From longlill at yahoo.com Wed Sep 15 07:18:38 2004 From: longlill at yahoo.com (Long Li) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] BioPython Homepage: Links not easily seen Message-ID: <20040915111839.38739.qmail@web52805.mail.yahoo.com> Hi, It is not easy to see the links when browsing BioPython homepage. I have to move the mouse to the text to know if it is a link. Could those links be underlined like BioPerl homepage or be displayed in another color? Best regards, Long _______________________________ Do you Yahoo!? Declare Yourself - Register online to vote today! http://vote.yahoo.com From longlill at yahoo.com Wed Sep 15 10:15:17 2004 From: longlill at yahoo.com (Long Li) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] bug: PDB.PDBList module "get_recent_filenames" Message-ID: <20040915141517.61563.qmail@web52810.mail.yahoo.com> In PDB.PDBList module, the method "get_recent_filenames" of the class "PDBList" has a bug. ____________________________________________________ def get_recent_filenames(self): ... ... file = url.readlines() maxdate = 0 for l in file: try: # check if this is a valid date date = int(l[54:62]) if date > maxdate: maxdate = date except: pass ... ... _____________________________________________________ The statement "date = int(l[54:62])" should be changed to "date = int( l[ 45:53 ] )". After I try the statement "file = url.readlines()" in the code above, it output like this: drwxrwxr-x 2 702 512 Aug 30 19:22 20040830 drwxrwxr-x 2 702 512 Sep 3 16:06 20040903 drwxrwxr-x 2 702 512 Sep 13 17:03 20040913 -rw-r--r-- 1 702 1218 Nov 26 2003 README not like that described in the module: drwxrwxr-x 2 1002 sysadmin 512 Oct 6 18:28 20031006 drwxrwxr-x 2 1002 sysadmin 512 Oct 14 02:14 20031013 -rw-r--r-- 1 1002 sysadmin 1327 Mar 12 2001 README I think it is not a good way to get the directory name by using the slice of result of "readlines()", could the directory name be read directly? Best regards, Long __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From bugzilla-daemon at portal.open-bio.org Fri Sep 24 06:59:14 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1698] Bio.Blast.Record.MultipleAlignment.to_generic bug Message-ID: <200409241059.i8OAxElc030309@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1698 ------- Additional Comments From j.a.casbon@qmul.ac.uk 2004-09-24 06:59 ------- Created an attachment (id=172) --> (http://bugzilla.open-bio.org/attachment.cgi?id=172&action=view) fix for Bio.Blast.Record ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Fri Sep 24 06:47:40 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1697] pdbparser should accpet pipes as well as filenames Message-ID: <200409241047.i8OAlec4030251@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1697 ------- Additional Comments From j.a.casbon@qmul.ac.uk 2004-09-24 06:47 ------- Created an attachment (id=171) --> (http://bugzilla.open-bio.org/attachment.cgi?id=171&action=view) allows parser to accept pipe ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Fri Sep 24 06:57:13 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1698] New: Bio.Blast.Record.MultipleAlignment.to_generic bug Message-ID: <200409241057.i8OAvDDS030297@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1698 Summary: Bio.Blast.Record.MultipleAlignment.to_generic 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: j.a.casbon@qmul.ac.uk The logic in this method was wrong. It was based on the uniqueness of the alignment sequence name. These need not be unique. This was reported by me: http://portal.open-bio.org/pipermail/biopython-dev/2004-June/002082.html Maybe it will get fixed if I leave the patch here instead! ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Fri Sep 24 06:45:25 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1697] New: pdbparser should accpet pipes as well as filenames Message-ID: <200409241045.i8OAjPKI030234@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1697 Summary: pdbparser should accpet pipes as well as filenames Product: Biopython Version: Not Applicable Platform: All OS/Version: Linux Status: NEW Severity: enhancement Priority: P2 Component: Main Distribution AssignedTo: biopython-dev@biopython.org ReportedBy: j.a.casbon@qmul.ac.uk see attached patch ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Fri Sep 24 09:53:35 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1697] pdbparser should accpet pipes as well as filenames Message-ID: <200409241353.i8ODrZTU031735@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1697 ------- Additional Comments From j.a.casbon@qmul.ac.uk 2004-09-24 09:53 ------- And while this is being fixed, perhaps the Parser returns a UnboundLocalError if the file passed in is empty. This is pretty dumb, maybe it shoud just return None. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Sat Sep 25 11:30:20 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1698] Bio.Blast.Record.MultipleAlignment.to_generic bug Message-ID: <200409251530.i8PFUKHf010960@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1698 jchang@biopython.org changed: What |Removed |Added ---------------------------------------------------------------------------- Status|NEW |RESOLVED Resolution| |FIXED ------- Additional Comments From jchang@biopython.org 2004-09-25 11:30 ------- I've patched the code and committed it into CVS. I had some problems with the patch and had to do it by hand. Could you check to make sure it is right? ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Sep 27 06:51:19 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1698] Bio.Blast.Record.MultipleAlignment.to_generic bug Message-ID: <200409271051.i8RApJXZ021389@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1698 ------- Additional Comments From j.a.casbon@qmul.ac.uk 2004-09-27 06:51 ------- The patch seems to be ok. What went wrong when applying? ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee. From bugzilla-daemon at portal.open-bio.org Mon Sep 27 11:26:08 2004 From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon@portal.open-bio.org) Date: Sat Mar 5 14:43:53 2005 Subject: [Biopython-dev] [Bug 1698] Bio.Blast.Record.MultipleAlignment.to_generic bug Message-ID: <200409271526.i8RFQ8DS024328@portal.open-bio.org> http://bugzilla.open-bio.org/show_bug.cgi?id=1698 ------- Additional Comments From jchang@biopython.org 2004-09-27 11:26 ------- One of the lines got split: + if parse_number == 1: # create on first_parse, append on all other s I fixed that manually. However, patch still rejected the whole block: sophie:~/remotecvs/biopython/Bio/Blast jchang$ patch < Record.patch patching file Record.py Hunk #1 FAILED at 175. 1 out of 1 hunk FAILED -- saving rejects to file Record.py.rej sophie:~/remotecvs/biopython/Bio/Blast jchang$ I didn't know what was wrong with it, so I just applied the patch by hand. ------- You are receiving this mail because: ------- You are the assignee for the bug, or are watching the assignee.