From bugzilla-daemon at portal.open-bio.org  Mon Apr  2 14:03:49 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 2 Apr 2007 14:03:49 -0400
Subject: [Biopython-dev] [Bug 2251] [PATCH] NumPy support for BioPython
In-Reply-To: <bug-2251-42@http.bugzilla.open-bio.org/>
Message-ID: <200704021803.l32I3nI9004963@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2251


edschofield at gmail.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
         OS/Version|Linux                       |All




------- Comment #6 from edschofield at gmail.com  2007-04-02 14:03 EST -------
Yes, you're right; this would lead to buggy behaviour in the cluster module on
64-bit platforms with arrays defined with more than 2^32 = 4294967296 rows or
columns.

Are you willing to change the sizes for the relevant array dimensions in
cluster.c from int to intptr_t? This is defined in stdint.h under the C99
standard.

If not, we'd need to stick with int definitions throughout clustermodule.c too,
converting to intp only when necessary for numpy.


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From sbassi at gmail.com  Mon Apr  2 14:32:58 2007
From: sbassi at gmail.com (Sebastian Bassi)
Date: Mon, 2 Apr 2007 15:32:58 -0300
Subject: [Biopython-dev] Changes in BLAST URLAPI
Message-ID: <b43bf2080704021132t1bfe0b85i244604318558a1b8@mail.gmail.com>

I wonder if net blast would be affected by this change (from April 16,
according to BLAST newsletter):

=====================================================

A Note About URLAPI

The new BLAST pages support URLAPI, a protocol that scripts and
programs use to run BLAST searches and retrieve results over
HTTP. (For more on URLAPI, see
http://www.ncbi.nlm.nih.gov/blast/Doc/urlapi.html). The following
information only applies to you if you develop or are responsible
for software that uses URLAPI.

The new pages have been tested and produce correct results with
the following URLAPI client programs:

* the BioPERL RemoteBlast module
* the NCBI demo script http://ncbi.nlm.nih.gov/blast/docs/web_blast.pl
* various scripts used in-house at NCBI

Users of URLAPI should be aware of the following minor
changes. In the new interface:

1. The Request ID (RID) format will be shorter.  The new format
   is 11 alphanumeric characters (e.g. RDEFEA5012) and will have no
   internal structure. The previous RID format was 36 or more
   characters long, including punctuation (e.g.,
   1175172712-21345-42512597310.BLASTQ3).

2. BLAST reports will show masked regions as lower-case letters
   by default (see
   http://nar.oxfordjournals.org/cgi/content/full/34/suppl_2/W6,
   figure 2. The current default behavior is to show masked
   regions as N's or X's. Users may recover the current behavior
   by adding &MASK_CHAR=0 to the query string for a URLAPI
   request.

3. BLAST reports will show alignments for 100 database sequences
   by default. The current reports show only 50 alignments by
   default.

If you have any questions please send them to mcginnis at ncbi.nlm.nih.gov

=======================================================

From bugzilla-daemon at portal.open-bio.org  Mon Apr  2 15:02:00 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 2 Apr 2007 15:02:00 -0400
Subject: [Biopython-dev] [Bug 2251] [PATCH] NumPy support for BioPython
In-Reply-To: <bug-2251-42@http.bugzilla.open-bio.org/>
Message-ID: <200704021902.l32J20s6007626@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2251





------- Comment #7 from edschofield at gmail.com  2007-04-02 15:02 EST -------
Forget the last comment. Here's a less invasive patch. It seems there's only a
need for explicit int/intp conversion in one function (parse_mask).


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From bugzilla-daemon at portal.open-bio.org  Mon Apr  2 15:04:13 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 2 Apr 2007 15:04:13 -0400
Subject: [Biopython-dev] [Bug 2251] [PATCH] NumPy support for BioPython
In-Reply-To: <bug-2251-42@http.bugzilla.open-bio.org/>
Message-ID: <200704021904.l32J4DpR007752@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2251


edschofield at gmail.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
 Attachment #611 is|0                           |1
           obsolete|                            |




------- Comment #8 from edschofield at gmail.com  2007-04-02 15:04 EST -------
Created an attachment (id=617)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=617&action=view)
Version 7 of patch for NumPy support


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From sbassi at gmail.com  Tue Apr 10 11:11:04 2007
From: sbassi at gmail.com (Sebastian Bassi)
Date: Tue, 10 Apr 2007 12:11:04 -0300
Subject: [Biopython-dev] Problem compiling Biopython 1.43 in Ubuntu
Message-ID: <b43bf2080704100811m1dd67174u6a51b3d0275e4c6a@mail.gmail.com>

Hello,

I tried to build biopython 1.43 in Ubuntu 6.10 (Edgy Eft). First I met
all dependencies and then I did:
python setup.py build and it failed. So the second try was with N in
the question about compiling Bio.KDTree and I got the same:

sbassi at inet2BALC:~/bioinfo/biopython-1.43$ python setup.py build
running build
running build_py

*** Bio.KDTree *** NOT built by default

The Bio.PDB.NeighborSearch module depends on the Bio.KDTree module,
which in turn, depends on C++ code that does not compile cleanly on
all platforms. Hence, Bio.KDTree is not built by default.

