file header change

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

Hello, Perl Monks;

I have a multi fasta file (with header > and sequence) in the following format:

>contig_1 # 498 # 1826 # 1 # ID=1_1;partial=00;start_type=ATG;rbs_motif=AGxAGG/AGGxGG;rbs_spacer=5-10bp;gc_cont=0.406

MNLTFDYTKEPSRDVLCIDVKSFYASVECVERG LDPLKTMLVVMSNSENSGGLVLAASPM

>contig_2 # 1823 # 2173 # 1 # ID=1_2;partial=00;start_type=ATG;rbs_motif=GGA/GAG/AGG;rbs_spacer=5-10bp;gc_cont=0.311

MKQNRKEFSSYFSRSIKQNKPLYLLLMSSETNPF PRPVIGTFRGYVEENKIIIGEDSYSI

.... ...

and i want to edit the header lines as just a simple number count:

MNLTFDYTKEPSRDVLCIDVKSFYASVECVERG LDPLKTMLVVMSNSENSGGLVLAASPM

MKQNRKEFSSYFSRSIKQNKPLYLLLMSSETNPF PRPVIGTFRGYVEENKIIIGEDSYSI

.... ...

may be it's a too simple questions, but I only started to learn perl and got stuck..

thanks in advance..

Comment on file header change

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Re: file header change by tmharish (Friar) on Feb 05, 2013 at 09:52 UTC
Where exactly are you stuck? Did you manage to open the file Can you print the contents of the file from your script Assuming that you can, all you need is: `if( $line =~ />contig_(\d+)\s/ ) { print ">$1\n"; } else { print "$lin +e\n"; }` [download]	[reply] [d/l]
Re^2: file header change by utpalmtbi (Acolyte) on Feb 05, 2013 at 10:30 UTC
thanks tmharish.. i used the following, but its not working.. : `use strict; use warnings; sub read_file { my( $filename ) = <STDIN>; my @lines; sub read_file { my( $filename ) = <STDIN>; my @lines; open( FILE, "< $filename" ) or die "Can't open $filename : $!" +; { if( @line =~ />contig_(\d+)\s/ ) { print ">$1\n"; } else { print "$line\n"; } }` [download] :-(	[reply] [d/l]
Re^3: file header change by tmharish (Friar) on Feb 05, 2013 at 10:42 UTC
, but its not working.. I am not surprised. Why do you have the same function defined twice? The second time inside the first?? Create two functions, one to get the file name and the other to read the file, modify the contents and print it CALL the functions And finally try to run your code and get rid of the syntax errors.	[reply]
Re^4: file header change by utpalmtbi (Acolyte) on Feb 05, 2013 at 11:20 UTC
Re: file header change by Anonymous Monk on Feb 05, 2013 at 09:50 UTC
may be it's a too simple questions, but I only started to learn perl and got stuck.. Great, show your code	[reply]
Re^2: file header change by utpalmtbi (Acolyte) on Feb 05, 2013 at 10:20 UTC
sorry for the previous post: `use strict; use warnings; sub read_file { my( $filename ) = <STDIN>; my @lines; sub read_file { my( $filename ) = <STDIN>; my @lines; open( FILE, "< $filename" ) or die "Can't open $filename : $!" +; { if( @line =~ />contig_(\d+)\s/ ) { print ">$1\n"; } else { print "$line\n"; } }` [download]	[reply] [d/l]
Re^3: file header change by Anonymous Monk on Feb 05, 2013 at 11:27 UTC
Um, wow, what tutorial are you reading? I suggest starting with perlintro , esp Files and I/O and Simple matching and perlfaq4#How do I find the first array element for which a condition is true? perlfaq4#How do I process/modify each element of an array? perlfaq5#How do I change, delete, or insert a line in a file, or append to the beginning of a file? Re: split line from one point Write to existing file with character insert I also reccomend you read Tutorials: Context tutorial, because an array in scalar context returns the number of elements in the array -- not that you need an array for this task, because you don't, as all the examples above show Also download a copy of Modern Perl and use it as a reference and see also http://perl-tutorial.org/	[reply]
Re^2: file header change by utpalmtbi (Acolyte) on Feb 05, 2013 at 10:17 UTC
use strict; use warnings; sub read_file { my( $filename ) = <STDIN>; my @lines; sub read_file { my( $filename ) = <STDIN>; my @lines; open( FILE, "< $filename" ) or die "Can't open $filename : $!"; { if( @line =~ />contig_(\d+)\s/ ) { print ">$1\n"; } else { print "$line\n"; } }	[reply]
Re: file header change by newbie1991 (Acolyte) on Feb 05, 2013 at 10:23 UTC
This might not be the most efficient way but it is easy to understand : I am assuming you are working with several pep files, so you read the input into an array. You can split this array at the '>' with the split function, this way each of the proteins gets their own element. To manipulate this further you can split each element into multiple lines by splitting at the \n. Now, your protein info will be in the [0]th element of the array, and you can manipulate it however you want. The 1, 2, 3 will be an incrementing counter. Like I said, not the most elegant, but it's a simple enough method that I've used. Glad if it helps. :)	[reply]
Re: file header change by Kenosis (Priest) on Feb 05, 2013 at 15:26 UTC
Try the following: `use strict; use warnings; my $i = 1; while (<>) { s/>\K.+/$i++/e; print; }` [download] Output from your data: `>1 MNLTFDYTKEPSRDVLCIDVKSFYASVECVERG LDPLKTMLVVMSNSENSGGLVLAASPM >2 MKQNRKEFSSYFSRSIKQNKPLYLLLMSSETNPF PRPVIGTFRGYVEENKIIIGEDSYSI` [download] Usage: `perl script.pl inFile >outFile` As the fasta `inFile` is read line-by-line, the regex will substitute all past the `>` with the value of `$i`. The `>outFile` notation directs the `print`ing to the file `outFile`. Hope this helps!	[reply] [d/l] [select]
Re^2: file header change by utpalmtbi (Acolyte) on Feb 05, 2013 at 16:36 UTC
it works.. thank u very much..	[reply]
Re^3: file header change by Kenosis (Priest) on Feb 05, 2013 at 17:07 UTC
You're most welcome, utpalmtbi!	[reply]