{"action":"created","issue":{"url":"https://api.github.com/repos/bioperl/bioperl-live/issues/117","labels_url":"https://api.github.com/repos/bioperl/bioperl-live/issues/117/labels{/name}","comments_url":"https://api.github.com/repos/bioperl/bioperl-live/issues/117/comments","events_url":"https://api.github.com/repos/bioperl/bioperl-live/issues/117/events","html_url":"https://github.com/bioperl/bioperl-live/issues/117","id":92376485,"number":117,"title":"File open for 'command |' not working","user":{"login":"nds","id":681476,"avatar_url":"https://avatars.githubusercontent.com/u/681476?v=3","gravatar_id":"","url":"https://api.github.com/users/nds","html_url":"https://github.com/nds","followers_url":"https://api.github.com/users/nds/followers","following_url":"https://api.github.com/users/nds/following{/other_user}","gists_url":"https://api.github.com/users/nds/gists{/gist_id}","starred_url":"https://api.github.com/users/nds/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nds/subscriptions","organizations_url":"https://api.github.com/users/nds/orgs","repos_url":"https://api.github.com/users/nds/repos","events_url":"https://api.github.com/users/nds/events{/privacy}","received_events_url":"https://api.github.com/users/nds/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-07-01T13:01:37Z","updated_at":"2015-07-01T13:20:17Z","closed_at":"2015-07-01T13:20:17Z","body":"In older versions of Bio/Root/IO.pm the following line was used to open files:\r\n\r\nopen ($fh,$file) || $self->throw(\"Could not open $file: $!\");\r\n\r\nIn newer versions, the following line is used with $mode defaulting to \"<\".\r\n\r\nopen $fh, $mode, $file or $self->throw(\"Could not $action file '$file': $!\");\r\n\r\nSo, for example, when we use:\r\n\r\n$fastq_obj =  Bio::SeqIO->new( -file => \"gunzip -c myfile.gz |\" , -format => 'Fastq');\r\n\r\nThis becomes:\r\n\r\nopen $fh, '<', 'gunzip -c myfile.gz |'\r\n\r\ncausing the following error:\r\n\r\nCould not read file 'gunzip -c myfile.gz |': No such file or directory"},"comment":{"url":"https://api.github.com/repos/bioperl/bioperl-live/issues/comments/117670381","html_url":"https://github.com/bioperl/bioperl-live/issues/117#issuecomment-117670381","issue_url":"https://api.github.com/repos/bioperl/bioperl-live/issues/117","id":117670381,"user":{"login":"nds","id":681476,"avatar_url":"https://avatars.githubusercontent.com/u/681476?v=3","gravatar_id":"","url":"https://api.github.com/users/nds","html_url":"https://github.com/nds","followers_url":"https://api.github.com/users/nds/followers","following_url":"https://api.github.com/users/nds/following{/other_user}","gists_url":"https://api.github.com/users/nds/gists{/gist_id}","starred_url":"https://api.github.com/users/nds/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/nds/subscriptions","organizations_url":"https://api.github.com/users/nds/orgs","repos_url":"https://api.github.com/users/nds/repos","events_url":"https://api.github.com/users/nds/events{/privacy}","received_events_url":"https://api.github.com/users/nds/received_events","type":"User","site_admin":false},"created_at":"2015-07-01T13:20:17Z","updated_at":"2015-07-01T13:20:17Z","body":"There are some examples in the documentation showing the use of 'command |' like in http://www.bioperl.org/wiki/HOWTO:SeqIO but I agree that passing commands into -file can get really messy. I've fixed this usage on our end. Thank you for responding so quickly."}}