Would you like to build Bio.KDTree ? (y/N)
running build_ext
building 'Bio.clistfns' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O2 -Wall
-Wstrict-prototypes -fPIC -I/usr/include/python2.4 -c
Bio/clistfnsmodule.c -o build/temp.linux-i686-2.4/Bio/clistfnsmodule.o
In file included from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/syslimits.h:7,
                 from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:11,
                 from /usr/include/python2.4/Python.h:18,
                 from Bio/clistfnsmodule.c:10:
/usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:122:61: error:
limits.h: No such file or directory
In file included from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/Python.h:32:19: error: stdio.h: No such file or directory
/usr/include/python2.4/Python.h:34:5: error: #error "Python.h requires
that stdio.h define NULL."
/usr/include/python2.4/Python.h:37:20: error: string.h: No such file
or directory
/usr/include/python2.4/Python.h:38:19: error: errno.h: No such file or directory
/usr/include/python2.4/Python.h:39:20: error: stdlib.h: No such file
or directory
/usr/include/python2.4/Python.h:41:20: error: unistd.h: No such file
or directory
/usr/include/python2.4/Python.h:53:20: error: assert.h: No such file
or directory
In file included from /usr/include/python2.4/Python.h:55,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pyport.h:7:20: error: stdint.h: No such file or directory
In file included from /usr/include/python2.4/Python.h:55,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pyport.h:73: error: expected '=', ',', ';',
'asm' or '__attribute__' before 'Py_uintptr_t'
/usr/include/python2.4/pyport.h:74: error: expected '=', ',', ';',
'asm' or '__attribute__' before 'Py_intptr_t'
/usr/include/python2.4/pyport.h:94:76: error: math.h: No such file or directory
/usr/include/python2.4/pyport.h:101:22: error: sys/time.h: No such
file or directory
/usr/include/python2.4/pyport.h:102:18: error: time.h: No such file or directory
/usr/include/python2.4/pyport.h:120:24: error: sys/select.h: No such
file or directory
/usr/include/python2.4/pyport.h:159:22: error: sys/stat.h: No such
file or directory
In file included from /usr/include/python2.4/Python.h:74,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pymem.h:50: warning: parameter names (without
types) in function declaration
/usr/include/python2.4/pymem.h:51: error: expected declaration
specifiers or '...' before 'size_t'
In file included from /usr/include/python2.4/Python.h:76,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/object.h:227: error: expected declaration
specifiers or '...' before 'FILE'
/usr/include/python2.4/object.h:371: error: expected declaration
specifiers or '...' before 'FILE'
In file included from /usr/include/python2.4/Python.h:77,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/objimpl.h:97: warning: parameter names (without
types) in function declaration
/usr/include/python2.4/objimpl.h:98: error: expected declaration
specifiers or '...' before 'size_t'
/usr/include/python2.4/objimpl.h:292: warning: parameter names
(without types) in function declaration
In file included from /usr/include/python2.4/Python.h:81,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/unicodeobject.h:55:19: error: ctype.h: No such
file or directory
/usr/include/python2.4/unicodeobject.h:118:21: error: wchar.h: No such
file or directory
In file included from /usr/include/python2.4/Python.h:81,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/unicodeobject.h:131: error: expected '=', ',',
';', 'asm' or '__attribute__' before 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:376: error: expected
specifier-qualifier-list before 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:422: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:422: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:429: error: expected '=', ',',
';', 'asm' or '__attribute__' before '*' token
/usr/include/python2.4/unicodeobject.h:440: error: expected '=', ',',
';', 'asm' or '__attribute__' before 'PyUnicodeUCS4_GetMax'
/usr/include/python2.4/unicodeobject.h:511: warning: type defaults to
'int' in declaration of 'wchar_t'
/usr/include/python2.4/unicodeobject.h:511: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:529: warning: type defaults to
'int' in declaration of 'wchar_t'
/usr/include/python2.4/unicodeobject.h:529: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:621: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:621: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:654: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:654: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:683: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:683: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:760: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:760: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:779: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:779: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:796: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:796: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:827: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:827: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:849: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:849: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:891: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:891: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:912: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:912: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:965: error: expected ')' before '*' token
/usr/include/python2.4/unicodeobject.h:1143: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1147: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1151: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1155: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1159: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1162: error: expected '=', ',',
';', 'asm' or '__attribute__' before '_PyUnicodeUCS4_ToLowercase'
/usr/include/python2.4/unicodeobject.h:1166: error: expected '=', ',',
';', 'asm' or '__attribute__' before '_PyUnicodeUCS4_ToUppercase'
/usr/include/python2.4/unicodeobject.h:1170: error: expected '=', ',',
';', 'asm' or '__attribute__' before '_PyUnicodeUCS4_ToTitlecase'
/usr/include/python2.4/unicodeobject.h:1175: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1179: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1183: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1187: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1191: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1195: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1199: error: expected ')' before 'ch'
In file included from /usr/include/python2.4/Python.h:82,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/intobject.h:35: error: expected ')' before '*' token
In file included from /usr/include/python2.4/Python.h:84,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/longobject.h:46: error: expected ')' before '*' token
/usr/include/python2.4/longobject.h:63: error: expected '=', ',', ';',
'asm' or '__attribute__' before '_PyLong_NumBits'
/usr/include/python2.4/longobject.h:79: error: expected declaration
specifiers or '...' before 'size_t'
/usr/include/python2.4/longobject.h:102: error: expected declaration
specifiers or '...' before 'size_t'
In file included from /usr/include/python2.4/Python.h:101,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/fileobject.h:12: error: expected
specifier-qualifier-list before 'FILE'
/usr/include/python2.4/fileobject.h:38: error: expected ')' before '*' token
/usr/include/python2.4/fileobject.h:40: error: expected '=', ',', ';',
'asm' or '__attribute__' before '*' token
/usr/include/python2.4/fileobject.h:57: error: expected declaration
specifiers or '...' before 'FILE'
/usr/include/python2.4/fileobject.h:58: error: expected '=', ',', ';',
'asm' or '__attribute__' before 'Py_UniversalNewlineFread'
In file included from /usr/include/python2.4/Python.h:112,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pyerrors.h:156: warning: type defaults to 'int'
in declaration of 'Py_UNICODE'
/usr/include/python2.4/pyerrors.h:156: error: expected ';', ',' or ')'
before '*' token
/usr/include/python2.4/pyerrors.h:160: warning: type defaults to 'int'
in declaration of 'Py_UNICODE'
/usr/include/python2.4/pyerrors.h:160: error: expected ';', ',' or ')'
before '*' token
/usr/include/python2.4/pyerrors.h:226: error: expected declaration
specifiers or '...' before 'size_t'
/usr/include/python2.4/pyerrors.h:227: error: format string argument
not a string type
/usr/include/python2.4/pyerrors.h:228: error: expected declaration
specifiers or '...' before 'size_t'
In file included from /usr/include/python2.4/Python.h:117,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pythonrun.h:32: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:33: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:35: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:36: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:40: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:41: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:42: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:43: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:44: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:45: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:46: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:49: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:55: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:59: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:60: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:64: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:66: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:82: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:123: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:125: error: expected ')' before '*' token
In file included from /usr/include/python2.4/Python.h:119,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/sysmodule.h:12: error: expected '=', ',', ';',
'asm' or '__attribute__' before '*' token
In file included from /usr/include/python2.4/Python.h:121,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/import.h:25: error: expected declaration
specifiers or '...' before 'size_t'
/usr/include/python2.4/import.h:25: error: expected declaration
specifiers or '...' before 'FILE'
In file included from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/Python.h:131: error: expected declaration
specifiers or '...' before 'size_t'
In file included from /usr/include/python2.4/Python.h:149,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pyfpe.h:129:20: error: signal.h: No such file
or directory
/usr/include/python2.4/pyfpe.h:130:20: error: setjmp.h: No such file
or directory
In file included from /usr/include/python2.4/Python.h:149,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pyfpe.h:132: error: expected '=', ',', ';',
'asm' or '__attribute__' before 'PyFPE_jbuf'
Bio/clistfnsmodule.c: In function 'clistfns_count':
Bio/clistfnsmodule.c:33: error: 'NULL' undeclared (first use in this function)
Bio/clistfnsmodule.c:33: error: (Each undeclared identifier is
reported only once
Bio/clistfnsmodule.c:33: error: for each function it appears in.)
Bio/clistfnsmodule.c: In function 'clistfns_contents':
Bio/clistfnsmodule.c:90: error: 'NULL' undeclared (first use in this function)
Bio/clistfnsmodule.c: At top level:
Bio/clistfnsmodule.c:149: error: 'NULL' undeclared here (not in a function)
error: command 'gcc' failed with exit status 1

From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 00:19:27 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 00:19:27 -0400
Subject: [Biopython-dev] [Bug 2266] New: setup.py test does not take options
Message-ID: <bug-2266-42@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2266

           Summary: setup.py test does not take options
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: chris.lasher at gmail.com


Currently, setup.py does not support passing options to the test command. The
Tests/run_tests.py script, however, takes the command line argument "--no-gui"
for running tests in non-GUI mode. This should be an option for setup.py test,
as well.


