use strict; 
use warnings; 

print "\n Running script for Jiggs \n";
my $infile = "foot.txt";                   # <foot.txt> is not legal q
+uotation in perl5

open my $in,  "<", $infile     or die $!;  # Don't quote a variable ag
+ain
open my $out, ">", "foot1.txt" or die $!;

my $line = <$in>;                          # Is $line the header? If s
+o, don't call it "line"
$line =~ s/\s+\Z/\n/;                      # When you chomp, you don't
+ get a "new" newline
$line =~ s/ +/,/g;
print $out $line;                          # Don't quote variable. It 
+now still has a newline
print $out scalar <$in>;                   # What is this second line?
+ Something special?

while (<$in>) {
    s/\s+\Z/\n/;
    s/ +/,/g;
    s/,length=/,/g;
    print $out $_;
    }

close $in; 
close $out; 
 
print "\n Done!\n";
[download]

Note that this might up being invalid CSV. Use Text::CSV or Text::CSV_XS to ensure valid CSV output.

Cool, thanks for the reply!

Using your example, I found out there is no need for the header part at all. I removed that part of the code, and then used the s//g; to get rid of the rest of the field names.

Here is the code:

use strict; 
use warnings; 

print "\n Running script for Jiggs \n";
my $infile = "foot.txt";                   

open my $in,  "<", $infile     or die $!;  
open my $out, ">", "foot1.txt" or die $!;

while (<$in>) {
    
    s/\s+\Z/\n/;
    s/ +/,/g;
    s/,length=/,/g;
    s/,xy=/,/g;
    s/,region=/,/g;
    s/,run=/,/g;
    
    print $out $_;
    }

close $in; 
close $out; 
 
print "\n Done!\n";
[download]

Here is the output:

>G9JVYGV01AJE8V,135,0104_0349,1,R_2011_09_20_15_00_06_
GGTGGTAGTGAAGAAGAGGAGATGAAAGTGGAAGAGGTTGAGGATGAGAAGGTTGAATTG
GAAGAAGAAGATGAGAAGGTTGAAGTGGAAGATGAGAAGGTTGAAGTGGAAGAAGATGAA
GTGGAAGAGAGGAGC
>G9JVYGV01A4910,90,0353_0150,1,R_2011_09_20_15_00_06_
GGTGCATGGCATTGTAGATGGTTGCTTGATAGTTGCCCATACGTGTACTACACTTGCAGA
GTGAAGCAACCATCTACAATGCCATGCACC
>G9JVYGV01A0SVP,70,0302_0163,1,R_2011_09_20_15_00_06_
GCACCATTCAGCACAGATATAGTAGCCACATCAACACAAGTTACCTAACTATATCTGTGC
TGAATGGTGC
>G9JVYGV01A221U,89,0328_0160,1,R_2011_09_20_15_00_06_
CTGGACATTTACATCCATAAGTAGGAGTTAGGACTCTGCACCAGCCTCTTGAGCTTGTGA
CGTCTCTTCTCCTCCTCCGGACTGGGACA
>G9JVYGV01BVCPK,46,0650_0134,1,R_2011_09_20_15_00_06_
GCAAGATCGCAAGCCAAGCAACGTTTCACGAACTGGCCAGAATGAG
>G9JVYGV01AOU3I,81,0166_0220,1,R_2011_09_20_15_00_06_
TCATTGACATCTGTGCAGCTGCAGGAGCGGATATGAGGAGATGGTTCTATCTGCACAGAT
GTCAATGAGTGTGACAGTGAT
>G9JVYGV01A0JEL,61,0299_0171,1,R_2011_09_20_15_00_06_
CGAGTGAAGGCATTGGTGATGCTGGTGTGAAGAGTGAGGGCATCGCCAATGCCTTCACTC
G
>G9JVYGV01AUKIG,119,0231_0198,1,R_2011_09_20_15_00_06_
GGCCACCAGGGCTTAACTTCCTGTGCCTCACCATCACGCAGTTGTCAGAGGATCCACATT
GAACAAAGTAGCAATTCTTTCCACTCTGTGACACACCAACATTCTTATACAGCACCAGG
>G9JVYGV01AJ8F7,29,0113_1333,1,R_2011_09_20_15_00_06_
CTGCTTCCAAGCCTCCAACCTCTAACCAG
>G9JVYGV01AMQ87,79,0142_0233,1,R_2011_09_20_15_00_06_
AGAGTCTCCTCATTGTTCTTTCCAAGTCCTCTATTGCTGAGCCTGGTTTCGTACCTTCTC
AGCTAGGCCCTCTTTCTCT
>G9JVYGV01A4W45,85,0348_3895,1,R_2011_09_20_15_00_06_
GCTTCACATCTCAGAAATATAACCGCTAATGATCTGAAACAAGTTACAATCTGACATTCT
GAAACCAAATGAAAGCAGCATAAAC
>G9JVYGV01A7TPA,66,0382_0140,1,R_2011_09_20_15_00_06_
ATGGCTTACCTCACTGTCGATGGAGATCGAATGCAAGCGATGTCCATCGACAGTGAGGTA
AGCCAT
[download]

Almost there, but I need to put a comma after the last field before the sequence. Then remove the returns within the sequence.

