perl脚本语言练习
perl脚本语⾔练习1、计算FASTA⽂件中各种碱基（A，T，C，G和代表未知碱基的N）的数⽬和百分数。
2、计算FASTA⽂件所包含序列的scaffold N50长度。
3、计算GFF3⽂件中所记录的各种类型repeat的总长，以及占FASTA⽂件序列总长的百分数。#!/usr/bin/perl -w
my $num_A=0;
my $num_T=0;
my $num_C=0;
my $num_G=0;
my $num_N=0;
my $num_total=0;
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open(IN, "./Test.fasta") or die;
my $index=1;
my $line;
my $line_num =0;
my $no_A_length;
my $no_T_length;
my $no_C_length;
my $no_G_length;
my $no_N_length;
while(<IN>)
{
#    print "\n\n$_\n\n";
$line_num = length($_);
$num_total +=($line_num-1);
#    print "$line_num  ";
$_=~s/A//g;
$no_A_length = length($_);
#print "$no_A_length    ";
$num_A += ($line_num-$no_A_length);
$_=~s/T//g;
$no_T_length = length($_);
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$num_T += ($no_A_length - $no_T_length);
$_=~s/C//g;
$no_C_length = length($_);
#    print "$no_C_length  ";
#    print "$no_C_length  ";
$num_C+=($no_T_length - $no_C_length);
$_=~s/G//g;
$no_G_length = length($_);
#  print "$no_G_length  ";
$num_G += ($no_C_length-$no_G_length);
$_=~s/N//g;
$no_N_length = length($_);
$num_N += ($no_G_length - $no_N_length);
}
print "TOTAL NUM IS $num_total\n";
print "A NUM IS $num_A\n";
print "T NUM IS $num_T\n";
print "C NUM IS $num_C\n";
print "G NUM IS $num_G\n";
print "N NUM IS $num_N\n";
print "A PERCENT IS ".($num_A*100/$num_total)."%\n"; print "T PERCENT IS ".($num_T*100/$num_total)."%\n"; print "C PERCENT IS ".($num_C*100/$num_total)."%\n"; print "G PERCENT IS ".($num_G*100/$num_total)."%\n"; print "N PERCENT IS ".($num_N*100/$num_total)."%\n"; exit;
#!/usr/bin/perl -w
my @repeatclass;
my @repeattmp;
my @repeatall;
my $classlen;
my @classier;
my $index=0;
my $i=0;
my $flag = 0;
open(IN, "./Repeat.gff") or die;
while(<IN>)
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{
chomp;
@repeattmp = split(/ /, $_);
$classlen = $repeattmp[4] - $repeattmp[3];    @repeatclass = split(/;/, $repeattmp[8]);
$i = 0;
while($i < $index)
{
#print "$repeatall[$i][0]\n";
if($repeatall[$i][0] eq $repeatclass[2])
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{
$flag =1;
last;
}
$i ++;
}
if($flag == 0)
{
@classier = [$repeatclass[2], $classlen];        push(@repeatall, @classier);
$index++;
}
else
{
$repeatall[$i][1] += $classlen;
$flag = 0;
}
}
exit;
#!/usr/bin/perl -w
#
my $line_num;
my $line_scafolld;
my $total_num =0;
my $i = 0;
open(IN, "./Test.fasta") or die;
my @scafolld = ();
my @temp;
while(<IN>)
{
chomp;
$line_num = length($_);
if(!(/^>/))
{
$total_num += $line_num;
@temp = [$line_scafolld,$line_num,$_];
push(@scafolld,@temp);
# push(@scafolld, $line_num);
$i++;
}
else
{
$line_scafolld = $_;
}
}
@scafolld = sort{$a->[1]<=>$b->[1]} @scafolld;
my $index = 0;
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my $num = 0;
while(1)
{
print "$scafolld[$index][1]\n";
$num += $scafolld[$index][1];
if($num*2 > $total_num)
{
print "$scafolld[$index][0]\n";
# print "$scafolld[$index][2]\n";
exit;
}
$index++;
if($index == $i)
{exit;}
}
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