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From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 00:32:16 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 00:32:16 -0400
Subject: [Biopython-dev] [Bug 2266] setup.py test does not take options
In-Reply-To: <bug-2266-42@http.bugzilla.open-bio.org/>
Message-ID: <200704110432.l3B4WGNm007098@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2266





------- Comment #1 from chris.lasher at gmail.com  2007-04-11 00:32 EST -------
Created an attachment (id=621)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=621&action=view)
Patch to add option --no-gui to setup.py test.

This patch affects setup.py as well as Tests/run_tests.py. The modification to
setup.py gives the option of --no-gui for the command "test", which is passed
to Tests/run_tests.py as an argument. The modification to run_tests.py includes
changing argv from being sys.argv by default to sys.argv[1:] by default, which
is more conventional, and also easier to substitute for cases such as this
where run_test.main() is called externally.


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From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 00:34:22 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 00:34:22 -0400
Subject: [Biopython-dev] [Bug 2266] setup.py test does not take options
In-Reply-To: <bug-2266-42@http.bugzilla.open-bio.org/>
Message-ID: <200704110434.l3B4YM1g007209@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2266


chris.lasher at gmail.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |ASSIGNED




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From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 00:55:30 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 00:55:30 -0400
Subject: [Biopython-dev] [Bug 2266] setup.py test does not take options
In-Reply-To: <bug-2266-42@http.bugzilla.open-bio.org/>
Message-ID: <200704110455.l3B4tUWo007910@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2266





------- Comment #2 from chris.lasher at gmail.com  2007-04-11 00:55 EST -------
I have committed the changes in this patch to the CVS repository.


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From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 00:56:52 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 00:56:52 -0400
Subject: [Biopython-dev] [Bug 2266] setup.py test does not take options
In-Reply-To: <bug-2266-42@http.bugzilla.open-bio.org/>
Message-ID: <200704110456.l3B4uqa3007970@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2266


chris.lasher at gmail.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|ASSIGNED                    |RESOLVED
         Resolution|                            |FIXED




------- Comment #3 from chris.lasher at gmail.com  2007-04-11 00:56 EST -------
Closing bug.


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From chris.lasher at gmail.com  Wed Apr 11 01:04:51 2007
From: chris.lasher at gmail.com (Chris Lasher)
Date: Wed, 11 Apr 2007 01:04:51 -0400
Subject: [Biopython-dev] Bugzilla Version Numbers
Message-ID: <128a885f0704102204p2872f42fh685919bb8b4656c3@mail.gmail.com>

Hi all,

Does anybody active with Biopython have administrative capabilities
for the project's Bugzilla tracker? The version numbers are a wee bit
out of date.

Chris

From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 11:56:39 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 11:56:39 -0400
Subject: [Biopython-dev] [Bug 2268] New: Cluster unit test suite runs
	indefinitely
Message-ID: <bug-2268-42@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2268

           Summary: Cluster unit test suite runs indefinitely
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: All
            Status: NEW
          Severity: critical
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: chris.lasher at gmail.com


The tests contained in Tests/test_Cluster.py seem to run indefinitely. This
prevents running all unit tests in the Biopython test suite to completion. I am
marking this bug as critical. The only workaround I have found has been to
disable these tests from being run by Tests/run_tests.py. This is not an
acceptable permanent solution.


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From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 12:04:07 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 12:04:07 -0400
Subject: [Biopython-dev] [Bug 2268] Cluster unit test suite runs indefinitely
In-Reply-To: <bug-2268-42@http.bugzilla.open-bio.org/>
Message-ID: <200704111604.l3BG47O0016964@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2268





------- Comment #1 from chris.lasher at gmail.com  2007-04-11 12:04 EST -------
Created an attachment (id=622)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=622&action=view)
run_tests_cluster.patch

This patch prevents the tests in test_Cluster.py from being run by default in
run_tests.py. This is not a permanent solution, it is a workaround.


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From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 12:17:42 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 12:17:42 -0400
Subject: [Biopython-dev] [Bug 2269] New: Shebang (hashbang) lines need
	cleanup
Message-ID: <bug-2269-42@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2269

           Summary: Shebang (hashbang) lines need cleanup
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: chris.lasher at gmail.com


The shebang/hashbang (i.e., "#!/usr/bin...") lines in the Biopython scripts
need to be tidied up. Currently there are 8 different shebang variations in the
Biopython library:

#! /usr/bin/env python
#!/usr/bin/env python
#!/usr/bin/env python2.3
#! /usr/bin/python
#!/usr/bin/python
#!/usr/bin/python 
#!/usr/bin/python -i
#!/usr/bin/python -OO

I propose to move these all to the following standard Python form:
#!/usr/bin/env python


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From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 12:26:22 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 12:26:22 -0400
Subject: [Biopython-dev] [Bug 2268] Cluster unit test suite runs indefinitely
In-Reply-To: <bug-2268-42@http.bugzilla.open-bio.org/>
Message-ID: <200704111626.l3BGQMEr018888@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2268





------- Comment #2 from mdehoon at ims.u-tokyo.ac.jp  2007-04-11 12:26 EST -------
Can you check which of the tests hangs?
You can run python test_Cluster.py to get more information.


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From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 12:32:33 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 12:32:33 -0400
Subject: [Biopython-dev] [Bug 2251] [PATCH] NumPy support for BioPython
In-Reply-To: <bug-2251-42@http.bugzilla.open-bio.org/>
Message-ID: <200704111632.l3BGWXs6019455@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2251





------- Comment #9 from mdehoon at ims.u-tokyo.ac.jp  2007-04-11 12:32 EST -------
In this patch, do you still need to define NPY_GENERIC_DIMENSION_FMT in
python/clustermodule.c? Since you don't seem to be using it.