If each entry starts with a carot, then I need 6 fields seperated by commas and then the new line: the opening entry, the length=, xy=, region=, run=, AAGGTTGGCC /n).

Apologies for not being clearer, but thanks for the help so far.

use strict;
use warnings;

while (<DATA>) {
    chomp;
    my @parts = split /\s+/,$_;
    ## $parts[0] = substr $parts[0],1,-1;
    $parts[1] = $1 if $parts[1] =~ /length=(\d+)/;
    print join(",",@parts),"\n";
}

__DATA__
>G9JVYGV01AJE8V length=135 xy=0104_0349 region=1 run=R_2011_09_20_15_0
+0_06_GGTGGTAGTGAAGAAGAGGAGATGAAAGTGGAAGAGGTTGAGGATGAGAAGGTTGAATTGGAAG
+AAGAAGATGAGAAGGTTGAAGTGGAAGATGAGAAGGTTGAAGTGGAAGAAGATGAAGTGGAAGAGAGGA
+GC
>G9JVYGV01A4910 length=90 xy=0353_0150 region=1 run=R_2011_09_20_15_00
+_06_GGTGCATGGCATTGTAGATGGTTGCTTGATAGTTGCCCATACGTGTACTACACTTGCAGAGTGAA
+GCAACCATCTACAATGCCATGCACC
>G9JVYGV01A0SVP length=70 xy=0302_0163 region=1 run=R_2011_09_20_15_00
+_06_GCACCATTCAGCACAGATATAGTAGCCACATCAACACAAGTTACCTAACTATATCTGTGCTGAAT
+GGTGC
>G9JVYGV01A221U length=89 xy=0328_0160 region=1 run=R_2011_09_20_15_00
+_06_CTGGACATTTACATCCATAAGTAGGAGTTAGGACTCTGCACCAGCCTCTTGAGCTTGTGACGTCT
+CTTCTCCTCCTCCGGACTGGGACA
>G9JVYGV01BVCPK length=46 xy=0650_0134 region=1 run=R_2011_09_20_15_00
+_06_GCAAGATCGCAAGCCAAGCAACGTTTCACGAACTGGCCAGAATGAG
>G9JVYGV01AOU3I length=81 xy=0166_0220 region=1 run=R_2011_09_20_15_00
+_06_TCATTGACATCTGTGCAGCTGCAGGAGCGGATATGAGGAGATGGTTCTATCTGCACAGATGTCAA
+TGAGTGTGACAGTGAT
>G9JVYGV01A0JEL length=61 xy=0299_0171 region=1 run=R_2011_09_20_15_00
+_06_CGAGTGAAGGCATTGGTGATGCTGGTGTGAAGAGTGAGGGCATCGCCAATGCCTTCACTCG
[download]

This can be done with a one-liner. See perlrun for the lowdown on the switches used.

c:\test>perl -l -0x3e -ane"@F||next; s/length=//for$F[1]; @F[5]=join''
+,@F[5..99]; $#F=5; print'>',join',',@F" junk.dat
>G9JVYGV01AJE8V,135,xy=0104_0349,region=1,run=R_2011_09_20_15_00_06_,G
+GTGGTAGTGAAGAAGAGGAGATGAAAGTGGAAGAGGTTGAGGATGAGAAGGTTGAATTGGAAGAAGAAG
+ATGAGAAGGTTGAAGTGGAAGATGAGAAGGTTGAAGTGGAAGAAGATGAAGTGGAAGAGAGGAGC
>G9JVYGV01A4910,90,xy=0353_0150,region=1,run=R_2011_09_20_15_00_06_,GG
+TGCATGGCATTGTAGATGGTTGCTTGATAGTTGCCCATACGTGTACTACACTTGCAGAGTGAAGCAACC
+ATCTACAATGCCATGCACC
>G9JVYGV01A0SVP,70,xy=0302_0163,region=1,run=R_2011_09_20_15_00_06_,GC
+ACCATTCAGCACAGATATAGTAGCCACATCAACACAAGTTACCTAACTATATCTGTGCTGAATGGTGC
>G9JVYGV01A221U,89,xy=0328_0160,region=1,run=R_2011_09_20_15_00_06_,CT
+GGACATTTACATCCATAAGTAGGAGTTAGGACTCTGCACCAGCCTCTTGAGCTTGTGACGTCTCTTCTC
+CTCCTCCGGACTGGGACA
>G9JVYGV01BVCPK,46,xy=0650_0134,region=1,run=R_2011_09_20_15_00_06_,GC
+AAGATCGCAAGCCAAGCAACGTTTCACGAACTGGCCAGAATGAG
>G9JVYGV01AOU3I,81,xy=0166_0220,region=1,run=R_2011_09_20_15_00_06_,TC
+ATTGACATCTGTGCAGCTGCAGGAGCGGATATGAGGAGATGGTTCTATCTGCACAGATGTCAATGAGTG
+TGACAGTGAT
>G9JVYGV01A0JEL,61,xy=0299_0171,region=1,run=R_2011_09_20_15_00_06_,CG
+AGTGAAGGCATTGGTGATGCTGGTGTGAAGAGTGAGGGCATCGCCAATGCCTTCACTCG
[download]

