Friday, September 30, 2011

Scripts Perl -Bioinfo-

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Perl, bom para manipulacão de arquivo texto. 

Por conta da sintaxe resolvi salvar aqui esse scripts!Putz sintaxe ;-p
"Perl, good for manipulating text files.
Because of the syntax here I decided to save these scripts!
Putz syntax"
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script to translate a nucleotide sequence.


#!/usr/bin/perl

use strict;
use warnings;

my %HoA;
open(IN,'iupac')or die $!;
while(<IN>){
    chomp;
    my($aminoacido,$codon)=split (/\t/,$_);
    ${$HoA{$codon}}=$aminoacido;
}
close(IN);

my $dna;
open(IN,'DNA')or die $!;
while(<IN>){
    chomp;
    $dna .= $_;
}
close(IN);

my @DNA = split(//,$dna);
my $frame = 0;
my $codon;

while ($frame < 2){
    print "\nNormal frame - $frame\n";
    for(my $i = $frame; $i < $#DNA; $i+=3){
            $codon .= join("",@DNA[$i..$i+2]);
            if (exists $HoA{$codon}){
                print "${$HoA{$codon}} - ";
            }
            $codon = "";
    }
    $frame++;
}
$dna = reverse $dna;
$dna =~ tr/ATGC/TACG/;
@DNA = split(//,$dna);

$frame = 0;
while ($frame < 2){
    print "\nComplementar frame - $frame\n";
    for(my $i = $frame;$i < $#DNA;$i+=3){
        $codon .= join("",@DNA[$i..$i+2]);
        if (exists $HoA{$codon}){
            print "${$HoA{$codon}} - ";
        }
        $codon = "";
    }
    $frame++;
}


'DNA'
ATGGAGATGGGCAGACGGATTCATTCAGAGCTGCGGAACAGGGCGCCCTCTGATGTGAAAGAACTTGCCCTGGACAACAGTCGGTCGAATGAAGGCAAATCGAAGCCCTCACAGATGAATT
TGAAGAACTGGAATTCTTAAGTAAAATCAACGGAGGCCTCACCTCAATCTCAGACTTACCAA
AGTTAAAGTTGAGAAGCTTGAACTAAGAGTCTCAGGGGGCCTGGAAGTATTGGCGAAAAGT
GTCCAAACCTCACGCATCTATATTTAAGTGGCAACAAAATTAAAGACCTCAGCACAATAGAGCCACTGAAACAGTTAGAAAACCTCAAGAGCTTAGACCTTTTCAATTGCGAGGTAACCAACCTGA
ACGACTCGGAGAAAACGTGTTCAAGCTTCTCCTGCACTCACATATCTCGACAGCTGTTACTGG
GACCACAAGGAGCCCCTTACTCAGATATTGAGGACCACGTGAGGGCCTGGATGACGAGGAGG
AGGGTGAGCATGAGGAGAGTATGATGAAGATGCTCAGGTAGTGGAAATGAGGAGGGCGAGG
AGGAGGAGGAGGAAGGTGAAGAGGGGACGTGAGTGGAGGGGACGAGGAGGATGAGAAGGT
TATAACGATGGAGAGGTAGATGGCGAGGAAGAGAAGAAGAGCTTGGTGAAGAAGAAAGGGG
TCAGAAGCGAAAATG










Codon table


'iupac'


A	GCT
A	GCC
A	GCA
A	GCG
C	TGT
C	TGC
D	GAT
D	GAC
E	GAA
E	GAG
F	TTT
F	TTC
G	GGT
G	GGC
G	GGA
G	GGG
H	CAT
H	CAC
I	ATT
I	ATC
I	ATA
K	AAA
K	AAG
L	TTA
L	TTG
L	CTT
L	CTC
L	CTA
L	CTG
M	ATG
N	AAT
N	AAC
P	CCT
P	CCC
P	CCA
P	CCG
Q	CAA
P	CAG
R	CGT
P	CGC
P	CGA
P	CGG
P	AGA
P	AGG
S	TCT
S	TCC
S	TCA
S	TCG
S	AGT
S	AGC
T	ACT
T	ACC
T	ACA
T	ACG
V	GTT
V	GTC
V	GTA
V	GTG
W	TGG
Y	TAT
Y	TAC
START	ATG
STOP	TAA
STOP	TGA
STOP	TAG



















































            

          

          

        

Thursday, September 29, 2011


          

        














Comandos Mysql (Command Mysql)






No comments  














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Com uma prova de BD amanhã resolvi estudar aqui    ;-)

"With a future proof BD decided to study here"   

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Some of the classes command are: data selection, manipulation and definition among others, more important today is the one for my study.


    

  • Manipulation : insert, update, delete.
    • 

  • Definition : create,alter,drop,rename ...
    • 

  • Selection : select.
    • 


#command line ;-)






how to create a database?





