in reply to Perl script help to convert .txt file to .csv

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

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Replies are listed 'Best First'.
Re^2: Perl script help to convert .txt file to .csv
by Seabass (Novice) on Dec 20, 2011 at 23:40 UTC

    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!

[reply]
[d/l]

      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]
[reply]
[d/l]
      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
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