脚本2perl求解，数据cd截图

Question

脚本2：
perl /mnt/sdb/share/bin/deal_fa.pl
数据路径：/mnt/sdb/share/bin/linux-demo/program/fasta
要求：

1. 过滤掉长度1000bp一下的序列
2. 提取目标区域（region.txt）内的序列
3. 计算每个scaffold序列的长度
4. 以100bp为窗口计算scaffold窗口内的GC含量
5. scaffold序列基本信息统计（N50，N90，最大长度，最小长度等）
6. 以300个N链接scaffold序列
7. scaffold的拆分为contig
8. 每两个序列拆分为一个文件
9. 反向互补scaffold的序列
10. 把不标准的scaffold的序列变成标准的scaffold的序列
11. fasta文件转化为fastq格式文件
12. 修改fasta序列前缀名称；前缀为： part

Answer 1

【以下回答由 GPT 生成】

对于上述任务，你可以使用Perl编写一个脚本来完成。下面是一个可以实现这些功能的Perl脚本的示例代码：

```perl

!/usr/bin/perl

use strict; use warnings;

Task 1: 过滤掉长度低于1000bp的序列。

sub filter_sequences { my ($input_file, $output_file) = @_; open(my $in_fh, "<", $input_file) or die "Cannot open file: $!"; open(my $out_fh, ">", $output_file) or die "Cannot open file: $!"; my $sequence = ""; my $header = ""; while (my $line = <$in_fh>) { chomp($line); if ($line =~ /^>/) { if ($sequence ne "" && length($sequence) >= 1000) { print $out_fh "$header\n$sequence\n"; } $header = $line; $sequence = ""; } else { $sequence .= $line; } } if ($sequence ne "" && length($sequence) >= 1000) { print $out_fh "$header\n$sequence\n"; } close($in_fh); close($out_fh); }

Task 2: 从名为"region.txt"的文件中提取目标区域内的序列。

sub extract_sequences { my ($input_file, $region_file, $output_file) = @_; open(my $in_fh, "<", $input_file) or die "Cannot open file: $!"; open(my $region_fh, "<", $region_file) or die "Cannot open file: $!"; open(my $out_fh, ">", $output_file) or die "Cannot open file: $!"; my %regions; while (my $region_line = <$region_fh>) { chomp($region_line); my ($region_start, $region_end) = split("\t", $region_line); $regions{$region_start} = $region_end; } my $current_seq = ""; my $current_header = ""; while (my $line = <$in_fh>) { chomp($line); if ($line =~ /^>/) { if ($current_seq ne "" && exists $regions{$current_header}) { my $end_position = $regions{$current_header} > length($current_seq) ? length($current_seq) : $regions{$current_header}; print $out_fh "$current_header\n", substr($current_seq, 0, $end_position), "\n"; } $current_header = $line; $current_seq = ""; } else { $current_seq .= $line; } } if ($current_seq ne "" && exists $regions{$current_header}) { my $end_position = $regions{$current_header} > length($current_seq) ? length($current_seq) : $regions{$current_header}; print $out_fh "$current_header\n", substr($current_seq, 0, $end_position), "\n"; } close($in_fh); close($region_fh); close($out_fh); }

Task 3: 计算每个scaffold序列的长度。

sub calculate_lengths { my ($input_file) = @_; open(my $in_fh, "<", $input_file) or die "Cannot open file: $!"; my %lengths; my $current_header = ""; while (my $line = <$in_fh>) { chomp($line); if ($line =~ /^>/) { $current_header = $line; $lengths{$current_header} = 0; } else { $lengths{$current_header} += length($line); } } close($in_fh); return \%lengths; }

Task 4: 使用100bp的窗口计算每个scaffold序列窗口内的GC含量。

sub calculate_gc_content { my ($input_file, $window_size) = @_; open(my $in_fh, "<", $input_file) or die "Cannot open file: $!"; my %gc_content; my $current_header = ""; my $current_seq = ""; while (my $line = <$in_fh>) { chomp($line); if ($line =~ /^>/) { if ($current_header ne "") { for (my $i = 0; $i < length($current_seq); $i += $window_size) { my $window_sequence = substr($current_seq, $i, $window_size); my $gc_count = ($window_sequence =~ tr/GC//); my $window_start = $i + 1; my $window_end = $i + $window_size; push(@{$gc_content{$current_header}}, "$window_start-$window_end: " . ($gc_count / $window_size) * 100 . "%"); } } $current_header = $line; $current_seq = ""; } else { $current_seq .= $line; } } if ($current_header ne "") { for (my $i = 0; $i < length($current_seq); $i += $window_size) { my $window_sequence = substr($current_seq, $i, $window_size); my $gc_count = ($window_sequence =~ tr/GC//); my $window_start = $i + 1; my $window_end = $i + $window_size; push(@{$gc_content{$current_header}}, "$window_start-$window_end: " . ($gc_count / $window_size) * 100 . "%"); } } close($in_fh); return \%gc_content; }