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From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 13:02:55 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 13:02:55 -0400
Subject: [Biopython-dev] [Bug 2251] [PATCH] NumPy support for BioPython
In-Reply-To: <bug-2251-42@http.bugzilla.open-bio.org/>
Message-ID: <200704111702.l3BH2tFh022804@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2251





------- Comment #10 from edschofield at gmail.com  2007-04-11 13:02 EST -------
(In reply to comment #9)
> In this patch, do you still need to define NPY_GENERIC_DIMENSION_FMT in
> python/clustermodule.c? Since you don't seem to be using it.

Yeah, I realized that as soon as I mailed off the last patch. Do you want me to
create a new patch just for this change? I figure such small changes can be
made more easily in-tree.


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From bugzilla-daemon at portal.open-bio.org  Fri Apr 13 17:55:10 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 13 Apr 2007 17:55:10 -0400
Subject: [Biopython-dev] [Bug 2268] Cluster unit test suite runs indefinitely
In-Reply-To: <bug-2268-42@http.bugzilla.open-bio.org/>
Message-ID: <200704132155.l3DLtAUB011430@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2268





------- Comment #3 from chris.lasher at gmail.com  2007-04-13 17:55 EST -------
It hangs on line 181 in "def test_kcluster"
clusterid, error, nfound = kcluster (data1, nclusters=nclusters, mask=mask1,
weight=weight1, transpose=0, npass=100, method='a', dist='e')


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From biopython-dev at maubp.freeserve.co.uk  Thu Apr 19 06:08:52 2007
From: biopython-dev at maubp.freeserve.co.uk (Peter)
Date: Thu, 19 Apr 2007 11:08:52 +0100
Subject: [Biopython-dev] Bugzilla Version Numbers
In-Reply-To: <128a885f0704102204p2872f42fh685919bb8b4656c3@mail.gmail.com>
References: <128a885f0704102204p2872f42fh685919bb8b4656c3@mail.gmail.com>
Message-ID: <46273FB4.4030805@maubp.freeserve.co.uk>

Chris Lasher wrote:
> Hi all,
> 
> Does anybody active with Biopython have administrative capabilities
> for the project's Bugzilla tracker? The version numbers are a wee bit
> out of date.

They are, aren't they!  I asked on the list last month about this, and 
updating the component fields too:

http://lists.open-bio.org/pipermail/biopython-dev/2007-March/002652.html

As no-one on the list has come forward, I guess one of us should get in 
touch with the relevant Open Bio people, probably by emailing "support" 
at the domain helpdesk.open-bio.org

Who needs/wants bugzilla admin rights?

Peter


From biopython-dev at maubp.freeserve.co.uk  Fri Apr 27 14:29:13 2007
From: biopython-dev at maubp.freeserve.co.uk (Peter)
Date: Fri, 27 Apr 2007 19:29:13 +0100
Subject: [Biopython-dev] Unified aligmment input/output, Bio.AlignIO?
Message-ID: <463240F9.8010907@maubp.freeserve.co.uk>

Following the release of Biopython 1.43 with Bio.SeqIO, I would like to 
do a better job for multiple sequence alignment file formats - creating 
a new module Bio.AlignIO

While most multiple sequence alignment files usually contain a single 
alignment (made up of multiple sequences), this is not the general case.

In the PHYLIP suite, concatenated alignments in phylip format are 
produced by the seqboot program for tasks like bootstrapping of a 
phylogenetic tree.  Currently SeqIO chokes on these!

Another example is the output of some the EMBOSS programs can contain 
many multiple sequences alignments, for example the water and needle 
tools can produce many pairwise alignments.

In such cases, being able to write code like the following seems to be 
the logical extension of the Bio.SeqIO style we have agreed on:

from Bio import AlignIO
for alignment in AlignIO.parse("many.phy", "phylip") :
     print "Alignment with %i sequences of length %i" \
         % (len(alignment.get_all_seqs()),
            alignment.get_alignment_length())
     ...

i.e. The AlignIO.parse() function would be an iterator returning 
alignment objects. Does this sound reasonable so far?

As part of this work, I would also like to introduce a "RichAlignment" 
or "AnnotatedAlignment" as a subclass of the generic Alignment class 
which would be able to hold all the alignment annotation found in 
pfam/stockholm files such as alignment ID, description, comments etc 
plus all the per column annotation.

Assuming the existence of this AnnotatedAlignment class, the existing 
PFAM/Stockholm parser in Bio.SeqIO would be turned into a Bio.AlignIO 
parser to take advantage of the rich annotation.

Note - I would intend to still allow Bio.SeqIO to be used on multiple 
sequence alignment files, however the implementation may well do this 
internally via Bio.AlignIO

---------------------------------------------------------------------

This also raises the related (but separate) issue of improving the 
generic Alignment object, raised in bug 1944:

http://bugzilla.open-bio.org/show_bug.cgi?id=1944

I personally would prefer the alignment class to act more like an 
array/matrix of residues/characters.

I would also like to be able to splice an alignment (both by the 
columns, or by the sequence numbers) to get a sub-alignment.  The 
suggested AnnotatedAlignment class would have to take care of also 
splicing any per sequence or per column annotation.

Peter


From mdehoon at c2b2.columbia.edu  Sun Apr 29 01:33:33 2007
From: mdehoon at c2b2.columbia.edu (Michiel de Hoon)
Date: Sun, 29 Apr 2007 14:33:33 +0900
Subject: [Biopython-dev] Problem compiling Biopython 1.43 in Ubuntu
In-Reply-To: <b43bf2080704100811m1dd67174u6a51b3d0275e4c6a@mail.gmail.com>
References: <b43bf2080704100811m1dd67174u6a51b3d0275e4c6a@mail.gmail.com>
Message-ID: <46342E2D.6000806@c2b2.columbia.edu>

Sorry for my late reply.

Sebastian Bassi wrote:
> I tried to build biopython 1.43 in Ubuntu 6.10 (Edgy Eft). First I met
> all dependencies and then I did:
> python setup.py build and it failed. So the second try was with N in
> the question about compiling Bio.KDTree and I got the same:

 From your output, Bio.KDTree does not seem to be the problem.

> sbassi at inet2BALC:~/bioinfo/biopython-1.43$ python setup.py build
> running build
> running build_py
 > ...
> running build_ext
> building 'Bio.clistfns' extension
> gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O2 -Wall
> -Wstrict-prototypes -fPIC -I/usr/include/python2.4 -c
> Bio/clistfnsmodule.c -o build/temp.linux-i686-2.4/Bio/clistfnsmodule.o
> In file included from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/syslimits.h:7,
>                  from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:11,
>                  from /usr/include/python2.4/Python.h:18,
>                  from Bio/clistfnsmodule.c:10:
> /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:122:61: error:
> limits.h: No such file or directory
> In file included from Bio/clistfnsmodule.c:10:
> /usr/include/python2.4/Python.h:32:19: error: stdio.h: No such file or directory
...

