I can't find my mistake here!!!

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

Replies are listed 'Best First'.
Re: I can't find my mistake here!!! by AppleFritter (Vicar) on Jul 02, 2014 at 11:07 UTC
Do you see anything wrong in the syntax??? Many things. You've got two opening parentheses in `if(($sequence=~/ABC/)`, but only one closing one. You've not populated `$sequence`. You've not populated `%hash_seqs_all`. You've not populated `$infile`. You've not populated `$id`. You've not populated `$protein`. You're not checking for errors after `open`ing your output file. I'd love to try to help you, as I'm sure my brothers here in the Monastery would, but you've not given us nearly enough to work with. We'd need the following, ideally: Complete, syntactically correct code; a minimal test case that demonstrates the problem you're having. Example data. Expected output. Actual output. As it is, we've got a code snippet that doesn't even compile, run on data we haven't seen, producing results we can only guess at. This isn't enough. Here are some further links to get you started: How do I post a question effectively? The SSCCE: Short, Self Contained, Correct (Compilable) Example Please help us help you!	[reply]
Re: I can't find my mistake here!!! by Corion (Patriarch) on Jul 02, 2014 at 10:26 UTC
Most likely, your `$sequence` never matches `ABC`. Alternatively, maybe opening the file failed. Use `open OUT, '>', "$infile.OUTFILE" or die "Couldn't create file '$infile.OUTFILE': $!";` [download] Also, consider printing both to STDOUT and to OUT, just to debug that what you think should be printed to the file really gets printed.	[reply] [d/l] [select]
Re: I can't find my mistake here!!! by baxy77bax (Deacon) on Jul 02, 2014 at 10:33 UTC
`if(($sequence=~/ABC/) ?????` [download] I guess two (( is a typing mistake. but that implies this is not copy-past of your code.... `$sequence= "ABC"; open (OUT, ">OUTFILE"); if($sequence=~/ABC/) { print OUT "blas\n"; } close (OUT);` [download] this works, so the error must be somewhere else. are you sure you are getting inside the if block ?	[reply] [d/l] [select]
Re: I can't find my mistake here!!! by jellisii2 (Hermit) on Jul 02, 2014 at 11:24 UTC
Tangential: PerlCritic balks at 2 arg `open`s. My understanding if the current best practice is `open(my $file, '>', "$infile.OUTFILE");`	[reply] [d/l] [select]
Re^2: I can't find my mistake here!!! by Anonymous Monk on Jul 02, 2014 at 12:00 UTC
Hi guys! Many thanks for all the posts! My problem is actually down to why this: `print ">$protein\n$respective_seq\n";` [download] works, and I see the results on my screen (so the if block is executed normally, while this: `print OUT ">$protein\n$respective_seq\n";` [download] does not work! The file IS created, but nothing is printed inside...I tried also with `open OUT, '>', "outfile";` but no luck! I don't get a warning either... I am so confused, I can't make sense of it...	[reply] [d/l] [select]
Re: I can't find my mistake here!!! by choroba (Cardinal) on Jul 02, 2014 at 11:08 UTC
What's $protein? Where does it get populated? لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ	[reply]
Re: I can't find my mistake here!!! by perlfan (Parson) on Jul 02, 2014 at 11:54 UTC
`use strict;` `use warnings;` Unmatched parans in `if (($sequence` Use the "3 argument" open with a scalar filehandle (no bareword). You don't need ">" in the print statement, this would be more clear to you if you used 3 argument open. You can skip the parens in close. If you are only writing in the case of /ABC/, just open and close inside of the if statement.	[reply] [d/l] [select]
Re^2: I can't find my mistake here!!! by choroba (Cardinal) on Jul 02, 2014 at 11:59 UTC
You don't need "`>`" in the print statement You do, if your output is in the FASTA format. لսႽ† ᥲᥒ⚪⟊Ⴙᘓᖇ Ꮅᘓᖇ⎱ Ⴙᥲ𝇋ƙᘓᖇ	[reply] [d/l]
Re^3: I can't find my mistake here!!! by perlfan (Parson) on Jul 03, 2014 at 00:11 UTC
Ah, tricky. I was just trying to cover all of my bases (pun intended). =)	[reply]
Re^3: I can't find my mistake here!!! by Anonymous Monk on Jul 02, 2014 at 12:07 UTC
Ok, something came up: It seems to work, if I do the `open`, within the if block... Any ideas why? But in that case it's not helpful because later on I will have to open it again, and all this `open file` it not time-efficient, right?	[reply] [d/l] [select]
Re^4: I can't find my mistake here!!! by Corion (Patriarch) on Jul 02, 2014 at 12:08 UTC
Re^4: I can't find my mistake here!!! by Anonymous Monk on Jul 02, 2014 at 12:38 UTC
Re: I can't find my mistake here!!! by Laurent_R (Canon) on Jul 02, 2014 at 21:31 UTC
Unless I missed something, nobody has pointed out that you are opening your output files probably multiple times (maybe million times) within a probable read loop (you did not show enough of your code for us to figure out exactly what your are doing) and that, each time you do that, you overwrite the content gathered the previous file version. So that, at the end, you get in the file what gathered for the last input line, which might be nothing if /ABC/ does not match. Whereas if you print to the screen, you get the full output. You might have solved the issue with another technique, but I think that if you showed us more of your code, we could give you a much better solution, probably based on the idea of opening the output file before entering the read loop.	[reply]