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From biopython-bugs at bioperl.org Wed Apr 2 13:16:31 2003 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] Notification: incoming/129 Message-ID: <200304021816.h32IGVRN018192@pw600a.bioperl.org> JitterBug notification new message incoming/129 Message summary for PR#129 From: "Eloy Hobbs" Subject: baw ynteger Date: Wed, 02 Apr 03 19:26:14 GMT 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From cpgkaqfc0@aol.com Wed Apr 2 13:16:22 2003 Received: from pool-151-201-26-2.pitt.east.verizon.net (pool-151-201-26-2.pitt.east.verizon.net [151.201.26.2]) by pw600a.bioperl.org (8.12.6/8.12.6) with SMTP id h32IG5RN018177; Wed, 2 Apr 2003 13:16:12 -0500 Received: from [209.252.217.90] by pool-151-201-26-2.pitt.east.verizon.net with SMTP; Wed, 02 Apr 2003 19:26:14 +0100 Message-ID: <0tpr$173f1-250b56-j@xbp.6e6.ek> From: "Eloy Hobbs" To: admin@bioperl.org Subject: baw ynteger Date: Wed, 02 Apr 03 19:26:14 GMT X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: The Bat! (v1.52f) Business MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="CF.B._2.A8516D.2BDEC" X-Spam-Status: No X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) This is a multi-part message in MIME format. --CF.B._2.A8516D.2BDEC Content-Type: text/html Content-Transfer-Encoding: quoted-printable

Hey how have you been?

--CF.B._2.A8516D.2BDEC-- From biopython-bugs at bioperl.org Wed Apr 2 22:41:29 2003 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] Notification: incoming/130 Message-ID: <200304030341.h333fTRN021454@pw600a.bioperl.org> JitterBug notification new message incoming/130 Message summary for PR#130 From: "" Subject: FW: RE: UNLOCK PPV from your Digital _Cable Box lwiuda u et eyqljz Date: Wed, 02 Apr 03 22:20:46 GMT 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From jpm@thefoxpro.prestel.co.uk Wed Apr 2 22:41:28 2003 Received: from INTI2002 ([200.72.60.98]) by pw600a.bioperl.org (8.12.6/8.12.6) with SMTP id h333f8RN021443; Wed, 2 Apr 2003 22:41:16 -0500 Received: from bog4l1up [127.231.58.122] by INTI2002 with ESMTP id HYNFCHCB; Wed, 02 Apr 03 22:38:46 +0400 Received: from 5q7u...98qf [184.175.39.252] by 127.231.58.122 with ESMTP id WAMTT; Wed, 02 Apr 03 22:20:46 +0400 Message-ID: > From: "" To: , , Subject: FW: RE: UNLOCK PPV from your Digital _Cable Box lwiuda u et eyqljz Date: Wed, 02 Apr 03 22:20:46 GMT X-Priority: 1 X-MSMail-Priority: High X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2910.0) MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="E1BB43D_E._.832" X-Spam-Warning: SpamAssassin says this message is SPAM X-Spam-Status: Yes X-Spam-Report: SPAM: ---- Start SpamAssassin results SPAM: 6.30 hits, 5 required; SPAM: * -0.1 -- Forwarded email (Outlook style) SPAM: * -0.0 -- X-Mailer header indicates a non-spam MUA (Outlook) SPAM: * 1.3 -- From: does not include a real name SPAM: * 0.4 -- Sent with 'X-Priority' set to high SPAM: * 0.4 -- Sent with 'X-Msmail-Priority' set to high SPAM: * 0.0 -- Message-Id is not valid, according to RFC 2822 SPAM: * 0.5 -- BODY: Claims to be Legal SPAM: * 0.3 -- BODY: Asks you to click below SPAM: * 1.3 -- BODY: Spam phrases score is 13 to 21 (high) SPAM: [score: 17] SPAM: * 0.3 -- BODY: Tells you to click on a URL SPAM: * 0.0 -- BODY: Contains a line >=199 characters long SPAM: * 1.4 -- Date: is 3 to 6 hours after Received: date SPAM: * 0.5 -- Message has X-MSMail-Priority, but no X-MimeOLE SPAM: SPAM: ---- End of SpamAssassin results X-Spam-Level: ****** (6.3) X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) This is a multi-part message in MIME format. --E1BB43D_E._.832 Content-Type: text/plain Content-Transfer-Encoding: quoted-printable This is the NEWEST and BEST Digital CATV Filter/PPV Tester that can test y= our digital cable pay-per-view purchase functions and can also eliminate u= nwanted interference caused by your broadband connection. This is a "True"= universal product. It will work on 99% of all digital cable systems in us= e today. This little filter has several different uses: Interference filte= r, PPV tester, and... it is even being sold as a "Digital Descrambler" by = some sites on the net. C= lick here This invaluable little tool is used by technicians on equipment they are r= epairing and testing. When the technician tests the "Buy" button on the re= mote and pay-per-view programming comes into view, confirming reception, t= he technician will then shut off the box so no one can watch the paid prog= ramming and the customer is not billed for the PPV that was ordered since = this device prevents the billing information from being transferred from t= he cable box to the cable company. 