Whilst you may not be interested in using a one-liner, especially if you need to do this regularly, it can be instructive to see the code that the one-liner produces when deparsed:

c:\test>perl -MO=Deparse -l -0x3e -ane"@F||next; s/length=//for$F[1]; 
+@F[5]=join'',@F[5..99]; $#F=5; print'>',join',',@F" junk.dat
BEGIN { $/ = ">"; $\ = "\n"; }
LINE: while (defined($_ = <ARGV>)) {
    chomp $_;
    our(@F) = split(' ', $_, 0);
    next unless @F;
    s/length=// foreach ($F[1]);
    @F[5] = join('', @F[5..99]);
    $#F = 5;
    print '>', join(',', @F);
}
-e syntax OK
[download]

You are correct, this needs to be run often and was hoping to use this code as a template for future applications. I am appreciative of your reply, but I am still new to one-liners.

You are correct, this needs to be run often and was hoping to use this code as a template for future applications. I am appreciative of your reply, but I am still new to one-liners.

Then you could cut&paste the Deparse output and use it as the basis of your own code.

---

With the rise and rise of 'Social' network sites: 'Computers are making people easier to use everyday'

Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.

"Science is about questioning the status quo. Questioning authority".

In the absence of evidence, opinion is indistinguishable from prejudice.

The start of some sanity?

Each entry begins with a carot

There is no caret (^) character in your data.    I assume you mean the (>) greater than character?

