writing array element to a file

francesca1987 has asked for the wisdom of the Perl Monks concerning the following question:

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Re: writing array element to a file by hdb (Monsignor) on Apr 25, 2013 at 09:42 UTC
At a first glance, it seems you need a pair of braces around the print statement. And the file handle in the print statement. `while ($line=<in>) { if($line=~/>/) { @vettore=split(/\s+/, $line); open my $fh, ">>seq_id.txt" or die "Cannot open output +.txt: $!"; foreach (@vettore) { # { was missing here, removed ; print $fh $_ . "\n"; # file handle was missing } # } was missing here close $fh; # removed my } }` [download] UPDATE: The regex for > at the beginning of line is /^>/. The name of the file you are trying to open for writing is inconsistent with the error message.	[reply] [d/l]
Re: writing array element to a file by Random_Walk (Prior) on Apr 25, 2013 at 09:46 UTC
Welcome to Perl Monks. The syntax problem with your code is that `foreach` runs a loop so you need to use it like this: `foreach (@vettore) { print $_ . "\n"; }` [download] But it looks like you may actually want to print the output to your filehandle $fh by replacing your `print` with `print $fh "$_\n"` Perhaps this script will help show some other ideas # The following two lines check your code and # alert you to many common errors use strict; use warnings; # Lets keep the filespec out the main code # using my when defining a variable limits its scope. my $infile = "rep_set_ass_tax.fna"; my $outfile = "seq_id.txt"; # No point going on if we can not open both files # You were opening the outfile in a loop before, lots of opens # and closes happening that were not needed open my $in, '<', $infile or die "Can't read $infile: $!\n"; open my $out, '>>', $outfile or die "Can't read $outfile: $!\n"; while (my $line=<$in>) { if($line=~/^>/) { # ^ added for only lines starting with +> my @vettore=split(/\s+/, $line); foreach (@vettore) { # can use for(@array) but they are the s +ame print $out "$_ \n"; # Variables can be interpolated in a stri +ng } # end foreach loop } } close $in; close $out; [download] If you are going to post more often it may be worth having a look at how to format your posts :) Cheers, R. Pereant, qui ante nos nostra dixerunt!	[reply] [d/l] [select]
Re^2: writing array element to a file by francesca1987 (Initiate) on Apr 25, 2013 at 11:17 UTC
Hi! Thanks everyone for the help, I know I did a lot of stupid errors, but I just started with perl. I tried to run the script you suggested me, but it wasn't exactly what I need to do. I need to copy in the stdout only the number after the >, without the following lines. These are few lines of my input file: > 0 CATCAAAATAATCATGTATTGGTAAAAGTTTAGTAAAAATACTAAAACTATTGACAATTCAAACTAATAC +TTGTATAATGGAAGCGTATTCAAAAAATAAACAGGAGGTTCTCATAATGAGAAAATCTAACGTTCAGAT +GAAGTCTCGTCTATCCTATGCAGCGGGTGCTTTTGGTAACGACGTCTTCTATGCAACGTTGTCAACATA +CTTTATT > 1 CATCAAAATAATCATGTATTAGTAAAAGTTTAGTAAAAAATACTAAAACTATTGACAATTCAAACTAATA +CTTGTATAATGGAAGCGTATTCAAAAAATAACAGGAGGTTCTCATAATGAGAAAATCTAACGTTCAGAT +GAAGTCTCGTCTATCCTATGCAGCGGGTGCTTTTGGTAACGACGTCTACTATGCAACGTTGTCAACATA +CTTTATT > 10 CATCAAGATAACCATGTATTAGTAAAATTTTAGTAAAAAACACTGAAATTATTGACTGCATAAACCAATT +TTCATATAATGTAAACGTATTCAAATAATAGGAGGTTTCCGAAATGGAAAAATCTAAAGGTCAGATGAA +GTCTCGTTTATCCTACGCAGCTGGTGCTTTTGATAACGACGTCTTCTATGCAACCTTGTCAACATTACT +TTATC > 100 CATCAAAATAATCATGTATTAGTAAAAGTTTAGTAAAAATACTAAAACTATTGACAATTCAAACTAATAC +TTGTATAATGGAAGCGTATTCAAAAAATGACAGGAGGTTCTCATAATGAGAAAATCTAACGTTCAGATG +AAGTCTCGTCTATCCTATGCAGCGGGTGCTTTTGGTAACGACGTCTTCTATGCAACGTTGTCAACATAC +TTTATT ... [download] I want to copy only the numers.... Running the sipt you suggested, I obtained this: `> 0 CATCAAAATAATCATGTATTGGTAAAAGTTTAGTAAAAATACTAAAACTATTGACAATTCAAACTAATAC +TTGTATAATGGAAGCGTATTCAAAAAATAAACAGGAGGTTCTCATAATGAGAAAATCTAACGTTCAGAT +GAAGTCTCGTCTATCCTATGCAGCGGGTGCTTTTGGTAACGACGTCTTCTATGCAACGTTGTCAACATA +CTTTATT > 1 CATCAAAATAATCATGTATTAGTAAAAGTTTAGTAAAAAATACTAAAACTATTGACAATTCAAACTAATA +CTTGTATAATGGAAGCGTATTCAAAAAATAACAGGAGGTTCTCATAATGAGAAAATCTAACGTTCAGAT +GAAGTCTCGTCTATCCTATGCAGCGGGTGCTTTTGGTAACGACGTCTACTATGCAACGTTGTCAACATA +CTTTATT` [download] How can I modify it? Man thanks for your help!! Francesca	[reply] [d/l] [select]
Re^3: writing array element to a file by Random_Walk (Prior) on Apr 25, 2013 at 13:11 UTC
