我正在尝试循环一个数组,递增200.我在200内构建一个子数组,在子数组上运行计算,然后将读取帧移动到下一组200并重复。但是,每当我进行第二次计算时,新的子数组都包含第一个子数组的值。这就像我无法重置或undef
子数组在for
循环的下一次迭代中重用它。
完整代码可在github上找到:https://github.com/bsima/yeast-TRX
要运行代码,您需要在与脚本相同的目录中使用以下基因组文件:https://raw.github.com/bsima/yeast-TRX/master/data/bayanus/genome.csv
以下是相关代码:
#!/usr/bin/perl
use strict;
use warnings;
use diagnostics;
use Statistics::Descriptive;
my $species = "bayanus";
open(SPECIES, "<./genome.csv") || die "Cannot open file: $!\n";
my @text = <SPECIES>;
my $geneNameRe = qr/(eY\w{5}[CW])/;
my $geneRe = qr/,([atgcATGC-]+)/;
foreach my $line (@text) {
chomp($line);
if ( defined $line && $line =~ m/e.{4,},[acgtACGT-]+/ ) {
my $gene = match($geneRe,$line);
my $geneName = match($geneNameRe,$line);
# Smoothing function
#
# This moves through the gene data and counts the position until it arrives
# at the end of the smoothing window (e.g. 200). Then it calculates the average
# of the selected data set and outputs it into the respecive `smooth.csv` file
# in the following format, to be read later by R's graphing functions:
# gene,position,trx.mean,energy.mean
open(my $smooth, ">>./smooth.csv") || die "Cannot open file $!";
my $smoothingWindow = 200;
# Loop through every 200 characters
for ( my $smoothing = 0; $smoothing < length($gene); $smoothing=$smoothing+$smoothingWindow ) {
my @trxValues;
my @energyScores;
# Loop through every character
for ( my $position = 0; $position <= $smoothingWindow; $position++ ) {
my $dinucleotide = substr($gene,$position,2);
if ( $dinucleotide =~ m/[actgACTG]{2}/ ) {
my $trxValue = trxScore($dinucleotide);
my $energyScore = energyScore($dinucleotide);
#print "trxValue = $trxValue\n";
push @trxValues, $trxValue;
push @energyScores, $energyScore;
}
}
# Now run the calculations and print to SMOOTH
my $trxStat = Statistics::Descriptive::Full->new();
$trxStat->add_data(@trxValues);
my $trxMean = $trxStat->mean();
my $energyStat = Statistics::Descriptive::Full->new();
$energyStat->add_data(@energyScores);
my $energyMean = $energyStat->mean();
print "$geneName $smoothing: TRX Values @trxValues\n";
print "$geneName $smoothing: TRX Mean is $trxMean.\n";
print $smooth $geneName . "," . $smoothing . "," . $trxMean . "," . $energyMean . "\n";
}
close $smooth;
}
}
# This just makes it easy to do regex matches
sub match {
my ( $re, $text ) = @_;
if ( $text =~ $re ) {
return $1;
}
}
# @name trxScore
# @description Calculates and returns the TRX value of a given phosphate linkage
# @param $dinucleotide {string} The nucleotide to be checked
# @return {integer} The TRX value
sub trxScore {
my ( $dinucleotide ) = @_;
my %trxScores = (
qr/(CG)/ => 43,
qr/(CA)/ => 42,
qr/(TG)/ => 42,
qr/(GG)/ => 42,
qr/(CC)/ => 42,
qr/(GC)/ => 25,
qr/(GA)/ => 22,
qr/(TC)/ => 22,
qr/(TA)/ => 14,
qr/(AG)/ => 9,
qr/(CT)/ => 9,
qr/(AA)/ => 5,
qr/(TT)/ => 5,
qr/(AC)/ => 4,
qr/(GT)/ => 4,
qr/(AT)/ => 0,
qr/(.-)/ => 0,
qr/(-.)/ => 0 # These last two are necessary for dealing with missing values in the genomes
);
foreach my $re (keys %trxScores) {
if ( match($re,$dinucleotide) ) {
return $trxScores{$re};
}
}
return 0;
}
# @name energyScore
# @description Calculates and returns the delta-E value of a given phosphate linkage
# @param $dinucleotide {string} The nucleotide to be checked
# @return {integer} The delta-E value
sub energyScore {
my ( $dinucleotide ) = @_;
my %energyScores = (
qr/(AA)/ => -18.5,
qr/(AC)/ => -19.0,
qr/(AG)/ => -23.6,
qr/(AU)/ => -15.7,
qr/(CA)/ => -20.0,
qr/(CC)/ => -21.4,
qr/(CG)/ => -26.9,
qr/(CU)/ => -17.2,
qr/(GA)/ => -23.7,
qr/(GC)/ => -22.9,
qr/(GG)/ => -24.3,
qr/(GU)/ => -18.9,
qr/(UA)/ => -19.6,
qr/(UC)/ => -28.2,
qr/(UG)/ => -23.3,
qr/(UU)/ => -15.8,
qr/(.-)/ => 0,
qr/(-.)/ => 0 # These last two are necessary for dealing with missing values in the genomes
);
foreach my $re (keys %energyScores) {
if ( match($re,$dinucleotide) ) {
return $energyScores{$re};
}
}
return 0;
}
如果您运行该代码块所属的较大脚本,它会将@trxValues
的内容打印到终端,您将看到$smoothing
变量正在递增,所以for
循环的步骤部分没有任何问题,但@trxValues
的内容永远不会改变。因此,在第一个for
循环结束和第二个循环开始之间的某个位置,数组@trxValues
无法正确清除。同样的事情发生在@energyScores
。
关于这个的任何想法?我尝试在undef
循环结束时使用for
,并在循环结束时将@trxValues
设置为零,两者都不起作用。我完全难过了。
编辑:将代码块更改为可自行运行。
答案 0 :(得分:0)
您似乎始终在内部for循环中使用相同的第一个平滑窗口。
尝试更改:
for ( my $position = 0; $position <= $smoothingWindow; $position++ ) {
到
for ( my $position = $smoothing; $position < $smoothing + $smoothingWindow; $position++ ) {
虽然内循环应检查平滑窗口和length($gene)
(除非你知道它总是200的偶数倍?)
您一次最多只能length($gene)
个位置,但您的substr正在提取两个字符,这似乎很奇怪。