I need help for a command that I wrote in perl

Question

[mark2020]

I wanna extract the header line from 2 protein sequences for example: I created the file, then I gave the file name, then I wanna extract header, then from the second sequence.

here I showed what's the header in below:

gi|628601924|ref|NP_001278775.1| DNA-binding protein Ikaros isoform 16 [Homo sapiens] These are my protein fasta with heder that i wanna extract the header from them:

gi|628601924|ref|NP_001278775.1| DNA-binding protein Ikaros isoform 16 [Homo sapiens] MDADEGQDMSQVSGKESPPVSDTPDEGDEPMPIPEDLSTTSGGQQSSKSDRVVVTYGADDFRDFHAIIPK SFSLLEL

gi|628601926|ref|NP_001278776.1| DNA-binding protein Ikaros isoform 16 [Homo sapiens] MDADEGQDMSQVSGKESPPVSDTPDEGDEPMPIPEDLSTTSGGQQSSKSDRVVVTYGADDFRDFHAIIPK SFSLLEL

I wrote this command:

   print "Please enter a file name: ";
   $file = <>;
   open INFILE, $file;

   $line = <INFILE>;

   while (defined($line = <INFILE>)){
   }
   chomp $line;

if ($line =~ /^>(S+)\s*(.*)$/;){

 $id = $1; # what should I write here to activate these $1 and $2

 $description = $2;

   print substr($1 $2); #what else should I add here
   }

   } else {# I need to write some thing here, like this it's not header don't  extract it 

   }
   next; # is this enough for going to the next sequence 

   close INFILE;

[GenoMax]

If you just need the header line then you could grep ">" .. no need for PERL.

[venu]

Why only perl? Is this homework? BTW, this was answered many a times in this forum.

[Chris Fields]

This sounds suspiciously homework-y.

[mark2020]

thanks for your comments I edited my question.

[GenoMax]

Please use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized.

The original question is still unanswered. Is this a homework question?

Hint: If you just need to print the header line then check to see if the line begins with "^>" otherwise go to next line.

Answer 1

[Eric Lim]

Google 'perl grep command line'.

[GenoMax]

When a question is suspiciously specific (e.g. need PERL solution) we try to encourage the OP to research a solution on their own (unless they provide an explanation that makes a compelling case). It is not helpful to provide a ready solution, especially if this is part of a homework assignment.

[Eric Lim]

I know, but it's Friday and I want to be nice. Answer changed.