If gcc cannot find standard headers such as limits.h or stdio.h, there 
seems to be a real problem with your installation. Can you compile a 
simple program with gcc if it #includes stdio.h? If not, try to solve 
that problem first. If so, try to find out why "gcc yourtestprogram.c" 
compiles, but "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O2 -Wall 
-Wstrict-prototypes -fPIC -I/usr/include/python2.4 -c 
Bio/clistfnsmodule.c -o build/temp.linux-i686-2.4/Bio/clistfnsmodule.o" 
doesn't. It may be that you have C_INCLUDE_PATH #defined somewhere, 
messing up the search paths.

--Michiel.

From sbassi at gmail.com  Sun Apr 29 01:58:44 2007
From: sbassi at gmail.com (Sebastian Bassi)
Date: Sun, 29 Apr 2007 02:58:44 -0300
Subject: [Biopython-dev] Problem compiling Biopython 1.43 in Ubuntu
In-Reply-To: <46342E2D.6000806@c2b2.columbia.edu>
References: <b43bf2080704100811m1dd67174u6a51b3d0275e4c6a@mail.gmail.com>
	<46342E2D.6000806@c2b2.columbia.edu>
Message-ID: <b43bf2080704282258r410bae75tb958c3e01a9e993@mail.gmail.com>

On 4/29/07, Michiel de Hoon <mdehoon at c2b2.columbia.edu> wrote:
>  From your output, Bio.KDTree does not seem to be the problem.
...
> If gcc cannot find standard headers such as limits.h or stdio.h, there
> seems to be a real problem with your installation. Can you compile a
....

I already fixed. Build-essential was missing (this was in a brand new
Ubuntu install). Then I updated the biopython wiki with the list of
packages that must be installed before installing BioPython in Ubuntu
on 13th April.
Thank you anyway for your help!
Best,
SB

From bugzilla-daemon at portal.open-bio.org  Sun Apr 29 06:18:22 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 29 Apr 2007 06:18:22 -0400
Subject: [Biopython-dev] [Bug 2268] Cluster unit test suite runs indefinitely
In-Reply-To: <bug-2268-42@http.bugzilla.open-bio.org/>
Message-ID: <200704291018.l3TAIMDP009802@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2268





------- Comment #4 from mdehoon at ims.u-tokyo.ac.jp  2007-04-29 06:18 EST -------
Which platform are you on (Windows/MacOSX/Unix/Linux)? I would like to
reproduce this bug.


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From bugzilla-daemon at portal.open-bio.org  Sun Apr 29 06:57:44 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 29 Apr 2007 06:57:44 -0400
Subject: [Biopython-dev] [Bug 2251] [PATCH] NumPy support for BioPython
In-Reply-To: <bug-2251-42@http.bugzilla.open-bio.org/>
Message-ID: <200704291057.l3TAvixC011222@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2251





------- Comment #11 from mdehoon at ims.u-tokyo.ac.jp  2007-04-29 06:57 EST -------
Looking at this patch again, it seems that it is still broken for 64-bits
platforms.

In NumPy, the struct PyArrayObject has a member npy_intp *dimensions. In
parse_array, we set nrows and ncols equal to dimensions[0] and dimensions[1],
respectively. The variables nrows and ncols are both int. What if npy_intp* is
not equal to int*?

By the way, I don't quite understand why the dimensions member is declared
npy_intp* in NumPy. In Numeric, the same member is int*, so in NumPy I would
expect to find npy_intp without the *.


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From bugzilla-daemon at portal.open-bio.org  Sun Apr 29 12:01:43 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 29 Apr 2007 12:01:43 -0400
Subject: [Biopython-dev] [Bug 2268] Cluster unit test suite runs indefinitely
In-Reply-To: <bug-2268-42@http.bugzilla.open-bio.org/>
Message-ID: <200704291601.l3TG1hgA021031@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2268





------- Comment #5 from chris.lasher at gmail.com  2007-04-29 12:01 EST -------
I experience this bug in Linux (Ubuntu 6.10 Edgy Eft) on 32-bit Intel boxes. Is
this bug not reproducible across all platforms?


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From bugzilla-daemon at portal.open-bio.org  Sun Apr 29 15:06:51 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 29 Apr 2007 15:06:51 -0400
Subject: [Biopython-dev] [Bug 2268] Cluster unit test suite runs indefinitely
In-Reply-To: <bug-2268-42@http.bugzilla.open-bio.org/>
Message-ID: <200704291906.l3TJ6p9K026799@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2268


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |biopython-
                   |                            |bugzilla at maubp.freeserve.co.
                   |                            |uk




------- Comment #6 from biopython-bugzilla at maubp.freeserve.co.uk  2007-04-29 15:06 EST -------
I can't reproduce this here.

I find test_Cluster.py runs very quickly (and passes) on my 64 bit Linux
machine (Ubuntu Linux 6.04 Dapper Drake) using python 2.4.3 and a freshly
downloaded biopython from CVS.

Barring the usual "import errors" for tests which depend on 3rd party resources
I don't have setup (like the SQL stuff) all the tests ran OK taking 2 minutes.


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From bugzilla-daemon at portal.open-bio.org  Sun Apr 29 15:26:18 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 29 Apr 2007 15:26:18 -0400
Subject: [Biopython-dev] [Bug 2284] New: Bio.GFF.easy uses Bio.SeqIO.FASTA
	which is now deprecated
Message-ID: <bug-2284-42@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2284

           Summary: Bio.GFF.easy uses Bio.SeqIO.FASTA which is now
                    deprecated
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


Specifically Bio.SeqIO.FASTA.FastaReader() and Bio.SeqIO.FASTA.FastaWriter()
are used by the following:

function fasta_single()
function fasta_multi()
function fasta_write()
class TempFastaWriter
class TempFastaWriterSingle

I'm not sure about the classes do, the doc-string unit test (and therefore
test_GFF.py) don't cover them.  Maybe we can deprecate/remove them?

Modifiying the functions to use Bio.SeqIO should be trivial.  I'm tempted to
suggest we deprecate/remove the fasta utility functions instead - and
genbank_single() too.


