Read in a template file, populate using user input and and generate a new file

Bioinfocoder has asked for the wisdom of the Perl Monks concerning the following question:

I am trying to read in a template config (template.config) file like ( which is little more complex then then the one posted earlier -

[module1]

;;path to speedseq package binary directory
$;SPEEDSEQ_BIN_DIR$; = /usr/local/packages/
;;Sequence file 1
$;Seq1File$; =
;;Sequence file 2
$;Seq2File$; =
;;Read Group
$;Read_Group$;='@RG\tID:NA12878\tSM:NA12878\tPL:ILLUMINA\tLB:NA12878\t
+PU:NA12878'
;;Reference
$;Reference$; =

[module2]

;;Output Chromosome
$;Chromosome$; = 
;;use --v for verbose summary
$;OTHER_ARGS$; = --v
[download]

whose fields will get populated by user input on command line eg

perl script.pl template.config --seq1 USER_INPUT.txt --Seq2 USER_INPT2.txt --Ref USER_INPUT_REF.txt --chr_list USER_INPUT_CHR.txt

and it will output a populated a new config file like -

[module1]

;;path to speedseq package binary directory
$;SPEEDSEQ_BIN_DIR$; = /usr/local/packages/
;;Sequence file 1
$;Seq1File$; = "USER_INPUT.txt"
;;Sequence file 2
$;Seq2File$; = "USER_INPT2.txt"
;;Read Group
$;Read_Group$;='@RG\tID:NA12878\tSM:NA12878\tPL:ILLUMINA\tLB:NA12878\t
+PU:NA12878'
;;Reference
$;Reference$; = "USER_INPUT_REF.txt"

[module2]

 ;;Output Chromosome
 $;Chromosome$; = "USER_INPUT_CHR.txt"
 ;;use --v for verbose summary
 $;OTHER_ARGS$; = --v
[download]

I tried with hash also, but that is not keeping the output order same as in the input file. I would really appreciate if anyone can provide suggestions on how to approach this.

Here is my Code -

my ($template_name, $Prefix, $Seq1File,$Seq2File,$Align_Reference,$Chr
+omosome_list,$Reference,$KnownSites ) = @ARGV;

GetOptions ('template_config=s' => \$template_name, 'Project=s' => \$P
+refix, 'Fasta_seq1=s' => \$Seq1File, 'Fasta_seq2=s' => \$Seq2File, 'R
+ef_align=s' => \$Align_Reference, 'Chr_list=s' => \$Chromosome_list, 
+'Ref=s' => \$Reference, 'Sites=s' => \$KnownSites);


open my $in_fh, '<', $template_name;
my %field = map { s/^\s+|\s*\n$//g; $_; } grep { !/^\s*#|^\s*$/ }  <$i
+n_fh>;
close $in_fh;


foreach my $spec (sort keys %field)
{
    if($spec =~ m/Output\s+Prefix/)
        {
        $field{$spec} = $field{$spec} .= $Prefix;
        }
        elsif ($spec =~ m/Sequence\s+file\s+1/)
        {
        $field{$spec} = $field{$spec} .= $Seq1File;
        }
        elsif ($spec =~ m/Sequence\s+file\s+2/)
        {
        $field{$spec} = $field{$spec} .= $Seq2File;
        }
        elsif ($spec =~ m/Align_Reference/)
        {
        $field{$spec} = $field{$spec} .= $Align_Reference;
        }
        elsif ($spec =~ m/Chromsome\s+List\s+file/)
        {
        $field{$spec} = $field{$spec} .= $Chromosome_list;
        }
        elsif ($spec =~ m/Reference/)
        {
        $field{$spec} = $field{$spec} .= $Reference;
        }
        elsif ($spec =~ m/Known\s+sites/)
        {
        $field{$spec} = $field{$spec} .= $KnownSites;
        }

}

# Print it to an output file

{
#open my $output_file = './test_processing.txt';
open my $out_fh, '>', './complete_nicu.txt';
foreach my $key (keys %field) {
    print $out_fh "$key\n";
    print $out_fh "$field{$key}\n";
   print "$field{$key}\n";
}
close $out_fh;
}
[download]

Thanks!

