我的代码循环遍历目录中的多个文件，解析每个文件并将每个文件的已解析内容追加到FinalVariantfile.txt。
代码有效，但会复制每个文件的内容。
当我用两个文件运行代码时，输出包含4个文件。有人可以解释为什么会发生这种情况以及如何解决这个问题？
#!/usr/bin/perl -w
use strict;
#directory structure
my $home = "/data/";
my $tsvdirectory = $home . "test_all_runs/" . $ARGV[0];
my $tsvfiles = $home . "test_all_runs/" . $ARGV[0] . "/tsv_files.txt";
my $FinalVariants = $home . "test_all_runs/" . $ARGV[0] . "/FinalVariantfile.txt";
my @tsvfiles = ();
my @currentlines = ();
my $currentline = '';
my $currentCNVline = '';
my @currentCNVlines = ();
my @HotSpotLines = ();
my @CNVLines = ();
# command to produce the vcf_files.txt file stored in each individual run
# directory; the file list includes solely vcf files which have not been
# previously prepared and/or annotated
my $cmd = `ls $tsvdirectory/FOCUS*\.tsv > $tsvfiles`;
# print "$cmd";
my $cmda = "ls $tsvdirectory/FOCUS*\.tsv > $tsvfiles";
# print "$cmda";
# this code opens the vcf_files.txt file and passes each line into an array for
# indidivudal manipulation
open( TXT2, "$tsvfiles" );
while ( <TXT2> ) {
push( @tsvfiles, $_ );
}
close(TXT2);
foreach ( @tsvfiles ) {
chop($_);
}
# this code then parses each of the files listed by name in the tsvfiles array
foreach ( @tsvfiles ) {
my $currenttsvfile = "$_"; # establishes the current file being manipulated
my $MDLfinaltsvfile = $currenttsvfile;
$MDLfinaltsvfile =~ s/\.tsv/_prepared\.txt/g;
# this series of variable calls names the various intermediate or
# final output files
my $MDLlinestsvfile = $currenttsvfile;
$MDLlinestsvfile =~ s/\.tsv/_withCNV\.txt/g;
my $Variantlinestsvfile = $currenttsvfile;
$Variantlinestsvfile =~ s/\.tsv/_HotSpot\.txt/g;
my $MDLtsvfile = $currenttsvfile;
$MDLtsvfile =~ s/\.tsv/_FilteredAllcolumns\.txt/g;
my $MDLsampleid = $currenttsvfile;
$MDLsampleid =~ s/\-oncogene.tsv//g;
print "The currentVCFis############# " . $currenttsvfile . "\n";
my @SampleID = ();
@SampleID = split /\//, $MDLsampleid;
print "The sampleIDis##############" . $SampleID[4] . "\n";
my $CNVdata = $currenttsvfile;
$CNVdata =~ s/\.tsv/_cnv\.txt/g;
my $FinalCNVdata = $currenttsvfile;
$FinalCNVdata =~ s/\.tsv/_finalcnv\.txt/g;
my $cmd2 = `fgrep -v "#" $currenttsvfile > $MDLlinestsvfile`;
print "$cmd2"; # this code extracts from the current vcf file all of the
# lines of data and outputs them into a separate file
my $cmd5 = `grep -vwE "(CNV|intronic|synonymous|utr_3|utr_5)"
#removes lines that contain CNV/intronic/synonymous/utr_3/utr_5"
$MDLlinestsvfile > $Variantlinestsvfile`;
print "$cmd5";
open( my $fh_in, '<', $Variantlinestsvfile )
or die "cannot open $Variantlinestsvfile: $!\n";
#removes lines that contain 0/0 and ./. genotypes from field 70.
open( my $fh_out, '>', $MDLtsvfile )
or die "cannot open $MDLtsvfile: $!\n";
while ( my $line = <$fh_in> ) {
# tab/field-based:
my @fields = split( /\s+/, $line );
print $fh_out $line unless ( $fields[70] =~ m|([0.])/\1| );
}
close($fh_in);
close($fh_out);
#open each filtered file with all columns and pushes it into array.
