Re^2: While loop with nested if statements

I've added an example of the input and output to my original post, and my code is currently looking like this, but again I am still not sure I am using the hash correctly, and the hash key is really throwing me. I'm not getting any errors with this code, but my output file is empty

#!/usr/bin/perl
use warnings;
use strict;
use diagnostics;

open( INFILE, "<", 'myosin.fasta') or die $!; #open original myosin.fa
+sta for reading
open( OUTFILE, ">", 'modifiedHeaders.fasta') or die $!; #open/create n
+ew fasta for writing

my %headerHash; #create hash for the header
my $seq;
my $header;

#loop through old file 
while (<INFILE>){
        chomp;
        my $line = $_;
# use if/then to seperate headers from seq, while regex to select only
+ species name in header
                if ($line =~ /^>/){
                 $header = $line;
                        if ($header =~ /(>gi.*)\[(.+)\](>g.*)\[(.+)\]/
+){
                                my $headerHash = $2;
                                $headerHash{$2} = $2;
}
                        }
                else {
                 $seq = $line;

        }
}
close INFILE;
for my $key(keys %headerHash){

print OUTFILE $headerHash{$key}, "\n", $seq, "\n";
}
[download]

Comment on Re^2: While loop with nested if statements Download Code

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Re^3: While loop with nested if statements by Marshall (Canon) on Apr 03, 2016 at 18:00 UTC
I still see multiple problems. Can you show what you expect the output lines to be? I guess there is some input now on the OP. I get now: Global symbol "$headerHash" requires explicit package name at C:\Proje +cts_Perl\anotherfastathing.pl line 30. Execution of C:\Projects_Perl\anotherfastathing.pl aborted due to comp +ilation errors (#1) (F) You've said "use strict" or "use strict vars", which indicates + that all variables must either be lexically scoped (using "my" or +"state"), declared beforehand using "our", or explicitly qualified to say which package the global variable is in (using "::"). Uncaught exception from user code: Global symbol "$headerHash" requires explicit package name at C:\P +rojects_Perl\anotherfastathing.pl line 30. Execution of C:\Projects_Perl\anotherfastathing.pl aborted due to +compilation errors. Process completed with exit code 255 [download] Update: Ok, this looks like what you want, why not? #!/usr/bin/perl use warnings; use strict; use diagnostics; my $firstline = <DATA>; my ($species) = $firstline =~ /\[(.+?)\]/; print "$species\n"; while (<DATA>) {print;} =Prints: Homo sapiens MSSDSEMAIFGEAAPFLRKSERERIEAQNKPFDAKTSVFVVDPKESFVKATVQSREGGKVTAKTEAGATV +TVKDDQVFPM NPPKYDKIEDMAMMTHLHEPAVLYNLKERYAAWMIYTYSGLFCVTVNPYKWLPVYNAEVVTAYRGKKRQE +APPHIFSISD NAYQFMLTDRENQSILITGESGAGKTVNTKRVIQYFATIAVTGEKKKEEVTSGKMQGTLEDQIISANPLL +EAFGNAKTVR NDNSSRFGKFIRIHFGTTGKLASADIETYLLEKSRVTFQLKAERSYHIFYQIMSNKKPDLIEMLLITTNP +YDYAFVSQGE ITVPSIDDQEELMATDSAIEILGFTSDERVSIYKLTGAVMHYGNMKFKQKQREEQAEPDGTEVADKAAYL +QNLNSADLLK ALCYPRVKVGNEYVTKGQTVQQVYNAVGALAKAVYDKMFLWMVTRINQQLDTKQPRQYFIGVLDIAGFEI +FDFNSLEQLC INFTNEKLQQFFNHHMFVLEQEEYKKEGIEWTFIDFGMDLAACIELIEKPMGIFSILEEECMFPKATDTS +FKNKLYEQHL GKSNNFQKPKPAKGKPEAHFSLIHYAGTVDYNIAGWLDKNKDPLNETVVGLYQKSAMKTLALLFVGATGA +EAEAGGGKKG GKKKGSSFQTVSALFRENLNKLMTNLRSTHPHFVRCIIPNETKTPGAMEHELVLHQLRCNGVLEGIRICR +KGFPSRILYA =cut __DATA__ >gi\|115527082\|ref\|NP_005954.3\| myosin-1 [Homo sapiens] >gi\|226694176\|s +p\|P12882.3\|MYH1_HUMAN RecName: Full=Myosin-1; AltName: Full=Myosin he +avy chain 1; AltName: Full=Myosin heavy chain 2x; Short=MyHC-2x; AltN +ame: Full=Myosin heavy chain IIx/d; Short=MyHC-IIx/d; AltName: Full=M +yosin heavy chain, skeletal muscle, adult 1 [Homo sapiens] >gi\|119610 +411\|gb\|EAW90005.1\| hCG1986604, isoform CRA_b MSSDSEMAIFGEAAPFLRKSERERIEAQNKPFDAKTSVFVVDPKESFVKATVQSREGGKVTAKTEAGATV +TVKDDQVFPM NPPKYDKIEDMAMMTHLHEPAVLYNLKERYAAWMIYTYSGLFCVTVNPYKWLPVYNAEVVTAYRGKKRQE +APPHIFSISD NAYQFMLTDRENQSILITGESGAGKTVNTKRVIQYFATIAVTGEKKKEEVTSGKMQGTLEDQIISANPLL +EAFGNAKTVR NDNSSRFGKFIRIHFGTTGKLASADIETYLLEKSRVTFQLKAERSYHIFYQIMSNKKPDLIEMLLITTNP +YDYAFVSQGE ITVPSIDDQEELMATDSAIEILGFTSDERVSIYKLTGAVMHYGNMKFKQKQREEQAEPDGTEVADKAAYL +QNLNSADLLK ALCYPRVKVGNEYVTKGQTVQQVYNAVGALAKAVYDKMFLWMVTRINQQLDTKQPRQYFIGVLDIAGFEI +FDFNSLEQLC INFTNEKLQQFFNHHMFVLEQEEYKKEGIEWTFIDFGMDLAACIELIEKPMGIFSILEEECMFPKATDTS +FKNKLYEQHL GKSNNFQKPKPAKGKPEAHFSLIHYAGTVDYNIAGWLDKNKDPLNETVVGLYQKSAMKTLALLFVGATGA +EAEAGGGKKG GKKKGSSFQTVSALFRENLNKLMTNLRSTHPHFVRCIIPNETKTPGAMEHELVLHQLRCNGVLEGIRICR +KGFPSRILYA [download]	[reply] [d/l] [select]
Re^4: While loop with nested if statements by v15 (Sexton) on Apr 04, 2016 at 05:57 UTC
`#!/usr/bin/perl-w use strict; use warnings; my %hash=(); my $key = ''; while(<>){ chomp; if($_ =~ /^>gi.\[(.+)\]\s>gi./){ $key = $1; }else{ $hash{$key} .= $_; } } foreach(keys %hash){ print join("\n",$_,$hash{$_}),"\n"; }` [download] This does what you need	[reply] [d/l]