Comment on Read in a template file, populate using user input and and generate a new file Select or Download Code

Replies are listed 'Best First'.
Re: Read in a template file, populate using user input and and generate a new file by toolic (Bishop) on Feb 25, 2016 at 21:08 UTC
xpost... http://stackoverflow.com/questions/35637816/read-in-a-template-file-populate-using-user-input-and-and-generate-a-new-file	[reply]
Re^2: Read in a template file, populate using user input and and generate a new file by ExReg (Priest) on Feb 25, 2016 at 22:19 UTC
I can only hope that some day I will also have attained enlightenment to the state where I am able answer an untitled node with no question asked!	[reply]
Re^3: Read in a template file, populate using user input and and generate a new file by Bioinfocoder (Novice) on Feb 26, 2016 at 16:46 UTC
My bad! the post dint get through!	[reply]
Re^4: Read in a template file, populate using user input and and generate a new file by ExReg (Priest) on Feb 26, 2016 at 17:32 UTC
Re: Read in a template file, populate using user input and and generate a new file by hippo (Archbishop) on Feb 26, 2016 at 09:26 UTC
If I've reverse engineered a spec from your post correctly, then something along these lines should suffice: `#!/usr/bin/env perl use strict; use warnings; use feature 'say'; my $infile = shift; open my $in, '<', $infile or die "Cannot open $infile: $!"; while (<$in>) { chomp; s/=\s$/"= " . shift/e; say; } close $in;` [download] Running it with your sample input gives: `$ ./bar.pl template.config list.txt file_list.txt ;; path to config file $;INPUT_FILE$; = list.txt ;; path to list of config files $;INPUT_FILE_LIST$; = file_list.txt ;; path to temporary directory $;TEMP_DIR$; = $;TMP_DIR$; ;; use --v for verbose summary $;OTHER_ARGS$; = --v` [download] Update:* removed a redundant mention of `@ARGV` in the substitution. Update 2: for the avoidance of any confusion resulting from the parent post having been rewritten to change both the data set and the invocation, here's the original input file: `;; path to config file $;INPUT_FILE$; = ;; path to list of config files $;INPUT_FILE_LIST$; = ;; path to temporary directory $;TEMP_DIR$; = $;TMP_DIR$; ;; use --v for verbose summary $;OTHER_ARGS$; = --v` [download] which was declared to be called as I have above and result in the output which I have also shown above.	[reply] [d/l] [select]
Re^2: Read in a template file, populate using user input and and generate a new file by Bioinfocoder (Novice) on Feb 26, 2016 at 16:49 UTC
Thanks! but I just came to know that the input is little different then teh earlier post, I will try your suggestion as well!	[reply]
Re^3: Read in a template file, populate using user input and and generate a new file by poj (Abbot) on Feb 26, 2016 at 18:47 UTC
If you can add placeholders `[% name %]` to your `template.config` file like this `[module1] ;;path to speedseq package binary directory $;SPEEDSEQ_BIN_DIR$; = /usr/local/packages/ ;;Sequence file 1 $;Seq1File$; = "[% seq1 %]" ;;Sequence file 2 $;Seq2File$; = "[% seq2 %]" ;;Read Group $;Read_Group$;='@RG\tID:NA12878\tSM:NA12878\tPL:ILLUMINA\tLB:NA12878\t +PU:NA12878' ;;Reference $;Reference$; = "[% ref %]" [module2] ;;Output Chromosome $;Chromosome$; = "[% chr_list %]" ;;use --v for verbose summary $;OTHER_ARGS$; = --v` [download] then you could use a templating module like Template::Toolkit or Template::Tiny Read more... (1039 Bytes) poj	[reply] [d/l] [select]
Re^4: Read in a template file, populate using user input and and generate a new file by Bioinfocoder (Novice) on Feb 26, 2016 at 20:32 UTC
Re^5: Read in a template file, populate using user input and and generate a new file by poj (Abbot) on Feb 26, 2016 at 21:09 UTC
Re: Read in a template file, populate using user input and and generate a new file by CountZero (Bishop) on Feb 26, 2016 at 07:35 UTC
What's in "script.pl"? Did it come with any documentation? CountZero A program should be light and agile, its subroutines connected like a string of pearls. The spirit and intent of the program should be retained throughout. There should be neither too little or too much, neither needless loops nor useless variables, neither lack of structure nor overwhelming rigidity." - The Tao of Programming, 4.1 - Geoffrey James My blog: Imperial Deltronics	[reply]
Re^2: Read in a template file, populate using user input and and generate a new file by Bioinfocoder (Novice) on Feb 26, 2016 at 16:48 UTC
its just the script with code in it, that user will use to run the job on command line	[reply]