Re^3: How to avoid using array in concatenating string of multiple lines

Running the while loop

while( my $seq = $in->next_seq  ) {
      print $i++, " : ", $seq->seq(), "\n";
   }
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will read until the end of the filehandle. (That is why the loop ended in the first place). So subsequently calling next_seq on the $in object will give you the error mesg you are seeing. You can

open SeqIO object outside of trial loop, and put seek(INFILE,0) inside the loop. Note that if the SeqIO object gets destroyed (or goes out of scope), you will need to add the flag -noclose => 1 option when initing the SeqIO object or else the filehandle is closed. But if you are going to do this, just move the initialization of the SeqIO object outside the loop.
re-open the file each time in the list (move the Bio::SeqIO initialization into the trial loop)

Or read all the sequences in at once and keep them in memory. (put them into an array).

my @seqs; 
while(my $s = $in->next_seq ) { push @seqs, $s; }
# now do your loop of trials
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#3 might not work depending on how many sequences and how big they are.

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Re^4: How to avoid using array in concatenating string of multiple lines by monkfan (Curate) on Dec 11, 2004 at 05:29 UTC
stajich: you will need to add the flag -noclose => 1 option when initing the SeqIO object or else the filehandle is closed. But if you are going to do this, just move the initialization of the SeqIO object outside the loop. Thanks stajich, it works ok now. But it will work with just adding the -noclose=>1 flag. So this will just work fine: `#!/usr/bin/perl -w use strict; use Bio::SeqIO; my $file = $ARGV[0]; open INFILE, "<$file" or die "$0: Can't open file $file: $!"; for (my $trial = 1; $trial <=2; $trial++) { seek(INFILE,0,0); print "Trial $trial\n"; my $i =1; my $in = Bio::SeqIO->new(-format => 'fasta', -noclose => 1, -fh => +\*INFILE); while( my $seq = $in->next_seq() ) { print $i++, " : ", $seq->seq(), "\n"; } }` [download] I don't understand why we still need to move the initialization of the seqIO outside the loop? Regards, Edward PS: BTW, I can't find any documentation of the -noclose flag in Bio::SeqIO perldoc. Where can I find that?	[reply] [d/l]
Re^5: How to avoid using array in concatenating string of multiple lines by stajich (Chaplain) on Dec 12, 2004 at 15:32 UTC
I don't understand why we still need to move the initialization of the seqIO outside the loop? Well did you try it.... You can write it this way since there is no need to initialize the SeqIO object each time since you are resetting the filehandle. I expect it is a miniscule performance different. `#!/usr/bin/perl -w use strict; use Bio::SeqIO; my $file = $ARGV[0]; open INFILE, "<$file" or die "$0: Can't open file $file: $!"; my $in = Bio::SeqIO->new(-format => 'fasta', -noclose => 1, -fh => \*INFILE); for (my $trial = 1; $trial <=2; $trial++) { seek(INFILE,0,0); print "Trial $trial\n"; my $i =1; while( my $seq = $in->next_seq() ) { print $i++, " : ", $seq->seq(), "\n"; } }` [download] As for the -noclose option, Bio::SeqIO ISA Bio::Root::IO so see the documenation for that module. Unfortunately perldoc does not allow one to pull in documentation from inherited modules so you have to read around to get the full list. The Pdoc generated documentation at our site doc.bioperl.org does have links up the inheritance hierarchy so you read the docs for the superclasses. So anything you can do with a Bio::Root::IO you can do with a Bio::SeqIO object. All the other Bio::XXIO modules also inherit from Bio::Root::IO.	[reply] [d/l]