get SeqIO working again as well

cjfields · Aug 10, 2015 · 0055530 · 0055530
1 parent d3cdcd9
commit 0055530
Show file tree

Hide file tree

Showing 3 changed files with 7 additions and 5 deletions.
diff --git a/lib/Bio/Role/IO.pm6 b/lib/Bio/Role/IO.pm6
@@ -5,7 +5,7 @@ use Bio::Role::Temp;
 role Bio::Role::IO does Bio::Role::Temp {
 
     # TODO: not sure we need to curry everything here, but list of methods is a rakudo bug
-    has IO::Handle $.fh; # handles IO::Handle;
+    has IO::Handle $.fh;
 
     # At the moment we force all IO consumers to initialize-io if they have this
     # simple signature

diff --git a/lib/Bio/SeqIO.pm6 b/lib/Bio/SeqIO.pm6
@@ -6,7 +6,7 @@ use Bio::Role::IO;
 
 class Bio::SeqIO does Bio::Role::Pluggable['SeqIO']
                  does Bio::Role::RecordFormat
-                 does Bio::Role::IO
+                 #does Bio::Role::IO
                  {
 
     has $!plugin handles <next-Seq write-Seq>;

diff --git a/lib/Bio/SeqIO/fasta.pm6 b/lib/Bio/SeqIO/fasta.pm6
@@ -1,6 +1,7 @@
 use v6;
 
 use Bio::Role::SeqStream;
+use Bio::Role::IO;
 use Bio::Grammar::Fasta;
 use Bio::PrimarySeq;
 
@@ -14,7 +15,7 @@ class Bio::Grammar::Fasta::Actions::PrimarySeq {
     }
 }
 
-class Bio::SeqIO::fasta does Bio::Role::SeqStream {
+class Bio::SeqIO::fasta does Bio::Role::SeqStream does Bio::Role::IO {
     has $.buffer  is rw;
     has $!actions = Bio::Grammar::Fasta::Actions::PrimarySeq.new();
     has $.width = 60;
@@ -30,9 +31,9 @@ class Bio::SeqIO::fasta does Bio::Role::SeqStream {
     # time; two future optimizations require implementation in Rakudo:
     # 1) Chunking in IO::Handle using nl => "\n>"
     # 2) Grammar parsing of a stream of data (e.g. Cat), which is now considered
-    # a close post-6.0 update
+    #    a post-6.0 update
     method !chunkify {
-        return if $.eof();
+        return if $.fh.eof();
         my $current_record;
         while $.fh.get -> $line {
             if $.buffer {
@@ -49,6 +50,7 @@ class Bio::SeqIO::fasta does Bio::Role::SeqStream {
             } else {
                 $current_record ~= $line;
             }
+            say "record: $current_record";
         }
         return $current_record;
     };