1. Are the filters you sell legal? Perfectly Legal. Yes... it is legal to own your own cable descrambling Click here 2. This descrambler is awesome. I've bought others before but either had problems connecting them or they were not compatible with my cable provide= r. I've told all my friends about it, thanks! DM - Des Moines, Iowa Click here 3. By having this device connected to your digital cable box...any and all programming that can be received by pressing the "Buy", "Order" or "Purchase" button on your remote can be viewed without the billing information reaching the cable company. Click here xmuedgsp tv ce y ilyrl --E1BB43D_E._.832-- From biopython-bugs at bioperl.org Fri Apr 4 02:00:53 2003 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] Notification: incoming/131 Message-ID: <200304040700.h3470rRN004361@pw600a.bioperl.org> JitterBug notification new message incoming/131 Message summary for PR#131 From: "Elvira Arellano" Subject: injent princitle Date: Fri, 04 Apr 03 11:05:48 GMT 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From uf30sy30pej@aol.com Fri Apr 4 02:00:51 2003 Received: from evrtwa1-ar8-4-65-016-093.evrtwa1.dsl-verizon.net (evrtwa1-ar8-4-65-016-093.evrtwa1.dsl-verizon.net [4.65.16.93]) by pw600a.bioperl.org (8.12.6/8.12.6) with SMTP id h3470WRN004354; Fri, 4 Apr 2003 02:00:40 -0500 Received: from kl.oodyl31.net [144.128.241.113] by evrtwa1-ar8-4-65-016-093.evrtwa1.dsl-verizon.net; Fri, 04 Apr 2003 11:05:48 +0400 Message-ID: <9li1$$82-399s-g-$xb40$8@37p6q.dkt68x> From: "Elvira Arellano" To: admin@bioperl.org Subject: injent princitle Date: Fri, 04 Apr 03 11:05:48 GMT X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: WorldClient 6.0.7 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="C_DF.D.C0.60.B_F.3D141F" X-Spam-Status: No X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) This is a multi-part message in MIME format. --C_DF.D.C0.60.B_F.3D141F Content-Type: text/html Content-Transfer-Encoding: quoted-printable

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--C_DF.D.C0.60.B_F.3D141F-- From biopython-bugs at bioperl.org Sat Apr 5 23:19:02 2003 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] Notification: incoming/132 Message-ID: <200304060419.h364J2RN020294@pw600a.bioperl.org> JitterBug notification new message incoming/132 Message summary for PR#132 From: movie Subject: =?gb2312?q?=D5=C5=B9=FA=C8=D9=BE=AB=D1=A1=B5=E7=D3=B0=CF=C2=D4=D8?= Date: Sun, 06 Apr 2003 12:21:49 0800 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From movie@263.com Sat Apr 5 23:19:01 2003 Received: from 46.21.47.06 ([218.109.50.45]) by pw600a.bioperl.org (8.12.6/8.12.6) with SMTP id h364IvRN020289 for ; Sat, 5 Apr 2003 23:18:59 -0500 Message-Id: <200304060418.h364IvRN020289@pw600a.bioperl.org> From: movie To: biopython-bugs@bioperl.org Reply-To: movie@263.com Subject: =?gb2312?q?=D5=C5=B9=FA=C8=D9=BE=AB=D1=A1=B5=E7=D3=B0=CF=C2=D4=D8?= Date: Sun, 06 Apr 2003 12:21:49 +0800 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="dd5ddabc-1a37-4fa8-8109-e4136fed9b1e" X-Spam-Status: No X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) This is a multi-part message in MIME format --dd5ddabc-1a37-4fa8-8109-e4136fed9b1e Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: quoted-printable =D5=C5=B9=FA=C8=D9=BE=AB=D1=A1=B5=E7=D3=B0=CF=C2=D4=D8=A3=BA http://www.17sky.com =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D =D5=C5=B9=FA=C8=D9=A1=B6=D2=EC=B6=C8=BF=D5=BC=E4=A1=B7 =D5=C5=B9=FA=C8=D9=A1=B6=D0=C2=C9=CF=BA=A3=C4=D1=A1=B7 =D5=C5=B9=FA=C8=D9=A1=B6=D7=DD=BA=E1=CB=C4=BA=A3=A1=B7 =D5=C5=B9=FA=C8=D9=A1=B6=B0=A2=B7=C9=D5=FD=B4=AB=A1=B7 =D5=C5=B9=FA=C8=D9=A1=B6=B4=BA=B9=E2=D5=A7=D0=B9=A1=B7=A1=AD=A1=AD =C6=E4=CB=FB=B5=E7=D3=B0=CD=C6=BC=F6 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D =A1=B6=B4=F3=BA=E8=C3=D7=B5=EA =A1=B7-----=D6=D0=B9=FA=B5=DA=D2=BB=B2=BF=C7=E9= =D3=FB=C6=AC =A1=B6=B7=D2=C4=DD=B5=C4=CE=A2=D0=A6=A1=B7-----=D6=D0=B9=FA=CA=D7=B2=BF=B3=A4= =C6=AA=B0=AE=C7=E9=BE=DE=C6=AC =A1=B6=D2=B9=C4=A7=CF=C0 =A1=B7 =A1=B6=BF=A8=C0=AD=CA=C7=CC=F5=B9=B7=A1=B7 =A1=B6=C4=A7=BD=E42=A1=B6=CB=AB=CB=FE=C6=E6=B1=F8=A1=B7 =A1=B6=D0=D0=D4=CB=B3=AC=C8=CB=A1=B7 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D =C8=E7=B9=FB=BE=F5=B5=C3=BA=C3=A3=AC=C7=EB=B0=D1=C9=CF=C3=E6=B5=C4=BB=B0=B7=A2= =B8=F8=C4=E3=B5=C410=CE=BBQQ=C9=CF=B5=C4=C5=F3=D3=D1=A3=AC=CE=D2=C3=C7=BD=AB= =B8=D0=D0=BB=C4=FA=B5=C4=D6=A7=B3=D6=A3=A1 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D =C8=E7=B9=FB=D5=E2=B7=E2=D0=C5=B4=F2=C8=C5=C1=CB=C4=FA=A3=AC=C7=EB=CB=FC=CB=FB= =C9=BE=B5=F4=A3=A1 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --dd5ddabc-1a37-4fa8-8109-e4136fed9b1e-- From biopython-bugs at bioperl.org Sat Apr 5 23:45:00 2003 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] Notification: incoming/133 Message-ID: <200304060445.h364j0RN021469@pw600a.bioperl.org> JitterBug notification new message incoming/133 Message summary for PR#133 From: movie Subject: =?gb2312?q?=D5=C5=B9=FA=C8=D9=BE=AB=D1=A1=B5=E7=D3=B0=CF=C2=D4=D8?= Date: Sun, 06 Apr 2003 12:47:46 0800 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From movie@263.com Sat Apr 5 23:44:59 2003 Received: from 46.47.39.06 ([218.109.50.45]) by pw600a.bioperl.org (8.12.6/8.12.6) with SMTP id h364inRN021459 for ; Sat, 5 Apr 2003 23:44:57 -0500 Message-Id: <200304060444.h364inRN021459@pw600a.bioperl.org> From: movie To: biopython-bugs@bioperl.org Reply-To: movie@263.com Subject: =?gb2312?q?=D5=C5=B9=FA=C8=D9=BE=AB=D1=A1=B5=E7=D3=B0=CF=C2=D4=D8?= Date: Sun, 06 Apr 2003 12:47:46 +0800 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="a10c7644-76ef-4859-8f2c-6518214c69c1" X-Spam-Status: No X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) This is a multi-part message in MIME format --a10c7644-76ef-4859-8f2c-6518214c69c1 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: quoted-printable =D5=C5=B9=FA=C8=D9=BE=AB=D1=A1=B5=E7=D3=B0=CF=C2=D4=D8=A3=BA http://www.17sky.com =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D =D5=C5=B9=FA=C8=D9=A1=B6=D2=EC=B6=C8=BF=D5=BC=E4=A1=B7 =D5=C5=B9=FA=C8=D9=A1=B6=D0=C2=C9=CF=BA=A3=C4=D1=A1=B7 =D5=C5=B9=FA=C8=D9=A1=B6=D7=DD=BA=E1=CB=C4=BA=A3=A1=B7 =D5=C5=B9=FA=C8=D9=A1=B6=B0=A2=B7=C9=D5=FD=B4=AB=A1=B7 =D5=C5=B9=FA=C8=D9=A1=B6=B4=BA=B9=E2=D5=A7=D0=B9=A1=B7=A1=AD=A1=AD =C6=E4=CB=FB=B5=E7=D3=B0=CD=C6=BC=F6 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D =A1=B6=B4=F3=BA=E8=C3=D7=B5=EA =A1=B7-----=D6=D0=B9=FA=B5=DA=D2=BB=B2=BF=C7=E9= =D3=FB=C6=AC =A1=B6=B7=D2=C4=DD=B5=C4=CE=A2=D0=A6=A1=B7-----=D6=D0=B9=FA=CA=D7=B2=BF=B3=A4= =C6=AA=B0=AE=C7=E9=BE=DE=C6=AC =A1=B6=D2=B9=C4=A7=CF=C0 =A1=B7 =A1=B6=BF=A8=C0=AD=CA=C7=CC=F5=B9=B7=A1=B7 =A1=B6=C4=A7=BD=E42=A1=B6=CB=AB=CB=FE=C6=E6=B1=F8=A1=B7 =A1=B6=D0=D0=D4=CB=B3=AC=C8=CB=A1=B7 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D =C8=E7=B9=FB=BE=F5=B5=C3=BA=C3=A3=AC=C7=EB=B0=D1=C9=CF=C3=E6=B5=C4=BB=B0=B7=A2= =B8=F8=C4=E3=B5=C410=CE=BBQQ=C9=CF=B5=C4=C5=F3=D3=D1=A3=AC=CE=D2=C3=C7=BD=AB= =B8=D0=D0=BB=C4=FA=B5=C4=D6=A7=B3=D6=A3=A1 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D =C8=E7=B9=FB=D5=E2=B7=E2=D0=C5=B4=F2=C8=C5=C1=CB=C4=FA=A3=AC=C7=EB=CB=FC=CB=FB= =C9=BE=B5=F4=A3=A1 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --a10c7644-76ef-4859-8f2c-6518214c69c1-- From biopython-bugs at bioperl.org Mon Apr 7 07:42:55 2003 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] Notification: incoming/134 Message-ID: <200304071142.h37BgtRN008154@pw600a.bioperl.org> JitterBug notification new message incoming/134 Message summary for PR#134 From: "Oscar Jaramillo" Subject: Prescription Diet Pills, and more prescribed online and shipped overnight Bioperl-l Date: Tue, 08 Apr 03 04:43:15 GMT 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From l62gtt5xze@earthlink.net Mon Apr 7 07:42:48 2003 Received: from ABERLANGA ([195.235.221.195]) by pw600a.bioperl.org (8.12.6/8.12.6) with SMTP id h37BgiRN008138; Mon, 7 Apr 2003 07:42:46 -0400 Received: from dja.5kcdvzl.com ([59.58.44.140]) by ABERLANGA with ESMTP id 19690450 for ; Tue, 08 Apr 2003 04:43:15 +0300 Message-ID: From: "Oscar Jaramillo" To: bioperl-l@bioperl.org Subject: Prescription Diet Pills, and more prescribed online and shipped overnight Bioperl-l Date: Tue, 08 Apr 03 04:43:15 GMT X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="A_1A3B406F.1F60_474C_" X-Spam-Status: No X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) This is a multi-part message in MIME format. --A_1A3B406F.1F60_474C_ Content-Type: text/html Content-Transfer-Encoding: quoted-printable