$ echo ">G9JVYGV01AJE8V length=135 xy=0104_0349 region=1 run=R_2011_09
+_20_15_00_06_
GGTGGTAGTGAAGAAGAGGAGATGAAAGTGGAAGAGGTTGAGGATGAGAAGGTTGAATTG
GAAGAAGAAGATGAGAAGGTTGAAGTGGAAGATGAGAAGGTTGAAGTGGAAGAAGATGAA
GTGGAAGAGAGGAGC
>G9JVYGV01A4910 length=90 xy=0353_0150 region=1 run=R_2011_09_20_15_00
+_06_
GGTGCATGGCATTGTAGATGGTTGCTTGATAGTTGCCCATACGTGTACTACACTTGCAGA
GTGAAGCAACCATCTACAATGCCATGCACC
>G9JVYGV01A0SVP length=70 xy=0302_0163 region=1 run=R_2011_09_20_15_00
+_06_
GCACCATTCAGCACAGATATAGTAGCCACATCAACACAAGTTACCTAACTATATCTGTGC
TGAATGGTGC
>G9JVYGV01A221U length=89 xy=0328_0160 region=1 run=R_2011_09_20_15_00
+_06_
CTGGACATTTACATCCATAAGTAGGAGTTAGGACTCTGCACCAGCCTCTTGAGCTTGTGA
CGTCTCTTCTCCTCCTCCGGACTGGGACA
>G9JVYGV01BVCPK length=46 xy=0650_0134 region=1 run=R_2011_09_20_15_00
+_06_
GCAAGATCGCAAGCCAAGCAACGTTTCACGAACTGGCCAGAATGAG
>G9JVYGV01AOU3I length=81 xy=0166_0220 region=1 run=R_2011_09_20_15_00
+_06_
TCATTGACATCTGTGCAGCTGCAGGAGCGGATATGAGGAGATGGTTCTATCTGCACAGAT
GTCAATGAGTGTGACAGTGAT
>G9JVYGV01A0JEL length=61 xy=0299_0171     region=1     run=R_2011_09_
+20_15_00_06_
CGAGTGAAGGCATTGGTGATGCTGGTGTGAAGAGTGAGGGCATCGCCAATGCCTTCACTC
G
" | perl -e'
my $line;     
while ( <> ) {
    chomp;
    s/length=//;
    tr/ /,/s;
    if ( /^>/ ) {
        print "$line\n" if $line;
        $line = $_;
        }
    else {
        $line .= $_;
        }
    }           
print "$line\n";
'
>G9JVYGV01AJE8V,135,xy=0104_0349,region=1,run=R_2011_09_20_15_00_06_GG
+TGGTAGTGAAGAAGAGGAGATGAAAGTGGAAGAGGTTGAGGATGAGAAGGTTGAATTGGAAGAAGAAGA
+TGAGAAGGTTGAAGTGGAAGATGAGAAGGTTGAAGTGGAAGAAGATGAAGTGGAAGAGAGGAGC
>G9JVYGV01A4910,90,xy=0353_0150,region=1,run=R_2011_09_20_15_00_06_GGT
+GCATGGCATTGTAGATGGTTGCTTGATAGTTGCCCATACGTGTACTACACTTGCAGAGTGAAGCAACCA
+TCTACAATGCCATGCACC
>G9JVYGV01A0SVP,70,xy=0302_0163,region=1,run=R_2011_09_20_15_00_06_GCA
+CCATTCAGCACAGATATAGTAGCCACATCAACACAAGTTACCTAACTATATCTGTGCTGAATGGTGC
>G9JVYGV01A221U,89,xy=0328_0160,region=1,run=R_2011_09_20_15_00_06_CTG
+GACATTTACATCCATAAGTAGGAGTTAGGACTCTGCACCAGCCTCTTGAGCTTGTGACGTCTCTTCTCC
+TCCTCCGGACTGGGACA
>G9JVYGV01BVCPK,46,xy=0650_0134,region=1,run=R_2011_09_20_15_00_06_GCA
+AGATCGCAAGCCAAGCAACGTTTCACGAACTGGCCAGAATGAG
>G9JVYGV01AOU3I,81,xy=0166_0220,region=1,run=R_2011_09_20_15_00_06_TCA
+TTGACATCTGTGCAGCTGCAGGAGCGGATATGAGGAGATGGTTCTATCTGCACAGATGTCAATGAGTGT
+GACAGTGAT
>G9JVYGV01A0JEL,61,xy=0299_0171,region=1,run=R_2011_09_20_15_00_06_CGA
+GTGAAGGCATTGGTGATGCTGGTGTGAAGAGTGAGGGCATCGCCAATGCCTTCACTCG
[download]

Yes you are correct, my mistake

By the way, thanks for the code!

It works great, here is the complete version that reads from and writes to files.

use strict; 
use warnings; 

print "\n Running script for Jiggs \n";
my $infile = "foot.txt";                   

open my $in,  "<", $infile     or die $!;  
open my $out, ">", "foot1.txt" or die $!;

my $line;     
while ( <$in> ) {
    chomp;
    s/length=//;
    s/xy=//g;
    s/region=//g;
    s/run=//g;
    tr/ /,/s;
    if ( /^>/ ) {
        print $out "$line\n" if $line;
        $line = $_;
        }
    else {
        $line .= $_;
        }
    }           
print $out "$line\n";


close $in; 
close $out; 
 
print "\n Done!\n";
[download]

Many thanks to all the responses, I learned so much today: Using RegEx's and substitution, file handling, split function, and joining arrays!

try this code ..

use strict;
use warnings;
open (  my $in ,"intxt.txt") || die "check the input file...not able t
+o open $!";
open (  my $out ,">output.txt") || die "check the input file...not abl
+e to open $!";
 $/="";
 my $in_whole= <$in>;
 $in_whole=~ s/\n//g;
 my @arr=split(">",$in_whole);
my $fout=join(">",@arr);
print $fout;
$fout=~ s/>/\n>/g;
$fout=~ s/^(\n)//;
$fout=~ s/\s/,/g;
$fout=~ s/length=//g;
@arr=split(">",$fout);
$fout=join(">",@arr);
$fout=~ s/>/\n>/g;
$fout=~ s/^(\n)//;
$fout=~ s/,\n/\n/g;
print $out $fout;
close($in);
close($out);
[download]

Hi, The above code is not working for me. My requirement is to convert tab delimited file to CSV file. I am pasting below records 0000709a1470a60284e3b243f713f5cb NULL 70304222 14165222 235588862 1 00010cc71380a0aa17070f07fc36a6be 734255876 70303022 14165222 235588862 1 000142841420a2a805916731fc6bad60 125729237 70303022 14165222 235588862 1 000144231480a5f162664e26ff3ca308 NULL 70304222 14165222 235588862 1 I want to replace tabs as comma.I will appreciate your help if any one can reply ASAP

Not many files, but each file contains thousands of entries (file size >35,936 KB). In fact, just opening the file in my text editor and it starts to slow down. Thanks for the idea though.