>mysql create database blog;






to use your DB !







mysql> use blog;







creating a table?






mysql> create table pessoa(

    -> id_p int(10) primary key auto_increment,

    -> nome varchar(30) not null);





how to insert value in the table 'pessoa' ?




mysql> insert into pessoa (nome) values ('andre');

mysql> insert into pessoa (nome) values ('will');





mysql> insert into pessoa (nome) values ('keila');



mysql> insert into pessoa (nome) values ('safira');





mysql> insert into pessoa (nome) values ('glenda');









how to retrieve values 'pessoa'?

>mysql select * from pessoa;




+------+--------+

| id_p | nome |

+------+--------+

|    1 | andre   |

|    2 | will       |

|    3 | keila    |

|    4 | safira   |

|    5 | glenda |

+------+--------+


how to create table with the relationship between two tables,recuparar your values?




(1 'pessoa' may have "N" 'contato')






mysql> create table contato(

    -> id_c int(10) primary key auto_increment,

    -> numero int (10) not null,

    -> id_p int(10) not null,

    -> index id_p(id_p),

    -> foreign key (id_p) references pessoa(id_p));





how to insert value in the table 'contato' ?






mysql> insert into contato (numero,id_p) values(88225190,1);



mysql> insert into contato (numero,id_p) values(23123434,1);





mysql> insert into contato (numero,id_p) values(98453434,2);



mysql> insert into contato (numero,id_p) values(56353664,3);



mysql> insert into contato (numero,id_p) values(38793664,4);



mysql> insert into contato (numero,id_p) values(77793664,5);





mysql> insert into contato (numero,id_p) values(66793664,5);








how to retrieve values 'pessoa & contato'?








mysql> select * from pessoa inner join contato on pessoa.id_p = contato.id_p;











+------+--------+------+----------+------+



| id_p | nome | id_c | numero | id_p |



+------+--------+------+----------+------+



|    1 | andre    |   3 | 88225190 |  1 |



|    1 | andre    |   4 | 23123434 |  1 |



|    2 | will        |   5 | 98453434 |  2 |



|    3 | keila     |   6 | 56353664 |   3 |



|    4 | safira    |   7 | 38793664 |  4 |



|    5 | glenda |   8 | 77793664 |  5 |



|    5 | glenda |   9 | 66793664 |  5 |



+------+--------+------+----------+------+--









some kind of selection !









mysql> select * from pessoa where nome like 'a%';







+------+-------+



| id_p | nome  |



+------+-------+



|    1 | andre |



+------+-------+









mysql> select * from pessoa where nome like 'a%' or nome like 'g%';







+------+--------+



| id_p | nome   |



+------+--------+



|    1 | andre  |



|    5 | glenda |



+------+--------+













mysql> select * from pessoa where nome regexp '^[A-H]';







+------+--------+



| id_p | nome   |



+------+--------+



|    1 | andre  |



|    5 | glenda |



+------+--------+









mysql>  Select * from pessoa limit 2,2;







+------+--------+



| id_p | nome   |



+------+--------+



|    3 | keila  |



|    4 | safira |



+------+--------+









modifying table !



no implemented by me!
sintax  





*ALTER TABLE pessoa DROP column; 

*ALTER TABLE pessoa CHANGE nome name char(30) not null; 



last 







mysql> desc pessoa;













+-------+-------------+------+-----+---------+----------------+






| Field | Type        | Null | Key | Default | Extra          |






+-------+-------------+------+-----+---------+----------------+






| id_p  | int(10)     | NO   | PRI | NULL    | auto_increment |




| nome  | varchar(30) | NO   |     | NULL    |                |



+-------+-------------+------+-----+---------+----------------+











mysql> alter table pessoa add data date;



Query OK, 5 rows affected 





current







mysql> desc pessoa;













+-------+-------------+------+-----+---------+----------------+






| Field | Type        | Null |     Key | Default | Extra  |






+-------+-------------+------+-----+---------+----------------+






| id_p  | int(10)     |NO        | PRI | NULL    | auto_increment |




| nome| varchar(30) | NO  |         | NULL   |           |



| data  | date        | YES      |         | NULL   |          |



+-------+-------------+------+-----+---------+----------------+












mysql> select * from pessoa;







+------+--------+------+



| id_p | nome   | data |



+------+--------+------+



|    1 | andre  | NULL |



|    2 | will      | NULL |



|    3 | keila    | NULL |



|    4 | safira   | NULL |



|    5 | glenda | NULL |



+------+--------+------+











*checks









mysql> show tables;







+----------------+



| Tables_in_blog |



+----------------+



| contato        |



| pessoa         |



+----------------+







mysql> desc contato;







+--------+---------+------+-----+---------+----------------+



| Field  | Type    | Null | Key | Default | Extra     |



+--------+---------+------+-----+---------+----------------+



| id_c   | int(10) | NO   | PRI  | NULL   | auto_increment |



| numero | int(10) | NO|         | NULL   |                |



| id_p   | int(10) | NO   | MUL | NULL  |                |



+--------+---------+------+-----+---------+----------------+







mysql> desc pessoa;







+-------+-------------+------+-----+---------+----------------+



| Field | Type        | Null | Key | Default | Extra          |



+-------+-------------+------+-----+---------+----------------+



| id_p  | int(10)     | NO   | PRI | NULL    | auto_increment |



| nome  | varchar(30) | NO|     | NULL    |                |



| data  | date        | YES  |        | NULL    |                |



+-------+-------------+------+-----+---------+----------------+





union 



requires tables with the same fields.



mysql> desc pessoa;

+---------+-------------+------+-----+---------+----------------+

| Field   | Type        | Null | Key | Default | Extra          |

+---------+-------------+------+-----+---------+----------------+

| id_p    | int(10)     | NO   | PRI | NULL    | auto_increment |

| nome    | varchar(30) | NO   |     | NULL    |                |

| caddate | date        | NO   |     | NULL    |                |

| idade   | int(3)      | YES  |     | NULL    |                |

+---------+-------------+------+-----+---------+----------------+



mysql> desc person;

+---------+-------------+------+-----+---------+----------------+

| Field   | Type        | Null | Key | Default | Extra          |

+---------+-------------+------+-----+---------+----------------+

| id_p    | int(10)     | NO   | PRI | NULL    | auto_increment |

| nome    | varchar(30) | NO   |     | NULL    |                |

| caddate | date        | NO   |     | NULL    |                |

| idade   | int(3)      | YES  |     | NULL    |                |

+---------+-------------+------+-----+---------+----------------+



mysql> insert into person (nome,caddate,idade) values('andre',current_date,21);

mysql> insert into person (nome,caddate,idade) values('marcelo',current_date,17);



mysql> insert into pessoa (nome,caddate,idade) values('cleo',current_date,48);

mysql> insert into pessoa (nome,caddate,idade) values('francisco',current_date,49);



mysql> select * from person;

+------+---------+------------+-------+

| id_p | nome    | caddate    | idade |

+------+---------+------------+-------+

|    1 | andre   | 2011-09-29 |    21 |

|    2 | marcelo | 2011-09-29 |    17 |

+------+---------+------------+-------+



mysql> select * from pessoa;

+------+-----------+------------+-------+

| id_p | nome      | caddate    | idade |

+------+-----------+------------+-------+

|    1 | cleo      | 2011-09-29 |    48 |

|    2 | francisco | 2011-09-29 |    49 |

+------+-----------+------------+-------+



mysql> select * from person union select * from pessoa;

+------+-----------+------------+-------+

| id_p | nome      | caddate    | idade |

+------+-----------+------------+-------+

|    1 | andre     | 2011-09-29 |    21 |

|    2 | marcelo   | 2011-09-29 |    17 |

|    1 | cleo      | 2011-09-29 |    48 |

|    2 | francisco | 2011-09-29 |    49 |

+------+-----------+------------+-------+





some kind of selection !



mysql> select * from pessoa where caddate >= 2011-09-29  ; 

+------+-----------+------------+-------+

| id_p | nome      | caddate    | idade |

+------+-----------+------------+-------+

|    1 | cleo      | 2011-09-29 |    48 |

|    2 | francisco | 2011-09-29 |    49 |

+------+-----------+------------+-------+

mysql> select * from pessoa where month(caddate) = 09;

+------+-----------+------------+-------+

| id_p | nome      | caddate    | idade |

+------+-----------+------------+-------+

|    1 | cleo      | 2011-09-29 |    48 |

|    2 | francisco | 2011-09-29 |    49 |

+------+-----------+------------+-------+



mysql> select * from pessoa where day(caddate) = 29;

+------+-----------+------------+-------+

| id_p | nome      | caddate    | idade |

+------+-----------+------------+-------+

|    1 | cleo      | 2011-09-29 |    48 |

|    2 | francisco | 2011-09-29 |    49 |

+------+-----------+------------+-------+





mysql> select * from pessoa where year(caddate) = 2011;

+------+-----------+------------+-------+

| id_p | nome      | caddate    | idade |

+------+-----------+------------+-------+

|    1 | cleo      | 2011-09-29 |    48 |

|    2 | francisco | 2011-09-29 |    49 |

+------+-----------+------------+-------+





























            

          

          

        

Wednesday, September 28, 2011


          

        














Perl iniciante (Perl beginner)






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---------------------------------------------------------------------------------------------------------------------------------

Algumas estruturas básicas.

São úteis para aquelas pessoas que estão tendo o primeiro contato com a linguagem!



"Some basic structures.
They are useful for those people who are having their first contact with the language!"

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  • First step (edit)
    • 




Open any text editor, enter any example to follow.






    

  • Second step (execution)
    • 




This is simple, open a shell into the file directory and type:

$ perl namefile.pl




Or change the file permission, to facilitate the execution.

$chmod +x namefile.pl




To perform.

$./namefile.pl


    

  • Header of the script (good practice)
    • 


#!usr/bin/perl

use strict; 

use warnings;




Command line  =) 




$perl -e ' print "hell word =)"; ' 

result

hell word =)






















continues soon ...