Split a multi-sequence file into individual files

[ela]

From google, no need to reinvent the wheel but this one line code is too
difficult to understand...

perl -ne 'BEGIN{ $/=">"; } if(/^\s*(\S+)/){ open(F,">$1.fsa")||warn"$1 write
failed:$!\n";chomp;print F ">", $_ }' fastafile

anybody helps?

 

[Tad J McClellan]

From google, no need to reinvent the wheel but this one line code is too
difficult to understand...

perl -ne 'BEGIN{ $/=">"; } if(/^\s*(\S+)/){ open(F,">$1.fsa")||warn"$1 write
failed:$!\n";chomp;print F ">", $_ }' fastafile

anybody helps?

BEGIN{ $/=">"; } # set the Input Record Separator (perlvar.pod)
while ( <> ) { # -n wraps in a while-diamond loop
if( /^\s*(\S+)/ ){ # grab the first non-whitespace characters
open(F,">$1.fsa") || warn"$1 write failed:$!\n"; # open a file
chomp; # remove ">" from end of string
print F ">", $_; # print ">" at beginning of string
}
}

 

[Mirco Wahab]

BEGIN{ $/=">"; } # set the Input Record Separator (perlvar.pod)
while ( <> ) { # -n wraps in a while-diamond loop
if( /^\s*(\S+)/ ){ # grab the first non-whitespace characters
open(F,">$1.fsa") || warn"$1 write failed:$!\n"; # open a file
chomp; # remove ">" from end of string
print F ">", $_; # print ">" at beginning of string
}
}

I don't understand the purpose of the chomp,
maybe it needs to be in front of the if():

...
local $/ = '>';
while (<>) {
chomp;
if( /\s*(\S+)/ ) {
open my $fh, '>', "$1.fsa" or warn "$1 $!";
print $fh '>'.$_
}
}
...

Regards

M.

 

[Tim Greer]

I don't understand the purpose of the chomp,
maybe it needs to be in front of the if():

...
local $/ = '>';
while (<>) {
chomp;
if( /\s*(\S+)/ ) {
open my $fh, '>', "$1.fsa" or warn "$1 $!";
print $fh '>'.$_
}
}
...

Regards

M.

perldoc -f chomp

Chomp removes any newline, if one exists (which it probably would on
<>).

It's the difference between (trying to) opening:
$1.fsa

and

$1
..fsa

 

[Tim Greer]

perldoc -f chomp

Chomp removes any newline, if one exists

Pardon... to be clear, it removes the new line at the end of the string
(not just any new line).

 

[Mirco Wahab]

perldoc -f chomp

Chomp removes any newline, if one exists (which it probably would on
<>).

No, it doesn't. It removes the $/, which is
here the '>'.

It's the difference between (trying to) opening:
$1.fsa

and

$1
.fsa

No way. In the above problem, it would on the
first record get the '>' in $1, which leads
to an open argument of ">>.fsa" which
creates a file '.fsa' that contains noting.

Regards

M.

 

[Tim Greer]

No, it doesn't. It removes the $/, which is
here the '>'.

My newsreader is interpreting / / and <> for some reason (and I'm not
seeing what I should be seeing), so I didn't see all of the code for
what it was, I guess. I saw while (<>) { chomp; ... } and hence my
reply. Disregard if it wasn't relevant after all.

 

[xhoster]

I don't understand the purpose of the chomp,

It is to remove the trailing ">", which is not wanted. In FASTA sequence
files, ">" is start of the next record, not the end of the current one.

maybe it needs to be in front of the if():

I don't see how that would make a difference. If the if fails, nothing
happens anyway. If the if succeeds, it makes no difference if the chomp
is done before or after.

Ah, but if the file starts out with the first character of ">", (which it
probably does) then the first record contains nothing but $/. By not
chomping the conditional is true you litter your file system with invisible
(on linux) empty files named .fsa. If you do chomp, the conditional is
false and nothing happens, which is what one wants. So yes, the chomp
should be before the if.


Xho

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