open( TXT2, "$MDLtsvfile" );
while (<TXT2>) {
push( @HotSpotLines, $_ );
}
close(TXT2);
foreach (@HotSpotLines) {
chop($_);
my @HotSpotEntries = ();
my $currentMDLline = $_;
@HotSpotEntries = split( /\t/, $currentMDLline );
my $chr = $HotSpotEntries[9];
my $position = $HotSpotEntries[10];
my $cosmicids = $HotSpotEntries[21];
my $refforward = $HotSpotEntries[67];
my $genotype = $HotSpotEntries[70];
my $altforward = $HotSpotEntries[77];
my $altreverse = $HotSpotEntries[78];
my $cDNA = $HotSpotEntries[81];
my $exon = $HotSpotEntries[83];
my $conseq = $HotSpotEntries[84];
my $location = $HotSpotEntries[88];
my $geneclass = $HotSpotEntries[92];
my $aachange = $HotSpotEntries[98];
my $transcript = $HotSpotEntries[100];
$currentline
= $SampleID[4] . "\t"
. $chr . "\t"
. $position . "\t"
. $cosmicids . "\t"
. $refforward . "\t"
. $refreverse . "\t"
. $genotype . "\t"
. $altforward . "\t"
. $altreverse . "\t"
. $cDNA . "\t"
. $exon . "\t"
. $conseq . "\t"
. $location . "\t"
. $geneclass . "\t"
. $aachange . "\t"
. $transcript;
# print "The currentVCFlineis ".$currentline."\n";
push( @currentlines, $currentline );
}
my $i;
for ( $i = 0; $i < @currentlines; $i += 1 ) {
my $currentguiline = $currentlines[$i];
my $cmd5 = `echo "$currentguiline" >> $FinalVariants`;
print "$cmd5";
#my $cmd9 = `sed -i '1i$SampleID[4]' $FinalVariants`; print $cmd9;
}
}
答案 0 :(得分：3)
没有必要启动这么多新的shell子进程来执行这样的基本操作。 ls，fgrep，grep和echo在Perl中都具有等价物，特别是对每行文本调用echo是一种非常糟糕的复制方式提交给另一个
我怀疑你的问题是因为行
my $cmd5 = `echo "$currentguiline" >> $FinalVariants`;
将追加 @currentlines的每个元素到文件的末尾。因此，第一次运行程序时，它将包含结果的单个副本，但每次后续运行只会在文件末尾添加更多数据，并且会不断增长
unlink $FinalVariants or die $!;
foreach ( @tsvfiles ) { ... }循环之前。这将删除文件并确保为程序的每次执行创建新版本。
好的，我仔细研究了你的代码，我认为这会做你想要的。没有任何数据甚至文件名样本我都无法测试它，除了确保它编译，所以如果它第一次工作将是一个奇迹，但我相信这是你得到一个连贯解决方案的最好机会< / p>
请注意，您在自己的代码中使用的$refreverse存在问题，但从未声明或定义它，因此您显示的代码无法创建您说它的问题，因为它在编译期间死亡错误消息
Global symbol "$refreverse" requires explicit package name
我猜测它正好在$ref_forward之后的索引68
请报告此功能的好坏
#!/usr/bin/perl
use strict;
use warnings 'all';
my $home = "/data";
my $tsv_directory = "$home/test_all_runs/$ARGV[0]";
my $final_variants = "$tsv_directory/final_variant_file.txt";
open my $out_fh, '>', $final_variants
or die qq{Unable to open "$final_variants" for output: $!};
my @tsv_files = glob "$tsv_directory/FOCUS*.tsv";
for my $tsv_file ( @tsv_files ) {
print "The current VCF is ############# $tsv_file\n";
$tsv_file =~ m|([^/]+)-oncogene.tsv$| or die "Cant extract Sample ID";
my $sample_id = $1;
print "The sample ID is ############## $sample_id\n";
open my $in_fh, '<', $tsv_file
or die qq{Unable to open "$tsv_file" for input: $!};
while ( <$in_fh> ) {
next if /^#/;
next if /\b(?:CNV|intronic|synonymous|utr_3|utr_5)\b/;
my @fields = split;
next if $fields[70] eq '0/0' or $fields[70] eq './.';
my @wanted = ( 9, 10, 21, 67, 68, 70, 77, 78, 81, 83, 84, 88, 92, 98, 100 );
my $current_line = join "\t", @fields[@wanted];
print $out_fh $current_line, "\n";
}
}