[英]Perl regular expression to match '>'
這就是數據在我的文件中的排列方式。
>Contig1
TGGCACCTTCGACAGTTGCTCCCTCCTGGGTGGGGGCCGTCTGACCTCGCTGTACTCCT
>Contig2
GGGCCTTGGGAAGCGCAGGTGCCGAGAACTTGGCTAGAGCGGTAGACAATGCGGTTCGTG
AAAAGAGCAACTTTAAATACTTGTACGACCTCAACCAGCCAGTCAAAGAGAAAATCGAG
>NODE_105957_length_443_cov_1.000000
TCAGAAGTTAATGCAATCTGGTCCATTAAGTAAATGGGTATCATGGTACATAAACTAAAA
GCACAGAACATGGATTATTTTCCCAATTTTAACTTTCCTAACCATTTTTATCTCTCTCAA
TAACTTCCACAGTAGTTTTTATTCGTCTCAATAACTTTATTAAAAGGGATCCCTCTATCC
CCAGAATTCAGTAGCTGCATACGACTTTCCTGTCACTAGAGATCCCTCAGATGTCGGTAG
TGCATTCATCTTAAGTGATAAATCAAATGTTAGTCAAGTTAGGAAGTGAGAATTGATACA
GAATTTCTACTTCAATACTAGCTATCCCAAAATGGTCATTGACGATTTATTTTTTTCCTA
CCAGCATATTCTTTTCTAGTATTTCAGATCTAGTGACTCAGAACTAGGACAATCATAAAT
TTGAAGGGAACCTTAAGTCTTTTTTCATGCTGAGACTGCCAAG
>NODE_105950_length_95_cov_1.000000
TCAGGTCCTACTTCATTTGTAAGGAAAACTGACAGGTAATTCAGTGGGACAGAATACCAT
GTGAAGAGTTTCCTCTCACCTGAGAGGAGACTTTTTGATGATGATGATGATCAAT
您能建議我如何提取序列,即僅在A,T,G,C的行中提取序列的每個連續序列之間的換行符。 這是我到目前為止的代碼
#!/usr/bin/perl
print "Enter the first filename\n";
$filename = <>;
print "Enter the output file for ids\n";
$filename1 = <>;
print "Enter the output file for sequences\n";
$filename2 = <>;
my $first = ">";
open(FILE, $filename) or die "Could not read from $filename, program halting.";
open(FIL, '>', $filename1) or die "Could not read from $filename1, program halting.";
open(FILES, '>', $filename2) or die "Could not read from $filename2, program halting.";
while(my $line = <FILE>)
{
if ($line =~ m//s)
{
print FILES $line, "\n";
}
if ($line =~ m/^>/)
{
print FIL $line;
}
}
close FILE;
close FIL;
close FILES;
這只是一個基本的常規,簡單的perl程序來匹配模式。 任何幫助表示贊賞。
您可以使用此正則表達式
/^[ATGC]+$/gm
演示在這里https://regex101.com/r/rQ9gN4/2
如果要提取
NODE_105957_length_443_cov_1.000000 NODE_105950_length_95_cov_1.000000
否定上述正則表達式
/^([^ATGC]+)$/gm
嘗試一下:
#!/usr/bin/perl
# ALLWAYS
use strict;
use warnings;
print "Enter the first filename\n";
chomp (my $filename = <>); # remove the line break
print "Enter the output file for ids\n";
chomp (my $filename1 = <>); # remove the line break
print "Enter the output file for sequences\n";
chomp (my $filename1 = <>); # remove the line break
# use three args open and show the reason when it fails
open(my $FILE, '<', $filename) or die "Unable to open '$filename', $!";
open(my $FILE1, '>', $filename1) or die "Unable to open '$filename1', $!";
open(my $FILE2, '>', $filename2) or die "Unable to open '$filename2', $!";
while(my $line = <$FILE>) {
chomp($line); # remove line break
if ($line =~ /^>/) {
print $FILE1 $line,"\n";
# add a line break to filename2 unless we are at first line.
print $FILE2 "\n" unless $. < 2;
}
else {
print $FILE2 $line;
}
}
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