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;


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 $no_N_length;
while(<IN>)
{ ??
# ? ?print "nn$_nn";
? ? $line_num = length($_);?


? ? $num_total +=($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;
? ? $no_T_length = length($_);
?# ? print "$no_T_length ?";
? ? $num_T += ($no_A_length - $no_T_length);
? ??
? ? $_=~s/C//g;
? ?
? ? $no_C_length = length($_);
# ? ?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_totaln";
print "A NUM IS $num_An";
print "T NUM IS $num_Tn";
print "C NUM IS $num_Cn";
print "G NUM IS $num_Gn";
print "N NUM IS $num_Nn";
print "A PERCENT IS ".($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>)
{
? ? 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 $repeatclass[2])
? ? ? ? {
? ? ? ? ? ? ?$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; 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;} }