Re: Find a sequence in a multifasta files and motifs

First things first. Generate a separate file for each amino acid sequence. Put these flat files into a separate folder. Label each file by the FASTA code. You may then be in a position to put each line of each sequence into the elements of an array. I'm assuming that the sequences correspond to particular proteins.

Looking at your code. I have never seen the following before:


if(!open(MY_HANDLE, "file.txt")){
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Try to keep to what you might find in a text book.

Your taking a single argument as an id and then worked with an array @id. That needs to be fixed.

~~I am assuming that you know that your regular expression does not match what you have said in the text.~~The standard input is the protein code ID but the regular expression that is search for is a protein motif. You are jumping ahead of yourself in the code. I expect that you will modify the program to then allow for alternative protein motifs to be inputed by the user.

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Re^2: Find a sequence in a multifasta files and motifs by haukex (Archbishop) on Jun 30, 2019 at 10:53 UTC
I have never seen the following before: `if(!open(MY_HANDLE, "file.txt")){` Try to keep to what you might find in a text book. TIMTOWTDI - `if(!open(MY_HANDLE, "file.txt")){ die "Cannot open the file\n"; }` is pretty much exactly* the same as `open MY_HANDLE, "file.txt" or die "Cannot open the file\n";`, but the former might be much more familiar to someone coming from a language such as C. Personally I'd just have pointed out that generally the three-argument open and lexical filehandles have several advantages over the two-argument open and bareword filehandles, and that it's usually nicer to include the filename and $! in the error message. * Update: One difference is that `if` introduces a new scope, which would become relevant when using lexical filehandles. But as currently written, they're the same.	[reply] [d/l] [select]
Re^2: Find a sequence in a multifasta files and motifs by rebkirl (Acolyte) on Jun 28, 2019 at 10:08 UTC
Thanks for your suggestions. I fixed the regex mistake	[reply]