Did you know you can get prescription medications prescribed online with
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%TO_= NAME --A_1A3B406F.1F60_474C_-- From biopython-bugs at bioperl.org Mon Apr 7 16:19:08 2003 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:21 2005 Subject: [Biopython-dev] Notification: incoming/135 Message-ID: <200304072019.h37KJ8RN010973@pw600a.bioperl.org> JitterBug notification new message incoming/135 Message summary for PR#135 From: "Flossie Madden" Subject: Apply online and re^fina-nce your home today Date: Mon, 07 Apr 03 14:16:41 GMT 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From dv9cwt64@freemail.absa.co.za Mon Apr 7 16:19:07 2003 Received: from ool-18baca72.dyn.optonline.net ([24.186.202.114]) by pw600a.bioperl.org (8.12.6/8.12.6) with SMTP id h37KIvRN010967; Mon, 7 Apr 2003 16:19:04 -0400 Received: from tkfki.mkf1l.net ([131.24.25.98]) by ool-18baca72.dyn.optonline.net id <1075088-74715>; Mon, 07 Apr 2003 14:16:41 -0700 Message-ID: From: "Flossie Madden" To: , , Subject: Apply online and re^fina-nce your home today Date: Mon, 07 Apr 03 14:16:41 GMT X-Mailer: Microsoft Outlook Express 5.00.2919.6700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="E3D_362F1A68.C" X-Priority: 3 X-MSMail-Priority: Normal X-Spam-Warning: SpamAssassin says this message is SPAM X-Spam-Status: Yes X-Spam-Report: SPAM: ---- Start SpamAssassin results SPAM: 5.40 hits, 5 required; SPAM: * 0.9 -- From: ends in numbers SPAM: * 0.3 -- From: contains numbers mixed in with letters SPAM: * 0.2 -- X-Mailer header indicates a non-spam MUA (Outlook Express) SPAM: * 0.4 -- BODY: Attempt at obfuscating the word "mortgage" SPAM: * 1.6 -- BODY: Spam phrases score is 05 to 08 (medium) SPAM: [score: 6] SPAM: * 0.3 -- BODY: FONT Size +2 and up or 3 and up SPAM: * 0.2 -- BODY: HTML font color is blue SPAM: * 0.7 -- RAW: Message text in HTML without specified charset SPAM: * 0.3 -- RAW: Quoted-printable line longer than 76 characters SPAM: * 0.5 -- Message has X-MSMail-Priority, but no X-MimeOLE SPAM: SPAM: ---- End of SpamAssassin results X-Spam-Level: ***** (5.4) X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) This is a multi-part message in MIME format. --E3D_362F1A68.C Content-Type: text/html; Content-Transfer-Encoding: quoted-printable
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When I do python setup.py build, I get syntax error: File "setup.py", line 184 i += 1 ^ I'm running python 2.2.2 ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at cvs.open-bio.org Wed Apr 16 03:18:59 2003 From: bugzilla-daemon at cvs.open-bio.org (bugzilla-daemon@cvs.open-bio.org) Date: Sat Mar 5 14:43:22 2005 Subject: [Biopython-dev] [Bug 1429] syntax error in setup.py Message-ID: <200304160718.h3G7IxH14808@cvs.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1429 jchang@biopython.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |ASSIGNED ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at cvs.open-bio.org Wed Apr 16 03:25:14 2003 From: bugzilla-daemon at cvs.open-bio.org (bugzilla-daemon@cvs.open-bio.org) Date: Sat Mar 5 14:43:22 2005 Subject: [Biopython-dev] [Bug 1429] syntax error in setup.py Message-ID: <200304160725.h3G7PES16869@cvs.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1429 ------- Additional Comments From jchang@biopython.org 2003-04-16 03:25 ------- Are you sure that the code is being executed with Python 2.2.2, and that the syntax error occurs on that line? That line should work correctly, since i is an integer. Can you check to see if the correct python is being run? Try doing: > which python and making sure the one being run is the one you expect. Also, try doing: python2.2 setup.py to make sure 2.2 is getting run. