Hi List,
I have been trying to follow one of code indentation guidelines from
wikipedia, but I have some questions that I can find answers, I would
appreciate if someone could help me or point me towards better references.
So here is something I have been working on:
-------------------------------Code------------------------------------------------
use strict;
my $seqnum = 0;
my @seq;
my @seqheader;
my @targets;
my $index = 0;
my $index1 = -1;
#Here we open the filehandle TARGETS to connect to the file containing the
names of the sequences we want to find.
open(TARGETS, "<$ARGV[0]");
@targets = <TARGETS>;
#Just printing the sequences we are looking for.
print "We are looking for:\n";
foreach (@targets)
{
print "\n$_";
}
As I understand I am supposed to align the start curly brace opening the
loop with the one closing, so I did it here. My first question is: should I
everything from now on be indented forward or should be aligned to the left?
close (TARGETS);
#Here we use the subroutine readFasta to read the FASTA file and store the
names in the array @seqheader and the sequences in the array @seq.
readFasta($ARGV[1]);
print "\nThere are $seqnum sequences in FASTA file\n";
print "\nWe found:\n\n";
#Here is where we interate the @seqheader array looking for the names we
wanted
The second question is the same as the first really: when I start a second
loop, should I indent it even further to the right?
foreach my $seqheaders(@seqheader)
{
$index1 = $index1 + 1;
if (grep {$seqheaders =~ /$_/} @targets)
{
print "$seqheaders\n";
print "$seq[$index1]\n";
$index = $index + 1;
}
next;
}
sub readFasta
{
my $line;
my $first;
if (@ARGV == 0){
die "No FASTA file specified.\n"
}
open(FILE, "<@_[0]");
$seqnum = 0;
$first = 0;
while (defined($line = <FILE>))
{
chomp($line);
if ($line =~ /^>/)
{
$seqheader[$seqnum] = $line;
$seqnum = $seqnum + 1;
if ($first == 0)
{
$first = 1;
}
next;
}
if ($first == 0){
die "Not a standard FASTA file. Stop.\n";
}
$seq[$seqnum - 1] = $seq[$seqnum - 1] .$line;
}
close(FILE);
}
--
"Education is not to be used to promote obscurantism." - Theodonius
Dobzhansky.
"Gracias a la vida que me ha dado tanto
Me ha dado el sonido y el abecedario
Con él, las palabras que pienso y declaro
Madre, amigo, hermano
Y luz alumbrando la ruta del alma del que estoy amando
Gracias a la vida que me ha dado tanto
Me ha dado la marcha de mis pies cansados
Con ellos anduve ciudades y charcos
Playas y desiertos, montañas y llanos
Y la casa tuya, tu calle y tu patio"
Violeta Parra - Gracias a la Vida
Tiago S. F. Hori
PhD Candidate - Ocean Science Center-Memorial University of Newfoundland