So you have a series of lines that look something like this `> 22 GATTGATGCC... > 2 GATGGATGTG... > 26 GATGCATGAT... > 52 GATGATGTGG...` [download] And in your output file you just want the numbers. The split we had in the original code splits each line on spaces into the `@vettore` array. If we only want to print the second element of this array (the number) then we do not need the `foreach` loop. We can alter our print to directly address the second element of the array`print $out "$vettore[1]\n";` (array indexing starts at 0). Here is our new line processing block: `while (my $line=<$in>) { if($line=~/^>/) { my @vettore=split(/\s+/, $line); print $out "$vettore[1]\n"; } }` [download] For fun it can also be done as a one liner. Here I added a bit more checking of the line to ensure it had some GATC characters following the number `perl -nle "if (/^>\s+(\d+)\s+[GATC]+/) {print $1}" rep_set_ass_tax.fna >> seq_id.txt` If you are not on windows you may need to change the two " quotes to ' quotes. Cheers, R. Pereant, qui ante nos nostra dixerunt!	[reply] [d/l] [select]
Re^4: writing array element to a file by francesca1987 (Initiate) on Apr 25, 2013 at 13:22 UTC
Re^5: writing array element to a file by Random_Walk (Prior) on Apr 25, 2013 at 14:31 UTC
Some notes below your chosen depth have not been shown here
Re: writing array element to a file by baxy77bax (Deacon) on Apr 25, 2013 at 09:58 UTC
you should really put your code in `<code></code>` tags. But from what I can see your code looks like this(more or less): open in, "rep_set_ass_tax.fna"; while ($line=<in>) { if($line=~/>/) { @vettore=split(/\s+/, $line); open my $fh, ">>seq_id.txt" or die "Cannot open output.txt: $!"; # + There is no need to open a file each time you need to print somethin +g into it if it is the same file. just open it once before the loop a +nd print to it foreach (@vettore); # What is a loop and what is a proper way to w +rite one. So you started a loop and what are you going to do with it( +I mean variables in the loop) print $_ . "\n"; # OK, so you want to print something, but where + to STDOUT or into a file that you have opened close my $fh; # again my doesn't have any effect if use strict is +not called. } } [download] First of all try to use strict and warnings, you will get a lot of info about your errors. Second, you have a some syntax errors(see comments in the above code). I I were you I would do something like this `use strict; use warnings; open(IN, "<", "rep_set_ass_tax.fna") or die "Died!!"; open (OUT , ">","seq_id.txt") or die "Cannot open output.txt: $!"; while (my $line=<IN>) { if($line=~/>/) { my @vettore=split(" ", $line); foreach (@vettore){ print OUT $_ . "\n"; } } } close IN; close OUT;` [download] now this maybe is not exactly what you need to do but it will get you started Cheers UPDATE: `use strict; use warnings; open(IN, "<", "rep_set_ass_tax.fna") or die "Died!!"; while (my $line=<IN>) { if($line=~/>(\d+)/) { print $1 . "\n"; } } close IN;` [download] UPDATE 2: Did you manage to get it working?? Also is this a fasta file orreally a one line file "> 1 ATTTAAA..."??? it is a bit strange if it is a one liner. usually those files look like this: `>1 ATGT... >2 ATGGTGC..` [download] also is there a space between > and 1? so you did several things wrong down there: it should look like this: `use strict; use warnings; my $infile = "rep_set_ass_tax.fna"; my $outfile = "seq_id.txt"; # you need to open this only if writing t +o a file open(IN, "<", $infile) or die "Died!!"; while (my $line=<IN>) { if($line=~/>\s*(\d+)/) { print $1 . "\n"; } } close IN;` [download] and use the code tags like: `<code>` My code; `</code>` baxy	[reply] [d/l] [select]
Re^2: writing array element to a file by francesca1987 (Initiate) on Apr 25, 2013 at 13:10 UTC
Hi baxy! I did as you suggested in the update, the script run, but the output was empty! I run: `use strict; use warnings; my $infile = "rep_set_ass_tax.fna"; my $outfile = "seq_id.txt"; open(IN, ">>", "rep_set_ass_tax.fna") or die "Died!!"; while (my $line=<IN>) { if($line=~/>(\d+)/) { print $1 . "\n"; } }` [download] What's the problem? `close IN;` [download]	[reply] [d/l] [select]
Re^3: writing array element to a file by poj (Abbot) on Apr 25, 2013 at 14:16 UTC
This opens IN for output `open(IN, ">>", "rep_set_ass_tax.fna") or die "Died!!";` [download] it should be `open(IN, "<", "rep_set_ass_tax.fna") or die "Died!!";` [download] poj	[reply] [d/l] [select]