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From MLModel at wesleyan.edu Wed Apr 16 11:41:42 2003 From: MLModel at wesleyan.edu (Mitchell L Model) Date: Sat Mar 5 14:43:22 2005 Subject: [Biopython-dev] broken link on www.biopython.org Message-ID: I apologize for the probably inappropriate destination of this message, but I couldn't find any information at http://www.biopython.org about who should be sent comments about the site itself, and I didn't think the biopython mailing list would be appropriate for that. So: I think there should be an email address on the home page, like there is on most, to which people can send site bug reports. (Webmaster@biopython.org, or whatever, which I'm cc'ing here in the vague hope that that works.) Or, a separate "Contacts" link in your left-side menu which then contains that information. I realize it's all volunteers and no-one really wants to hear about the site itself, but someone must be responsible for site maintenance. The link to the "BITS Online Journal" is broken. -- Mitchell L Model Visiting Associate Professor Computer Science (860) 685-3915 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://portal.open-bio.org/pipermail/biopython-dev/attachments/20030416/d7915a3f/attachment.htm From chapmanb at uga.edu Wed Apr 16 11:58:04 2003 From: chapmanb at uga.edu (Brad Chapman) Date: Sat Mar 5 14:43:22 2005 Subject: [Biopython-dev] broken link on www.biopython.org In-Reply-To: References: Message-ID: <20030416155804.GC25210@uga.edu> Hi Mitchell; > I apologize for the probably inappropriate destination of this > message, but I couldn't find any information at > http://www.biopython.org about who should be sent comments about the > site itself, and I didn't think the biopython mailing list would be > appropriate for that. So: This isn't too bad a place -- we'll all probably live with a few web page e-mails :-). Although your point about having an e-mail address to write about stuff like this is a good one (biopython-dev is probably the right list, I would think). In response to your mail, I actually have a new website all finished and ready to go (you can check it out at http://evostick.agtec.uga.edu/biopython/ -- comments on this are always appreciated). We are currently working on setting up a new web server where it'll go (and running in the usual sort of issues in setting something up), and then we'll be able to get rid of the old page which has quite a few out of date things. Thanks for the report and the suggestion! 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We can help you Date: Wed, 23 Apr 2003 13:49:10 +0900 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_24D_5ADC_2232C472.2E880871" X-Priority: 1 X-MSMail-Priority: High X-Mailer: Microsoft Outlook, Build 10.0.4510 X-Spam-Warning: SpamAssassin says this message is SPAM X-Spam-Status: Yes X-Spam-Report: SPAM: ---- Start SpamAssassin results SPAM: 7.20 hits, 5 required; SPAM: * 1.3 -- From: does not include a real name SPAM: * 0.6 -- To: has a malformed address SPAM: * 0.4 -- Sent with 'X-Priority' set to high SPAM: * 0.4 -- Sent with 'X-Msmail-Priority' set to high SPAM: * 0.8 -- BODY: Spam phrases score is 02 to 03 (medium) SPAM: [score: 2] SPAM: * 0.3 -- BODY: HTML mail with non-white background SPAM: * 1.4 -- RAW: Message text disguised using base-64 encoding SPAM: * 1.5 -- Forged hotmail.com 'Received:' header found SPAM: * 0.5 -- Message has X-MSMail-Priority, but no X-MimeOLE SPAM: SPAM: ---- End of SpamAssassin results X-Spam-Level: ******* (7.2) X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) ------=_NextPart_24D_5ADC_2232C472.2E880871 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit ------=_NextPart_24D_5ADC_2232C472.2E880871 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: base64 PEhUTUw+PEJPRFkgQkdDT0xPUj0iIzAwMDBhMCI+PGZvbnQgY29sb3I9IiMw MDAwYTAiPg0KVTZuRHdPaVQyeWxSdUhtUzBpUDBxWDRyWGUxWWdSdVVqUnRI NGhFMEZsMlhoNUFuMVl2OEZpMFBwSmlDcExjTHcwUm9LNHZDNHQ8YnI+Mm5I eEo2ZFMyeVgzYlR5NVRmVnlYb1dnNlhzM0tuM0lnMkhhTmZZbFB3TDdpSThj SjRmRXFPalRvQzNhUjF2VzFrTWxPNGlBbjxicj48YnI+DQo8Y2VudGVyPjxi Pg0KPGEgaHJlZj0iaHR0cDovL0FZbEtqTWFTeVRpOFZpWUlwRXgzTmQ3TmU0 THA3SmFOalBuQDE5My4yMzEuMjQ4LjcyL3YyL2luZGV4LnBocD9ib3VnaGV0 dG8iPg0KDQo8Zm9udCBjb2xvcj0id2hpdGUiIHNpemU9IjUiPmNsaWNrIGhl cmUgdG8gYWRkIGluY2hlcyAtJi0gc3RtYWluYSB0b2RheSENCg0KPC9hPjwv Yj48YnI+PC9mb250PjwvZm9udD4odGhpcyBpcyBhIGZyZWUgdGlja2V0KTwv