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From bugzilla-daemon at portal.open-bio.org  Sun Apr 29 15:49:44 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 29 Apr 2007 15:49:44 -0400
Subject: [Biopython-dev] [Bug 2284] Bio.GFF.easy uses Bio.SeqIO.FASTA which
	is now deprecated
In-Reply-To: <bug-2284-42@http.bugzilla.open-bio.org/>
Message-ID: <200704291949.l3TJniBs028138@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2284


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
         AssignedTo|biopython-dev at biopython.org |biopython-
                   |                            |bugzilla at maubp.freeserve.co.
                   |                            |uk
             Status|NEW                         |ASSIGNED




------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2007-04-29 15:49 EST -------
Created an attachment (id=642)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=642&action=view)
Patch to Bio/GFF/easy.py

Updates fasta utility functions to use Bio.SeqIO instead of Bio.SeqIO.FASTA
Removes classes TempFastaWriter and TempFastaWriterSingle


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From biopython-dev at maubp.freeserve.co.uk  Sun Apr 29 18:56:19 2007
From: biopython-dev at maubp.freeserve.co.uk (Peter)
Date: Sun, 29 Apr 2007 23:56:19 +0100
Subject: [Biopython-dev] UniGene flat file parser
In-Reply-To: <4542ED32.8060702@c2b2.columbia.edu>
References: <200610261056.25883.sdavis2@mail.nih.gov>	<4540F7F4.2050003@c2b2.columbia.edu>	<014DBF86B19310419F0DF8910FC56457240CEA@nihcesmlbx10.nih.gov>
	<4542ED32.8060702@c2b2.columbia.edu>
Message-ID: <46352293.8030004@maubp.freeserve.co.uk>

Hello Sean,

Late last year there was a thread talking about adding your UniGene flat 
file parser to Biopython - which you did on Oct 31st 2006 according to CVS.

I've just checked in a very simple unit test - please feel free to 
improve or add to this if needed.

Peter


From bugzilla-daemon at portal.open-bio.org  Mon Apr 30 05:20:37 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 30 Apr 2007 05:20:37 -0400
Subject: [Biopython-dev] [Bug 2285] New: Creating Bio.AlignIO to cope with
	alignments like Bio.SeqIO does sequences
Message-ID: <bug-2285-42@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2285

           Summary: Creating Bio.AlignIO to cope with alignments like
                    Bio.SeqIO does sequences
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


I would like to introduce an alignment equivalent of the SeqRecord based
Bio.SeqIO module, sample usage:

from Bio import AlignIO
for alignment in AlignIO.parse(open("many.phy"), "phylip") :
     print "Alignment with %i sequences of length %i" \
         % (len(alignment.get_all_seqs()),
            alignment.get_alignment_length())

As with Bio.SeqIO, I would have an input function "parse" which returns an
iterator - but giving Alignment objects.  Based on my own experience, most
alignment files usually contain a single alignment, but this is not the general
case.

For example, given a concatenated PHLYIP alignment (e.g. produced by seqboot)
containing five alignments of four sequences, then AlignIO.parse() would return
an interator giving five Alignment objects. Currently Bio.SeqIO won't parse
such PHLYIP files, but I would make it return twenty SeqRecords.

Clustalw and Stockholm files can also be concatenated and can use used to hold
many different multiple sequence alignments.

Another example is the EMBOSS simple/pairs alignment format, which again is
frequently used to hold more than one alignment. I would plan to add support
for this file format in Bio.AlignIO

Details:
I would move and rewrite the existing Bio.SeqIO code for clustal, stockholm and
phylip formats to Bio.AlignIO, and modify the Bio.SeqIO parse and write
functions to offload work to Bio.AlignIO when there is no Bio.SeqIO handler
defined.

Progress:
I have this working for parsing clustal, stockholm and phylip files already -
and converting the writers is underway.

I aim to attach a (big) patch shortly, and would like some feedback/discussion
on the idea.

See also Bug 1944 to enhance the Alignment class - Bio.AlignIO can be
implemented without that work.


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From bugzilla-daemon at portal.open-bio.org  Mon Apr 30 10:51:28 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 30 Apr 2007 10:51:28 -0400
Subject: [Biopython-dev] [Bug 2268] Cluster unit test suite runs indefinitely
In-Reply-To: <bug-2268-42@http.bugzilla.open-bio.org/>
Message-ID: <200704301451.l3UEpS3I001417@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2268





------- Comment #7 from chris.lasher at gmail.com  2007-04-30 10:51 EST -------
I installed Ubuntu 7.04 (Feisty Fawn) on 32-bit Intel, and this bug persists
with the latest CVS on that distribution.


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From bugzilla-daemon at portal.open-bio.org  Mon Apr  2 18:03:49 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 2 Apr 2007 14:03:49 -0400
Subject: [Biopython-dev] [Bug 2251] [PATCH] NumPy support for BioPython
In-Reply-To: <bug-2251-42@http.bugzilla.open-bio.org/>
Message-ID: <200704021803.l32I3nI9004963@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2251


edschofield at gmail.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
         OS/Version|Linux                       |All




------- Comment #6 from edschofield at gmail.com  2007-04-02 14:03 EST -------
Yes, you're right; this would lead to buggy behaviour in the cluster module on
64-bit platforms with arrays defined with more than 2^32 = 4294967296 rows or
columns.

Are you willing to change the sizes for the relevant array dimensions in
cluster.c from int to intptr_t? This is defined in stdint.h under the C99
standard.

If not, we'd need to stick with int definitions throughout clustermodule.c too,
converting to intp only when necessary for numpy.


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From sbassi at gmail.com  Mon Apr  2 18:32:58 2007
From: sbassi at gmail.com (Sebastian Bassi)
Date: Mon, 2 Apr 2007 15:32:58 -0300
Subject: [Biopython-dev] Changes in BLAST URLAPI
Message-ID: <b43bf2080704021132t1bfe0b85i244604318558a1b8@mail.gmail.com>

I wonder if net blast would be affected by this change (from April 16,
according to BLAST newsletter):

=====================================================

A Note About URLAPI

The new BLAST pages support URLAPI, a protocol that scripts and
programs use to run BLAST searches and retrieve results over
HTTP. (For more on URLAPI, see
http://www.ncbi.nlm.nih.gov/blast/Doc/urlapi.html). The following
information only applies to you if you develop or are responsible
for software that uses URLAPI.

The new pages have been tested and produce correct results with
the following URLAPI client programs:

* the BioPERL RemoteBlast module
* the NCBI demo script http://ncbi.nlm.nih.gov/blast/docs/web_blast.pl
* various scripts used in-house at NCBI

Users of URLAPI should be aware of the following minor
changes. In the new interface:

1. The Request ID (RID) format will be shorter.  The new format
   is 11 alphanumeric characters (e.g. RDEFEA5012) and will have no
   internal structure. The previous RID format was 36 or more
   characters long, including punctuation (e.g.,
   1175172712-21345-42512597310.BLASTQ3).

