| 1              | read and write      | read, write    |
-+----------------+---------------------+----------------+
-| 2              | read and execute    | read           |
-+----------------+---------------------+----------------+
-| 3              | read only           | read           |
-+----------------+---------------------+----------------+
-| 4              | write and execute   | write          |
-+----------------+---------------------+----------------+
-| 5              | write only          | write          |
-+----------------+---------------------+----------------+
-| 6              | execute only        | no permissions |
-+----------------+---------------------+----------------+
-| 7              | no permissions      | no permissions |
-+----------------+---------------------+----------------+
-setting the umask
-=================
-* **umask octal_value**
-* **umask -S symbolic value**
-::
-   umask 001
-   umask -S
-   u=rwx,g=rx,o=rx
-   umask -S o+w
-   u=rwx,g=rx,o=rwx
-exercise:
-| create dir and files (use touch) with different umask
-| check their permisions with ``ls -l``
-.. role:: red
-:red:`To set x on file you need to use chmod.`
-change owner/group
-==================
-chown command (for **ch**\ ange **ow** ner)
-* **chown owner file/dir**  
-* **chown owner.group file/dir**
-:red:`the ownership of a file may only be altered by a super-user`
-* **chgrp group file/dir**
-.. warning::
-   * Only a member of a group can change a file's group
-   * And only to one of which they are a member.
-* **-R** option recurse through subdirectories.
--- a/source/Unix/jokers.rst
+++ b/source/Unix/jokers.rst
@@ -171,6 +171,7 @@ there is various solutions to escape special characters.
 * enclose file name in **'** (single-quotes) or **"** (double-quotes)
 .. warning::
    backslashes, single-quotes and double-quotes present different levels of protection
 ::

--- a/source/Unix/scripting.rst
+++ b/source/Unix/scripting.rst
@@ -36,7 +36,7 @@ exercise
 syntax ::
    # use the bashrc
-    source ${HOOME}/.bashrc
+    source ${HOME}/.bashrc
 #. make a copy of the *.bashrc* file
 #. use vim to edit the *.bashrc* file and add the alias.

--- a/source/Unix/search_filter.rst
+++ b/source/Unix/search_filter.rst
@@ -89,24 +89,21 @@ grep with Regular Expressions
    * more information on regular expression in *man grep*
-sed
-===
 Regular expression vs shell special characters.
 ===============================================
-    **warning**
+.. warning::
    * remember some characters have a special meaning for the shell, eg *>*, *>>*, *2>*, *\**, *?*, *|*, ...
    * remember shell evaluation is executed **before** command execution
    example: what do you expect in the following **wrong** examples:
    * grep > file
    * grep * file
-    regular expression and shell share some metacharacters that do not have the same meaning, when you want to search for those characters you have to protect them.
+regular expression and shell share some metacharacters that do not have the same meaning,
+when you want to search for those characters you have to protect them.
 **hint:** **always** protect your search pattern by enclosing it in double quotes *"*

--- a/source/Unix/transform.rst
+++ b/source/Unix/transform.rst
@@ -5,6 +5,8 @@
 replace pattern
 ***************
+.. role:: red
 tr
 ==
@@ -52,6 +54,11 @@ or the program dos2unix
 dos2unix transforms the file *inplace*.
+exercice
+--------
+transform sequence in lower case in upper case
 sed.
 ====
@@ -83,7 +90,7 @@ replace pattern
 * **sed 's<SEP>pattern<SEP>replace' file** NB <SEP> may be any single character. usual <SEP> ones are  */*, *|*, *,*, *#*.
 * ``sed 's/chromosome/chr/' arrayAnnot.txt``
-  replaces **only the 1st** occurence of *chromosome* by 'chr' in **each line** of *arrayAnnot.txt*
+  replaces **only the 1st** occurence of *chromosome* by 'chr' in :red:`each line` of *arrayAnnot.txt*
 * ``sed 's/chromosome/chr/' arrayAnnot.txt``
  does the same.
 * ``sed 's/chromosome/chr/g' arrayAnnot.txt``
@@ -95,7 +102,7 @@ expression
 ----------
 * ``\w``  match word (alphanumeric and _)
-* [0-9] digits
+* ``\d`` digits
 * keep only the field bank|accession number|entry_name (*sp|P80874|GS69_BACSU*)
@@ -148,6 +155,36 @@ The "-n" option will not print anything unless an explicit request to print is f
 **sed -n -e'/pattern/p'** will print only line containing pattern
+special characters
+------------------
+* useful metacharacters:
+    * **\.** any character
+    * **\[\]** bracket expressions: defines a set of characters
+        * *[abc]* : matches character *"a"* or *"b"* or *"c"*
+        * *[a-z]* : matches on character in the range from *"a"* to *"z"*, ie *"a"* or *"b"* ... or *"z"*
+        * *\\w*    : matches word (alphanumeric and \_)
+        * *\\s*    : matches blank characters (spaces, tabulation)
+* Anchoring.
+    * **\^** represent start of the string.
+    * **\$** represent end of the string.
+* Repetition.
+    * **\?** match at most once the preceding element. ie **A?** represent zero or **1** A => "" or "A"
+    * **\+** match one or more times the preceding element. ie **A+** represent **1** A to any number of successive A => "A" or "AA" or "AAA" etc ...
+    * **\*** match zero or more times the preceding element. ie **a\*** represent **0** to any number of successive A => "" or "A" or "AA" or "AAA" etc ...
+    * **{n}** match exactly **n** times the preceding element. ie **A{5}** represent exactly **5** successives A  => "AAAAA"
+    * **{m,n}** match *m* to *n* times the preceding element. ie **A{2,5}** represent from **2** to **5**  successives A => "AA" or "AAA" or "AAAA" or "AAAAA"
+* Logical OR.
+    * **(one|two)** match the strings "one" or "two"
+* Recording
+    * **\\(pattern\\)** : will record the pattern that matched
+* Negation
+    * **!** : negate the pattern it precedes
+more information on regular expression in *man sed*
 Addresses
 ---------