UD48Zm9udCBjb2xvcj0iIzAwMDBhMCI+DQo8YnI+PGJyPm5ON29ZOHhGN3JC YkhpZ1IzdFcwakM4cU1zWHJIdk5qN1ZzNk1uT2k4RXg3Rmg0SWE0SWQ0Q284 VWkwUGpVdlVuU29GdjVTbE41dEczZTxicj48YnI+PGJyPjhvWGRCMmdYNnVQ TGZWeVBpQnBXNzB5UDhrTTZsQzJ5ZEltSmZRZFRrRG5YaFhiU29ONHNVNHZP M284Rm01TmUwUXAwUWMwUHdLMWRTOHRJPGJyPjxicj4NCjxicj48YnI+PGJy Pjxicj48YnI+PGJyPjxicj48YnI+PGJyPjxicj4NCjxicj5SazdwaWVXN3RS NXhMNGVEMXdBcjFDd1BmTXA3WXczTW0wWHcwRWpUZUlpTmpPNmFEMWhQMG9J d1VoVGxDOGhWNXJZNmpHaVQ2akdvPGJyPjxicj5HSHVYcERpMU5zNmdCckxs TG9LZkc3dVI1ZVF3V2NQMWlING1WN3ZFM2VCM2pGNGdKNGdIeTNIazFMd1U8 YnI+PGJyPjwvY2VudGVyPjxmb250IHNpemU9IjEiPg0KPEEgSFJFRj0ibWFp bHRvOnJlbW92ZW1lbm93LWR1aEBsaXN0LnJ1P3N1YmplY3Q9cmVtb3ZlLW1l LWxpYW10b2giPg0KPGZvbnQgY29sb3I9IndoaXRlIj48Zm9udCBzaXplPSIx Ij5DbGljayBIZXJlPC9BPiB0byByZW1vdmUgeW91cnNlbGYgZnJvbSB0aGlz IG9wdC1pbi9vdXQgbGlzdDxicj4NCjwvZm9udD48YnI+PGZvbnQgY29sb3I9 IiMwMDAwYTAiPktTdU1wUG41VWQ1QXA4dUpwUWRKajZrWGZPb1I1d1ExZlY0 b0MycEExc0U4YUI3aEdwMlNnMEplUjxicj4= ------=_NextPart_24D_5ADC_2232C472.2E880871-- From bugzilla-daemon at cvs.open-bio.org Thu Apr 24 10:42:04 2003 From: bugzilla-daemon at cvs.open-bio.org (bugzilla-daemon@cvs.open-bio.org) Date: Sat Mar 5 14:43:22 2005 Subject: [Biopython-dev] [Bug 1434] Syntax error in triemodule.c. Won't compile with ANSI C Message-ID: <200304241442.h3OEg4A14287@cvs.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1434 ------- Additional Comments From jonathan.gilligan@vanderbilt.edu 2003-04-24 10:42 ------- Created an attachment (id=46) --> (http://bugzilla.bioperl.org/attachment.cgi?id=46&action=view) Proposed patch to resolve bug 1434 ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at cvs.open-bio.org Thu Apr 24 10:38:09 2003 From: bugzilla-daemon at cvs.open-bio.org (bugzilla-daemon@cvs.open-bio.org) Date: Sat Mar 5 14:43:22 2005 Subject: [Biopython-dev] [Bug 1434] New: Syntax error in triemodule.c. Won't compile with ANSI C Message-ID: <200304241438.h3OEc9X14237@cvs.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1434 Summary: Syntax error in triemodule.c. Won't compile with ANSI C Product: Biopython Version: 1.10 Platform: PC OS/Version: Windows 2000 Status: NEW Severity: blocker Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: jonathan.gilligan@vanderbilt.edu Line 576 of Bio/triemodule.c is legal C++, but not C. Thus, it will not build with an ANSI C compiler. The following patch should work. Index: Bio/triemodule.c =================================================================== RCS file: /home/repository/biopython/biopython/Bio/triemodule.c,v retrieving revision 1.4 diff -u -b -r1.4 triemodule.c --- Bio/triemodule.c 2003/04/10 19:34:42 1.4 +++ Bio/triemodule.c 2003/04/24 14:26:51 @@ -571,7 +571,12 @@ _read_value_from_handle(void *handle) { int length; +#if defined(__cplusplus) // ANSI spec, sect. 16.8: __cplusplus defined to be 199711L const int MAX_KEY_LENGTH = 2000; +#else +# define MAX_KEY_LENGTH 2000 +#endif + unsigned char KEY[MAX_KEY_LENGTH]; if(!_read_from_handle((void *)&length, sizeof(length), (void *)handle)) ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at cvs.open-bio.org Thu Apr 24 15:05:58 2003 From: bugzilla-daemon at cvs.open-bio.org (bugzilla-daemon@cvs.open-bio.org) Date: Sat Mar 5 14:43:22 2005 Subject: [Biopython-dev] [Bug 1434] Syntax error in triemodule.c. Won't compile with ANSI C Message-ID: <200304241905.h3OJ5wN25326@cvs.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1434 jchang@biopython.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From jchang@biopython.org 2003-04-24 15:05 ------- Thanks for the fix. Since it is supposed to be C-code, I've just gone ahead and #defined it as a constant. Jeff ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From jpaint at u.washington.edu Fri Apr 25 16:56:41 2003 From: jpaint at u.washington.edu (Jay Painter) Date: Sat Mar 5 14:43:22 2005 Subject: [Biopython-dev] Preliminary release of PyMMLib Message-ID: <200304251656.41501.jpaint@u.washington.edu> Hello, I have just put together the first tarball of a project I've been working on called PyMMLib. It is a set of Python modules for manipulating and analyzing biological macromolecules. I'd like to eventually merge this package with one of the other bio-python packages out there, so I'm hoping to get