Download 4-MoreLoops

4.1
Revision
4.2
if, elsif, else
It’s convenient to test several conditions in one if structure:
print "Please enter your grades average:\n";
my $number = <STDIN>;
if ($number < 0 or $number > 100) {
print "ERROR: The average must be between 0 and 100.\n";
} elsif ($number > 90) {
print "wow!\n";
} elsif ($number > 80) {
print "well done.\n";
} else {
print "oh well...\n";
}
Note the
indentation:
a single tab in each
‘}’ that ends the block
line of new block
should be in the same
indentation as where it
started
4.3
Comparison operators
Comparison Numeric
String
Equal
==
eq
Not equal
!=
ne
Less than
<
lt
Greater than
>
gt
Less than or
equal to
>=
le
Greater than
or equal to
<=
ge
if ($age == 18){
...
}
if ($name eq "Yossi")...
if ($name ne "Yossi")...
if ($name lt "n")...
if ($age = 18)...
Found = in conditional, should be == at ...
if ($name == "Yossi")...
Argument "Yossi" isn't numeric in numeric eq (==) at ...
4.4
Loops
Commands inside a loop are executed repeatedly (iteratively):
my $num=0;
print "Guess a number.\n";
while ($num != 31) {
$num = <STDIN>;
}
print "correct!\n";
my @names = <STDIN>;
chomp(@names);
my $name;
foreach $name (@names) {
print "Hello $name!\n";
}
4.5
Loops: foreach
The foreach loop passes through all the elements of an array
my @numArr = (1,1,2,3,5);
foreach my $number (@numArr) {
$number++;
}
Note:
The array is
actually
changed
4.6
Fasta format
Fasta format sequence begins with a single-line description, that start with '>', followed by
lines of sequence data that contains new-lines after a fixed number of characters:
>gi|229608964|ref|NM_014600.2| Homo sapiens EH-domain
AAACATGGCGGCGCCCTGCGCGGCTTCCCGTCGCCGCAACCGTGGGGCCGGCCCTGCCTT
GGAGCGGAGCCGAAGCATCCCTTGCTGCACGCAGGGCAGAGCAGGCGAGGGCTGGGGGCC
GTATAACTTATTTTATATCCATATTCAGACTATATAGAGAATATTCTATGCATCTATGAC
GTGCTTAC
>gi|197099147|ref|NM_001131576.1| Pongo abelii EH-domain
AGAGCTGAGCGCCTGCCCACAAACATGGCGGCGCCCTGCGCGGCTTCCCTTCGCCGGGAC
CGCCTGGGGCTGCAGGATGCTGCTGCGGATGCTGAGCTGTCCGCGGGTTGGGCAGCGTCG
CTGCGCGGCTTCCCTT
>gi|55742034|ref|NM_001006733.1| Xenopus tropicalis EH-domain
CGGGCAAGACCACCTTCATCCGCCACCTCATAGAGCAGGACTTCCCCGGCATGAGGATCG
GGCCCGAACCGGGGACTTCCTCTGCGCGCCGGCTTCCTGCCCAGCTGGCATTTAAACCAC
ACATGGCGGCGCCCTGCGCGGCTTCCCGTCGCCGCAACCGTGGGGCCGGCC
4.7
Breaking out of loops
next – skip to the next iteration
last – skip out of the loop
my @lines = <STDIN>;
foreach $line (@lines) {
if (substr($line,0,1) eq ">") { next; }
if (substr($line,0,8) eq "**stop**") { last; }
print($line);
}
4.8
More loops
4.9
Scope of variable declaration
If you declare a variable inside a loop it will only exist in that loop
This is true for every {block}:
my $name="";
while ($name ne "Yossi") {
chomp($name = <STDIN>);
print "Hello $name, what is your age?\n";
my $age;
$age = <STDIN>;
}
print $name;
print $age;
Global symbol "$age" requires explicit package name
4.10
Never declare the same variable name twice
If you declare a variable name twice, outside and inside – you are creating
two distinct variables… don’t do it!
my $name = "Ruti";
print "Hello $name!\n";
my $number;
foreach $number (1,2,3) {
my $name = "Nimrod";
print "Hello $name!\n";
}
print "Hello $name!\n";
Hello
Hello
Hello
Hello
Hello
Ruti!
Nimrod!
Nimrod!
Nimrod!
Ruti!
4.11
Never declare the same variable name twice
If you declare a variable name twice, outside and inside – you are creating
two distinct variables… don’t do it!
my $name = "Ruti";
print "Hello $name!\n";
my $number;
foreach $number (1,2,3) {
$name = "Nimrod";
print "Hello $name!\n";
}
print "Hello $name!\n";
Hello
Hello
Hello
Hello
Hello
Ruti!