Task 5: 统计scaffold序列的基本信息，包括N50、N90、最大长度和最小长度。

sub calculate_basic_stats { my ($input_file) = @_; open(my $in_fh, "<", $input_file) or die "Cannot open file: $!"; my @sequence_lengths; my $total_length = 0; my $current_length = 0; my $current_header = ""; my $max_length = 0; my $min_length; while (my $line = <$in_fh>) { chomp($line); if ($line =~ /^>/) { if ($current_length > 0) { push(@sequence_lengths, $current_length); $total_length += $current_length; if ($current_length > $max_length) { $max_length = $current_length; } if (!defined $min_length || $current_length < $min_length) { $min_length = $current_length; } } $current_header = $line; $current_length = 0; } else { $current_length += length($line); } } if ($current_length > 0) { push(@sequence_lengths, $current_length); $total_length += $current_length; if ($current_length > $max_length) { $max_length = $current_length; } if (!defined $min_length || $current_length < $min_length) { $min_length = $current_length; } } close($in_fh);

@sequence_lengths = sort { $b <=> $a } @sequence_lengths;
my $n50 = calculate_n(50, \@sequence_lengths, $total_length);
my $n90 = calculate_n(90, \@sequence_lengths, $total_length);

return ($max_length, $min_length, $n50, $n90);

}

Helper function for calculating N50 and N90

sub calculate_n { my ($percentage, $lengths, $total_length) = @_; my $threshold = $total_length * ($percentage / 100); my $current_length = 0; foreach my $length (@{$lengths}) { $current_length += $length; if ($current_length >= $threshold) { return $length; } } }

Task 6: 使用300个N将scaffold序列连接起来。

sub join_sequences { my ($input_file, $output_file) = @_; open(my $in_fh, "<", $input_file) or die "Cannot open file: $!"; open(my $out_fh, ">", $output_file) or die "Cannot open file: $!"; my $current_seq = ""; while (my $line = <$in_fh>) { chomp($line); if ($line =~ /^>/) { if ($current_seq ne "") { print $out_fh join("", ("N") x 300), "\n$current_seq\n"; } $current_seq = ""; } else { $current_seq .= $line; } } if ($current_seq ne "") { print $out_fh join("", ("N") x 300), "\n$current_seq\n"; } close($in_fh); close($out_fh); }

Task 7: 将scaffold序列拆分为contig。

sub split_sequences { my ($input_file) = @; open(my $in_fh, "<", $input_file) or die "Cannot open file: $!"; my $output_count = 1; my $output_file = "contig$output_count.fasta"; open(my $out_fh, ">", $output_file) or die "Cannot open file: $!"; while (my $line = <$in_fh>) { if ($line =~ /^>/) { close($out_fh); $output_count++; $output_file = "contig_$output_count.fasta"; open($out_fh, ">", $output_file) or die "Cannot open file: $!"; } print $out_fh $line; } close($in_fh); close($out_fh); }

Task 8: 将每两个序列拆分为一个文件。

sub split_files { my ($input_file) = @; open(my $in_fh, "<", $input_file) or die "Cannot open file: $!"; my $output_count = 1; my $current_header = ""; my $output_file = "output$output_count.fasta"; open(my $out_fh, ">", $output_file) or die "Cannot open file: $!"; while (my $line = <$in_fh>) { if ($line =~ /^>/) { if ($current_header ne "") { close($out_fh); $output_count++; $output_file = "output_$output_count.fasta"; open($out_fh, ">", $output_file) or die "Cannot open file: $!"; } $current_header = $line; } print $out_fh $line; } close($in_fh); close($out_fh); }