some feedback on the work I've done so far. Some of what is included is: * mmCIF file parser (read/write) * PDB v2.2 file parser (all records, read/write, some type checking) * MTZ file parser (CCP4 HKL reflection files) * object-oriented structural representation * minimal element/amino acid/nucleic acid dictionary * Gtk/OpenGL example molecular viewer, 100% Python There are more docs on the web site: http://pymmlib.sourceforge.net/ Regards, Jay Painter From biopython-bugs at bioperl.org Mon Apr 28 03:21:30 2003 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:22 2005 Subject: [Biopython-dev] Notification: incoming/145 Message-ID: <200304280721.h3S7LUwU001952@pw600a.bioperl.org> JitterBug notification new message incoming/145 Message summary for PR#145 From: HIPAA Compliance Office Subject: Important HIPAA Update. Date: Mon, 28 Apr 2003 03:21:46 -0400 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From ptytrevlaws@sfo.com Mon Apr 28 03:21:30 2003 Received: from 24.165.149.195 (cpe-024-165-149-195.midsouth.rr.com [24.165.149.195]) by pw600a.bioperl.org (8.12.6/8.12.6) with SMTP id h3S7LPwU001947 for ; Mon, 28 Apr 2003 03:21:29 -0400 Message-Id: <200304280721.h3S7LPwU001947@pw600a.bioperl.org> Received: from mta6.snfc21.pbi.net ([39.26.127.61]) by ssymail.ssy.co.kr with esmtp; Apr, 28 2003 2:16:25 AM +0400 Received: from rly-yk04.mx.aol.com ([99.100.131.137]) by rly-xw01.mx.aol.com with NNFMP; Apr, 28 2003 12:59:22 AM -0800 From: HIPAA Compliance Office To: biopython-bugs@bioperl.org Subject: Important HIPAA Update. 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--0.C_F0__EE4EDA_..D4BCCAF-- From bugzilla-daemon at cvs.open-bio.org Tue Apr 29 15:24:58 2003 From: bugzilla-daemon at cvs.open-bio.org (bugzilla-daemon@cvs.open-bio.org) Date: Sat Mar 5 14:43:22 2005 Subject: [Biopython-dev] [Bug 1437] New: Parse Error in NCBIStandalone.py Message-ID: <200304291924.h3TJOwR21969@cvs.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1437 Summary: Parse Error in NCBIStandalone.py Product: Biopython Version: 1.10 Platform: PC OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: gckettle@cs.uchicago.edu The blast parser will return an inaccurate query length if it is long enough to include a comma. It looks like _HeaderConsumer.query_info() should be using something like r"([0-9,]+) letters" not r"(\d+) letters" ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at cvs.open-bio.org Tue Apr 29 16:50:34 2003 From: bugzilla-daemon at cvs.open-bio.org (bugzilla-daemon@cvs.open-bio.org) Date: Sat Mar 5 14:43:22 2005 Subject: [Biopython-dev] [Bug 1437] Parse Error in NCBIStandalone.py Message-ID: <200304292050.h3TKoYU23158@cvs.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1437 jchang@biopython.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From jchang@biopython.org 2003-04-29 16:50 ------- Good catch! I've applied your fix to the current repository. Thanks, Jeff ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From biopython-bugs at bioperl.org Wed Apr 30 03:20:40 2003 From: biopython-bugs at bioperl.org (biopython-bugs@bioperl.org) Date: Sat Mar 5 14:43:22 2005 Subject: [Biopython-dev] Notification: incoming/147 Message-ID: <200304300720.h3U7KewU021737@pw600a.bioperl.org> JitterBug notification new message incoming/147 Message summary for PR#147 From: "Bianca Alvarez" Subject: Mortgage Rates down to Lowest since 1966! 123 qgx jbsptwy o Date: Sat, 12 Jan 02 08:05:51 GMT 0 replies 0 followups ====> ORIGINAL MESSAGE FOLLOWS <==== >From kwty68a63m@yahoo.com Wed Apr 30 03:20:38 2003 Received: from COMUNICACION31 ([200.93.35.58]) by pw600a.bioperl.org (8.12.6/8.12.6) with SMTP id h3U7KQwU021729; Wed, 30 Apr 2003 03:20:34 -0400 Received: from ([201.66.94.86]) by COMUNICACION31 with ESMTP id <525640-89487>; Sat, 12 Jan 2002 08:05:51 -0700 Message-ID: <7793k$kls4we@gzb6n.jq> From: "Bianca Alvarez" To: admin@bioperl.org Cc: , , Subject: Mortgage Rates down to Lowest since 1966! 