Nimrod!
Nimrod!
Nimrod!
Nimrod!
4.12
Reminder:
Uninitialized (undefined) variables
If uninitialized variables are used (before assignment) awarnings
is issued:
my $a;
print($a+3);
Use of uninitialized value in addition (+)
3
my $line;
print("line is $line");
Use of uninitialized value in concatenation (.) or string
line is
4.13
Is this variables defined?
defined check whether a variable was defined.
my $a;
if (defined $a){
print($a+3);
}
ctrl-z to
indicate end
of input
my $line = <STDIN>;
while (defined $line){
print "line is $line";
$line = <STDIN>;
}
print "done!!!\n"
4.14
Is this variables defined?
defined check whether a variable was defined.
my $line = <STDIN>;
while (defined $line){
if (substr($line,0,1) eq ">"){
print "$line";
}
$line = <STDIN>;
}
4.15
FASTA: Analyzing complex input
Assignment:
Write a script that reads several DNA sequences
in FASTA format, and prints for each sequence print
its header and its G+C content
|
Obtain from the assignment:
 Input
 Required Output
 Required processes (functions)
4.16
Start
FASTA: Analyzing complex input
Overall design:
Read the FASTA file (several sequences).
For each sequence:
1.
Read the FASTA sequence
1.1. Read FASTA header
Read line
Save header
Read line
Concatenate
to sequence
Read line
1.2. Read each line until next FASTA header
2.
For each sequence: Do something
2.1. Compute G+C content
2.2. Print header and G+C content
Header or
end of input
No
Yes
Do something
Let’s see how it’s done…
End of input?
End
No
4.17
Start
# 1. Read FASTA sequece
$fastaLine = <STDIN>;
while (defined $fastaLine) {
Read line
Save header
# 1.1. Read FASTA header
$header = substr($fastaLine,1);
$fastaLine = <STDIN>;
# 1.2. Read sequence until next FASTA header
while ((defined $fastaLine) and
(substr($fastaLine,0,1) ne ">" ))
{
$seq .= $fastaLine;
$fastaLine = <STDIN>;
}
# 2. Do something
... # 2.1 compute $gcContent
print "$header: $gcContent\n";
}
Read line
Concatenate
to sequence
Read line
Header or
end of input
No
Yes
Do something
End of input?
End
No
4.18
1.
Class exercise 4a
Write a script that reads lines of names and expenses:
Yossi 6.10,16.50,5.00
Dana 21.00,6.00
Refael 6.10,24.00,7.00,8.00
END
Output:
Yossi 27.6
Dana 27
Refael 45.1
For each line print the name and the sum. Stop when you reach "END"
2.
Change your script to read names and expenses on separate lines, Identify
lines with numbers by a "+" sign as the first character in the string:
Yossi
+6.10
+16.50
+5.00
Dana
+21.00
+6.00
Refael
+6.10
+24.00
+7.00
+8.00
END
Sum the numbers
while there is a '+'
sign before them.
4.19
3.
Class exercise 4a
(Home Ex. 2 Q. 5) Write a script that reads several protein sequences
in FASTA format, and prints the name and length of each sequence.
Start with the example code from the last lesson.
4*. Write a script that reads several DNA sequences in FASTA format,
and prints FASTA output of the sequences whose header starts with
'Chr07'.
5*. As in Q4, but now concatenate all the sequences whose header starts
with 'Chr07'.
4.20
A bit about
Reading and writing files
4.21
Reading files
Open a file for reading, and link it to a filehandle:
open(IN, "<EHD.fasta");
And then read lines from the filehandle, exactly like you would from <STDIN>:
my $line = <IN>;
my @inputLines = <IN>;
foreach $line (@inputLines) ...
Every filehandle opened should be closed:
close(IN);
4.22
Writing to files
Open a file for writing, and link it to a filehandle:
open(OUT, ">EHD.analysis")
NOTE: If a file by that name already exists it will be overwritten!
Print to a file:
print OUT "The mutation is in exon $exonNumber\n";
And don't forget to:
close(IN);
no comma here
4.23
Class exercise 4b
1. Change the script for class exercise 4a.1 to read the lines
from an input file (instead of reading lines from
keyboard).
2. Now, in addition, write the output of the previous
question to a file named "class.ex.4a1.out" (instead of
printing to the screen).
3*. Change the script for class exercise 4.a3 to receive from
the user two strings: 1) a name of FASTA file 2) a name
of an output file. And then - read from a FASTA file
given by the user, and write to an output file also supplied
by the user.