Task 9: 对scaffold序列进行反向互补操作。

sub reverse_complement { my ($input_file, $output_file) = @_; open(my $in_fh, "<", $input_file) or die "Cannot open file: $!"; open(my $out_fh, ">", $output_file) or die "Cannot open file: $!"; while (my $line = <$in_fh>) { chomp($line); if ($line =~ /^>/) { print $out_fh "$line\n"; } else { $line = reverse($line); $line =~ tr/ACGTacgt/TGCAtgca/; print $out_fh "$line\n"; } } close($in_fh); close($out_fh); }

Task 10: 将不标准的scaffold序列转换为标准的scaffold序列。

sub convert_sequences { my ($input_file, $output_file) = @; open(my $in_fh, "<", $input_file) or die "Cannot open file: $!"; open(my $out_fh, ">", $output_file) or die "Cannot open file: $!"; while (my $line = <$in_fh>) { chomp($line); if ($line =~ /^>/) { $line =~ s//-/g; } print $out_fh "$line\n"; } close($in_fh); close($out_fh); }

Task 11: 将FASTA文件转换为FASTQ格式文件。

sub convert_to_fastq { my ($input_file, $output_file) = @_; open(my $in_fh, "<", $input_file) or die "Cannot open file: $!"; open(my $out_fh, ">", $output_file) or die "Cannot open file: $!"; my $sequence = ""; my $header = ""; while (my $line = <$in_fh>) { chomp($line); if ($line =~ /^>/) { if ($sequence ne "") { $header =~ s/^>//; print $out_fh '@', $header, "\n", $sequence, "\n+\n", ("I" x length($sequence)), "\n"; } $header = $line; $sequence = ""; } else { $sequence .= $line; } } if ($sequence ne "") { $header =~ s/^>//; print $out_fh '@', $header, "\n", $sequence, "\n+\n", ("I" x length($sequence)), "\n"; } close($in_fh); close($out_fh); }

Task 12: 修改FASTA序列的前缀名称，将前缀改为"part"。

sub modify_prefix { my ($input_file, $output_file) = @; open(my $in_fh, "<", $input_file) or die "Cannot open file: $!"; open(my $out_fh, ">", $output_file) or die "Cannot open file: $!"; while (my $line = <$in_fh>) { chomp($line); if ($line =~ /^>/) { $line =~ s/^>.+?/>part_/; } print $out_fh "$line\n"; } close($in_fh); close($out_fh); }

Run the functions

Task 1: 过滤掉长度低于1000bp的序列。

filter_sequences("input.fasta", "filtered.fasta");

Task 2: 从名为"region.txt"的文件中提取目标区域内的序列。

extract_sequences("input.fasta", "region.txt", "extracted.fasta");

Task 3: 计算每个scaffold序列的长度。

my $lengths = calculate_lengths("input.fasta"); foreach my $header (keys %{ $lengths }) { print "Length of $header: ", $lengths->{$header}, "bp\n"; }

Task 4: 使用100bp的窗口计算每个scaffold序列窗口内的GC含量。

my $gc_content = calculate_gc_content("input.fasta", 100); foreach my $header (keys %{ $gc_content }) { print "GC Content of $header:\n"; foreach my $window (@{ $gc_content->{$header} }) { print "$window\n"; } }

Task 5: 统计scaffold序列的基本信息，包括N50、N90、最大长度和最小长度。

my ($max_length, $min_length, $n50, $n90) = calculate_basic_stats("input.fasta"); print "Max Length: $max_length\n"; print "Min Length: $min_length\n"; print "N50: $n50\n"; print "N90: $n90\n";

Task 6: 使用300个N将scaffold序列连接起来。

join_sequences("input.fasta", "joined.fasta");

Task 7: 将scaffold序列拆分为contig。

split_sequences("input.fasta");

Task 8: 将每两个序列拆分为一个文件。

split_files("input.fasta");

Task 9: 对scaffold序列进行反向互补操作。

reverse_complement("input.fasta", "reverse_complemented.fasta");

Task 10: 将不标准的scaffold序列转换为标准的scaffold序列。

convert_sequences("input.fasta", "converted.fasta");

Task 11: 将FASTA文件转换为FASTQ格式文件。

convert_to_fastq("input.fasta", "output.fastq");

Task 12: 修改FASTA序列的前

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