123 qgx jbsptwy o Date: Sat, 12 Jan 02 08:05:51 GMT X-Mailer: AOL 7.0 for Windows US sub 118 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="FB_BF20A1.50_1" X-Priority: 3 X-MSMail-Priority: Normal X-Spam-Warning: SpamAssassin says this message is SPAM X-Spam-Status: Yes X-Spam-Report: SPAM: ---- Start SpamAssassin results SPAM: 6.30 hits, 5 required; SPAM: * -0.2 -- X-Mailer header indicates a non-spam MUA (AOL) SPAM: * 0.3 -- From: contains numbers mixed in with letters SPAM: * 0.6 -- BODY: Information on mortgage rates SPAM: * 0.4 -- BODY: Attempt at obfuscating the word "mortgage" SPAM: * 0.8 -- BODY: Spam phrases score is 00 to 01 (low) SPAM: [score: 0] SPAM: * 0.7 -- RAW: Message text in HTML without specified charset SPAM: * 0.7 -- URI: URL of page called "remove" SPAM: * 1.4 -- 'From' yahoo.com does not match 'Received' headers SPAM: * 0.5 -- Message has X-MSMail-Priority, but no X-MimeOLE SPAM: * 1.1 -- Message looks like Outlook, but isn't SPAM: SPAM: ---- End of SpamAssassin results X-Spam-Level: ****** (6.3) X-Scanned-By: MIMEDefang 2.26 (www . roaringpenguin . com / mimedefang) This is a multi-part message in MIME format. --FB_BF20A1.50_1 Content-Type: text/html; Content-Transfer-Encoding: quoted-printable bolshevismAdmin
No mail! brushwork yackrk hdxy jlezicsesiiwtbokaa mxxro nahkipr v nlg --FB_BF20A1.50_1-- From bugzilla-daemon at cvs.open-bio.org Wed Apr 30 12:31:46 2003 From: bugzilla-daemon at cvs.open-bio.org (bugzilla-daemon@cvs.open-bio.org) Date: Sat Mar 5 14:43:22 2005 Subject: [Biopython-dev] [Bug 1438] New: fssp parsing bug Message-ID: <200304301631.h3UGVkI09712@cvs.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1438 Summary: fssp parsing bug Product: Biopython Version: Not Applicable Platform: All OS/Version: Linux Status: NEW Severity: normal Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: idoerg@burnham.org reported by Shaheen Ahmed: Dear all, I have problems when trying to generate a clustalw alignment of the fssp database file -> 1ycc.fssp. I use the following biopython script: ------------------------------------------------------------------- #!/usr/bin/python from Bio import FSSP from Bio.FSSP import FSSPTools from Bio import Align from Bio.Align import AlignInfo from Bio.Align.FormatConvert import FormatConverter from Bio import SubsMat from Bio.SubsMat import SeqMat from Bio import Alphabet from Bio.Alphabet import IUPAC from Bio import Clustalw from Bio.SeqRecord import SeqRecord import sys import string for arg in sys.argv[1:]: my_header, my_sum, my_align = FSSP.read_fssp(open(arg)) # To Filter From The Alignment Only Those Alignments With A Percent Id # Above 30%: filtered_sum, filtered_alignment = FSSPTools.filter( my_sum,my_align,'pID',30,100) filtered_ali = FSSPTools.mult_align(filtered_sum, filtered_alignment) converter = FormatConverter(filtered_ali) clustal_align = converter.to_clustal() print clustal_align ---------------------------------------------------------------------- The alignment is not generated, but I get the following error messages: ---------------------------------------------------------------------- File "./fssp_example.py", line 30, in ? filtered_ali = FSSPTools.mult_align(filtered_sum, filtered_alignment) File "/usr/lib/python2.0/site-packages/Bio/FSSP/FSSPTools.py", line 22, in mult_align for j in align_dict.abs(1).pos_align_dict.keys(): File "/usr/lib/python2.0/site-packages/Bio/FSSP/__init__.py", line 168, in abs return self[self.abs_res_dict[num]] KeyError: 1 ---------------------------------------------------------------------- Does anybody have a clue what's going wrong? I'd be greatful for any suggestions. Best wishes, Shaheen P.S.: For most of the other fssp database files I tried, the above script seems to work and a clustalw alignment is generated and printed. -- Shaheen Ahmed Department of Biochemistry University of Zuerich Winterthurerstrasse 190 8057 Zuerich (Switzerland) tel: ++41 1 635 55 68 mailto:ahmed@bioc.unizh.ch ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at cvs.open-bio.org Wed Apr 30 12:49:52 2003 From: bugzilla-daemon at cvs.open-bio.org (bugzilla-daemon@cvs.open-bio.org) Date: Sat Mar 5 14:43:22 2005 Subject: [Biopython-dev] [Bug 1438] fssp parsing bug Message-ID: <200304301649.h3UGnqu10124@cvs.open-bio.org> http://bugzilla.bioperl.org/show_bug.cgi?id=1438 idoerg@burnham.org changed: What |Removed |Added ---------------------------------------------------------------------------- AssignedTo|biopython-dev@biopython.org |idoerg@burnham.org ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee.