[Bioperl-l] writing sequences to a file

Mon, 22 Oct 2001 15:59:34 -0700

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Spinoff from an earlier post...
Per Seq::IO, I'm using
$stream =3D Bio::SeqIO->newFh(-file =3D> ">$output";
...
print $stream $seq;
to write to my $output file once retrieved from a local db.  How do I =
also write the (FASTA formatted) names of these sequences?  Previously =
(as in BLAST parsing) I had used:
open(OUT, ">$output);
...
print OUT ">",$hit->name;
But combining the parsing and retrieval scripts (i.e. mixing print OUT =
with the print $stream $seq above doesn't give the desired output of a =
nicely formatted file).

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<DIV><FONT face=3DArial size=3D2>Spinoff from an earlier =
post...</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>Per Seq::IO, I'm using</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>$stream =3D Bio::SeqIO-&gt;newFh(-file =
=3D&gt;=20
"&gt;$output";</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>...</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>print $stream $seq;</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>to write to my $output file once =
retrieved from a=20
local db.&nbsp; How do I also write the (FASTA formatted) names of these =

sequences?&nbsp; Previously (as&nbsp;in BLAST parsing) I had =
used:<BR>open(OUT,=20
"&gt;$output);</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>...</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>print OUT =
"&gt;",$hit-&gt;name;</FONT></DIV>
<DIV><FONT face=3DArial size=3D2>But combining the parsing and retrieval =
scripts=20
(i.e. mixing&nbsp;print OUT with the print $stream&nbsp;$seq above =
doesn't give=20
the desired output of a nicely formatted file).</FONT></DIV>
<DIV>&nbsp;</DIV>
<DIV>&nbsp;</DIV></BODY></HTML>

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