From MAILER-DAEMON@bioruby.org Sun Dec 11 13:02:00 2005 Return-Path: <> Delivered-To: ktym@hgc.jp Received: (qmail 25529 invoked from network); 11 Dec 2005 13:02:42 +0900 Received: from localhost (HELO agari) (127.0.0.1) by localhost with SMTP; 11 Dec 2005 13:02:41 +0900 Received: from eforward2.name-services.com (eforward2.name-services.com [216.52.184.242]) by agari (Postfix) with ESMTP id 3EDEDFF93F for ; Sun, 11 Dec 2005 13:02:41 +0900 (JST) Received: from c9mailgw24.amadis.com ([216.163.188.221]) by eforward2.name-services.com with Microsoft SMTPSVC(6.0.3790.211); Sat, 10 Dec 2005 20:03:21 -0800 Received: from kumamushi.bioruby.org (asf-cable.c-able.ne.jp [218.223.192.34]) by c9mailgw24.amadis.com (Postfix) with ESMTP id 6249A110550 for ; Sat, 10 Dec 2005 19:47:49 -0800 (PST) Received: by kumamushi.bioruby.org (Postfix) id 802D8212031; Sun, 11 Dec 2005 13:02:03 +0900 (JST) Date: Sun, 11 Dec 2005 13:02:03 +0900 (JST) From: MAILER-DAEMON@bioruby.org (Mail Delivery System) Subject: Undelivered Mail Returned to Sender To: k@bioruby.org MIME-Version: 1.0 Message-Id: <20051211040203.802D8212031@kumamushi.bioruby.org> X-CTCH-RefID: str=0001.0A090216.439BA4B2.0080,ss=1,fgs=0 X-CTASD-IP: 218.223.192.34 X-CTASD-Sender: MAILER-DAEMON@bioruby.org x-ctasd:uncategorized x-ctasd-vod:uncategorized X-OriginalArrivalTime: 11 Dec 2005 04:03:22.0069 (UTC) FILETIME=[D3BF6850:01C5FE07] Content-Type: multipart/report; report-type=delivery-status; boundary="16A5D21202D.1134273723/kumamushi.bioruby.org" Content-Length: 4842 This is a MIME-encapsulated message. --16A5D21202D.1134273723/kumamushi.bioruby.org Content-Description: Notification Content-Type: text/plain This is the Postfix program at host kumamushi.bioruby.org. I'm sorry to have to inform you that your message could not be be delivered to one or more recipients. It's attached below. For further assistance, please send mail to If you do so, please include this problem report. You can delete your own text from the attached returned message. The Postfix program : host mail.corevx.com[207.7.108.149] said: 554 Service unavailable; Client host [218.223.192.34] blocked using sbl-xbl.spamhaus.org; http://www.spamhaus.org/query/bl?ip=218.223.192.34 (in reply to RCPT TO command) --16A5D21202D.1134273723/kumamushi.bioruby.org Content-Description: Delivery report Content-Type: message/delivery-status Reporting-MTA: dns; kumamushi.bioruby.org X-Postfix-Queue-ID: 16A5D21202D X-Postfix-Sender: rfc822; k@bioruby.org Arrival-Date: Sun, 11 Dec 2005 13:02:01 +0900 (JST) Final-Recipient: rfc822; trevor@corevx.com Action: failed Status: 5.0.0 Diagnostic-Code: X-Postfix; host mail.corevx.com[207.7.108.149] said: 554 Service unavailable; Client host [218.223.192.34] blocked using sbl-xbl.spamhaus.org; http://www.spamhaus.org/query/bl?ip=218.223.192.34 (in reply to RCPT TO command) --16A5D21202D.1134273723/kumamushi.bioruby.org Content-Description: Undelivered Message Content-Type: message/rfc822 Received: from [127.0.0.1] (localhost [127.0.0.1]) by kumamushi.bioruby.org (Postfix) with ESMTP id 16A5D21202D; Sun, 11 Dec 2005 13:02:01 +0900 (JST) In-Reply-To: <20051211035957.783A121201C@kumamushi.bioruby.org> References: <20051211035957.783A121201C@kumamushi.bioruby.org> Mime-Version: 1.0 (Apple Message framework v746.2) Content-Type: text/plain; charset=ISO-2022-JP Message-Id: <6AEE9C5C-5759-4F4D-B3F1-3B1834C8FBC3@bioruby.org> Content-Transfer-Encoding: 7bit From: Toshiaki Katayama Subject: Re: Bio::NucleicAcid na.rb to_re bug (Re: Undelivered Mail Returned to Sender) Date: Sun, 11 Dec 2005 13:02:00 +0900 To: Trevor Wennblom X-Mailer: Apple Mail (2.746.2) Trevor, Please accept this mail. :) Toshiaki On 2005/12/11, at 12:59, Mail Delivery System wrote: > This is the Postfix program at host kumamushi.bioruby.org. > > I'm sorry to have to inform you that your message could not be > be delivered to one or more recipients. It's attached below. > > For further assistance, please send mail to > > If you do so, please include this problem report. You can > delete your own text from the attached returned message. > > The Postfix program > > : host mail.corevx.com[207.7.108.149] said: 554 Service > unavailable; Client host [218.223.192.34] blocked using > sbl-xbl.spamhaus.org; http://www.spamhaus.org/query/bl?ip=218.223.192.34 > (in reply to RCPT TO command) > Reporting-MTA: dns; kumamushi.bioruby.org > X-Postfix-Queue-ID: 511DB212019 > X-Postfix-Sender: rfc822; k@bioruby.org > Arrival-Date: Sun, 11 Dec 2005 12:59:46 +0900 (JST) > > Final-Recipient: rfc822; trevor@corevx.com > Action: failed > Status: 5.0.0 > Diagnostic-Code: X-Postfix; host mail.corevx.com[207.7.108.149] said: 554 > Service unavailable; Client host [218.223.192.34] blocked using > sbl-xbl.spamhaus.org; http://www.spamhaus.org/query/bl?ip=218.223.192.34 > (in reply to RCPT TO command) > > From: Toshiaki Katayama > Date: 2005年12月11日 12:59:44:JST > To: Trevor Wennblom > Subject: Re: Bio::NucleicAcid na.rb to_re bug > > > Trevor, > > To embed all possible combinations would be most efficient, after all... > > def to_re(seq, rna = false) > replace = { > 'y' => '[tcy]', > 'r' => '[agr]', > 'w' => '[atw]', > 's' => '[gcw]', > 'k' => '[tgk]', > 'm' => '[acm]', > 'b' => '[tgcyskb]', > 'd' => '[atgrwkd]', > 'h' => '[atcwmyh]', > 'v' => '[agcmrsv]', > 'n' => '[atgcyrwskmbdhvn]' > } > > str = seq.to_s > str.gsub!(/[^atgcu]/) { |base| > replace[base] || base > } > if rna > str.tr!("t", "u") > end > Regexp.new(str) > end > > Toshiaki > > On 2005/12/11, at 3:34, Trevor Wennblom wrote: > >> Toshiaki Katayama wrote: >> >>> And the below is a ad-hoc implementation to include all possible combination of the ambiguous bases. >>> I removed brackets and sorted the bases contained in the ambiguous bases for easier implementation... >>> >> >> >> Great, I'll try to play with the ad-hoc code later this week. >> >> Thanks again for all your help Toshiaki! >> Trevor > > > --16A5D21202D.1134273723/kumamushi.bioruby.org--