2. BLAST reports will show masked regions as lower-case letters
   by default (see
   http://nar.oxfordjournals.org/cgi/content/full/34/suppl_2/W6,
   figure 2. The current default behavior is to show masked
   regions as N's or X's. Users may recover the current behavior
   by adding &MASK_CHAR=0 to the query string for a URLAPI
   request.

3. BLAST reports will show alignments for 100 database sequences
   by default. The current reports show only 50 alignments by
   default.

If you have any questions please send them to mcginnis at ncbi.nlm.nih.gov

=======================================================


From bugzilla-daemon at portal.open-bio.org  Mon Apr  2 19:02:00 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 2 Apr 2007 15:02:00 -0400
Subject: [Biopython-dev] [Bug 2251] [PATCH] NumPy support for BioPython
In-Reply-To: <bug-2251-42@http.bugzilla.open-bio.org/>
Message-ID: <200704021902.l32J20s6007626@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2251





------- Comment #7 from edschofield at gmail.com  2007-04-02 15:02 EST -------
Forget the last comment. Here's a less invasive patch. It seems there's only a
need for explicit int/intp conversion in one function (parse_mask).


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From bugzilla-daemon at portal.open-bio.org  Mon Apr  2 19:04:13 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 2 Apr 2007 15:04:13 -0400
Subject: [Biopython-dev] [Bug 2251] [PATCH] NumPy support for BioPython
In-Reply-To: <bug-2251-42@http.bugzilla.open-bio.org/>
Message-ID: <200704021904.l32J4DpR007752@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2251


edschofield at gmail.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
 Attachment #611 is|0                           |1
           obsolete|                            |




------- Comment #8 from edschofield at gmail.com  2007-04-02 15:04 EST -------
Created an attachment (id=617)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=617&action=view)
Version 7 of patch for NumPy support


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From sbassi at gmail.com  Tue Apr 10 15:11:04 2007
From: sbassi at gmail.com (Sebastian Bassi)
Date: Tue, 10 Apr 2007 12:11:04 -0300
Subject: [Biopython-dev] Problem compiling Biopython 1.43 in Ubuntu
Message-ID: <b43bf2080704100811m1dd67174u6a51b3d0275e4c6a@mail.gmail.com>

Hello,

I tried to build biopython 1.43 in Ubuntu 6.10 (Edgy Eft). First I met
all dependencies and then I did:
python setup.py build and it failed. So the second try was with N in
the question about compiling Bio.KDTree and I got the same:

sbassi at inet2BALC:~/bioinfo/biopython-1.43$ python setup.py build
running build
running build_py

*** Bio.KDTree *** NOT built by default

The Bio.PDB.NeighborSearch module depends on the Bio.KDTree module,
which in turn, depends on C++ code that does not compile cleanly on
all platforms. Hence, Bio.KDTree is not built by default.

Would you like to build Bio.KDTree ? (y/N)
running build_ext
building 'Bio.clistfns' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O2 -Wall
-Wstrict-prototypes -fPIC -I/usr/include/python2.4 -c
Bio/clistfnsmodule.c -o build/temp.linux-i686-2.4/Bio/clistfnsmodule.o
In file included from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/syslimits.h:7,
                 from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:11,
                 from /usr/include/python2.4/Python.h:18,
                 from Bio/clistfnsmodule.c:10:
/usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:122:61: error:
limits.h: No such file or directory
In file included from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/Python.h:32:19: error: stdio.h: No such file or directory
/usr/include/python2.4/Python.h:34:5: error: #error "Python.h requires
that stdio.h define NULL."
/usr/include/python2.4/Python.h:37:20: error: string.h: No such file
or directory
/usr/include/python2.4/Python.h:38:19: error: errno.h: No such file or directory
/usr/include/python2.4/Python.h:39:20: error: stdlib.h: No such file
or directory
/usr/include/python2.4/Python.h:41:20: error: unistd.h: No such file
or directory
/usr/include/python2.4/Python.h:53:20: error: assert.h: No such file
or directory
In file included from /usr/include/python2.4/Python.h:55,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pyport.h:7:20: error: stdint.h: No such file or directory
In file included from /usr/include/python2.4/Python.h:55,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pyport.h:73: error: expected '=', ',', ';',
'asm' or '__attribute__' before 'Py_uintptr_t'
/usr/include/python2.4/pyport.h:74: error: expected '=', ',', ';',
'asm' or '__attribute__' before 'Py_intptr_t'
/usr/include/python2.4/pyport.h:94:76: error: math.h: No such file or directory
/usr/include/python2.4/pyport.h:101:22: error: sys/time.h: No such
file or directory
/usr/include/python2.4/pyport.h:102:18: error: time.h: No such file or directory
/usr/include/python2.4/pyport.h:120:24: error: sys/select.h: No such
file or directory
/usr/include/python2.4/pyport.h:159:22: error: sys/stat.h: No such
file or directory
In file included from /usr/include/python2.4/Python.h:74,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pymem.h:50: warning: parameter names (without
types) in function declaration
/usr/include/python2.4/pymem.h:51: error: expected declaration
specifiers or '...' before 'size_t'
In file included from /usr/include/python2.4/Python.h:76,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/object.h:227: error: expected declaration
specifiers or '...' before 'FILE'
/usr/include/python2.4/object.h:371: error: expected declaration
specifiers or '...' before 'FILE'
In file included from /usr/include/python2.4/Python.h:77,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/objimpl.h:97: warning: parameter names (without
types) in function declaration
/usr/include/python2.4/objimpl.h:98: error: expected declaration
specifiers or '...' before 'size_t'
/usr/include/python2.4/objimpl.h:292: warning: parameter names
(without types) in function declaration
In file included from /usr/include/python2.4/Python.h:81,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/unicodeobject.h:55:19: error: ctype.h: No such
file or directory
/usr/include/python2.4/unicodeobject.h:118:21: error: wchar.h: No such
file or directory
In file included from /usr/include/python2.4/Python.h:81,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/unicodeobject.h:131: error: expected '=', ',',
';', 'asm' or '__attribute__' before 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:376: error: expected
specifier-qualifier-list before 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:422: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:422: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:429: error: expected '=', ',',
';', 'asm' or '__attribute__' before '*' token
/usr/include/python2.4/unicodeobject.h:440: error: expected '=', ',',
';', 'asm' or '__attribute__' before 'PyUnicodeUCS4_GetMax'
/usr/include/python2.4/unicodeobject.h:511: warning: type defaults to
'int' in declaration of 'wchar_t'
/usr/include/python2.4/unicodeobject.h:511: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:529: warning: type defaults to
'int' in declaration of 'wchar_t'
/usr/include/python2.4/unicodeobject.h:529: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:621: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:621: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:654: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:654: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:683: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:683: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:760: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:760: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:779: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:779: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:796: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:796: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:827: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:827: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:849: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:849: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:891: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:891: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:912: warning: type defaults to
'int' in declaration of 'Py_UNICODE'
/usr/include/python2.4/unicodeobject.h:912: error: expected ';', ','
or ')' before '*' token
/usr/include/python2.4/unicodeobject.h:965: error: expected ')' before '*' token
/usr/include/python2.4/unicodeobject.h:1143: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1147: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1151: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1155: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1159: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1162: error: expected '=', ',',
';', 'asm' or '__attribute__' before '_PyUnicodeUCS4_ToLowercase'
/usr/include/python2.4/unicodeobject.h:1166: error: expected '=', ',',
';', 'asm' or '__attribute__' before '_PyUnicodeUCS4_ToUppercase'
/usr/include/python2.4/unicodeobject.h:1170: error: expected '=', ',',
';', 'asm' or '__attribute__' before '_PyUnicodeUCS4_ToTitlecase'
/usr/include/python2.4/unicodeobject.h:1175: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1179: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1183: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1187: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1191: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1195: error: expected ')' before 'ch'
/usr/include/python2.4/unicodeobject.h:1199: error: expected ')' before 'ch'
In file included from /usr/include/python2.4/Python.h:82,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/intobject.h:35: error: expected ')' before '*' token
In file included from /usr/include/python2.4/Python.h:84,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/longobject.h:46: error: expected ')' before '*' token
/usr/include/python2.4/longobject.h:63: error: expected '=', ',', ';',
'asm' or '__attribute__' before '_PyLong_NumBits'
/usr/include/python2.4/longobject.h:79: error: expected declaration
specifiers or '...' before 'size_t'
/usr/include/python2.4/longobject.h:102: error: expected declaration
specifiers or '...' before 'size_t'
In file included from /usr/include/python2.4/Python.h:101,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/fileobject.h:12: error: expected
specifier-qualifier-list before 'FILE'
/usr/include/python2.4/fileobject.h:38: error: expected ')' before '*' token
/usr/include/python2.4/fileobject.h:40: error: expected '=', ',', ';',
'asm' or '__attribute__' before '*' token
/usr/include/python2.4/fileobject.h:57: error: expected declaration
specifiers or '...' before 'FILE'
/usr/include/python2.4/fileobject.h:58: error: expected '=', ',', ';',
'asm' or '__attribute__' before 'Py_UniversalNewlineFread'
In file included from /usr/include/python2.4/Python.h:112,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pyerrors.h:156: warning: type defaults to 'int'
in declaration of 'Py_UNICODE'
/usr/include/python2.4/pyerrors.h:156: error: expected ';', ',' or ')'
before '*' token
/usr/include/python2.4/pyerrors.h:160: warning: type defaults to 'int'
in declaration of 'Py_UNICODE'
/usr/include/python2.4/pyerrors.h:160: error: expected ';', ',' or ')'
before '*' token
/usr/include/python2.4/pyerrors.h:226: error: expected declaration
specifiers or '...' before 'size_t'
/usr/include/python2.4/pyerrors.h:227: error: format string argument
not a string type
/usr/include/python2.4/pyerrors.h:228: error: expected declaration
specifiers or '...' before 'size_t'
In file included from /usr/include/python2.4/Python.h:117,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pythonrun.h:32: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:33: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:35: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:36: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:40: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:41: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:42: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:43: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:44: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:45: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:46: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:49: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:55: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:59: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:60: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:64: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:66: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:82: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:123: error: expected ')' before '*' token
/usr/include/python2.4/pythonrun.h:125: error: expected ')' before '*' token
In file included from /usr/include/python2.4/Python.h:119,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/sysmodule.h:12: error: expected '=', ',', ';',
'asm' or '__attribute__' before '*' token
In file included from /usr/include/python2.4/Python.h:121,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/import.h:25: error: expected declaration
specifiers or '...' before 'size_t'
/usr/include/python2.4/import.h:25: error: expected declaration
specifiers or '...' before 'FILE'
In file included from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/Python.h:131: error: expected declaration
specifiers or '...' before 'size_t'
In file included from /usr/include/python2.4/Python.h:149,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pyfpe.h:129:20: error: signal.h: No such file
or directory
/usr/include/python2.4/pyfpe.h:130:20: error: setjmp.h: No such file
or directory
In file included from /usr/include/python2.4/Python.h:149,
                 from Bio/clistfnsmodule.c:10:
/usr/include/python2.4/pyfpe.h:132: error: expected '=', ',', ';',
'asm' or '__attribute__' before 'PyFPE_jbuf'
Bio/clistfnsmodule.c: In function 'clistfns_count':
Bio/clistfnsmodule.c:33: error: 'NULL' undeclared (first use in this function)
Bio/clistfnsmodule.c:33: error: (Each undeclared identifier is
reported only once
Bio/clistfnsmodule.c:33: error: for each function it appears in.)
Bio/clistfnsmodule.c: In function 'clistfns_contents':
Bio/clistfnsmodule.c:90: error: 'NULL' undeclared (first use in this function)
Bio/clistfnsmodule.c: At top level:
Bio/clistfnsmodule.c:149: error: 'NULL' undeclared here (not in a function)
error: command 'gcc' failed with exit status 1


From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 04:19:27 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 00:19:27 -0400
Subject: [Biopython-dev] [Bug 2266] New: setup.py test does not take options
Message-ID: <bug-2266-42@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2266

           Summary: setup.py test does not take options
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: chris.lasher at gmail.com


Currently, setup.py does not support passing options to the test command. The
Tests/run_tests.py script, however, takes the command line argument "--no-gui"
for running tests in non-GUI mode. This should be an option for setup.py test,
as well.


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From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 04:32:16 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 00:32:16 -0400
Subject: [Biopython-dev] [Bug 2266] setup.py test does not take options
In-Reply-To: <bug-2266-42@http.bugzilla.open-bio.org/>
Message-ID: <200704110432.l3B4WGNm007098@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2266





------- Comment #1 from chris.lasher at gmail.com  2007-04-11 00:32 EST -------
Created an attachment (id=621)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=621&action=view)
Patch to add option --no-gui to setup.py test.

This patch affects setup.py as well as Tests/run_tests.py. The modification to
setup.py gives the option of --no-gui for the command "test", which is passed
to Tests/run_tests.py as an argument. The modification to run_tests.py includes
changing argv from being sys.argv by default to sys.argv[1:] by default, which
is more conventional, and also easier to substitute for cases such as this
where run_test.main() is called externally.


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From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 04:34:22 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 00:34:22 -0400
Subject: [Biopython-dev] [Bug 2266] setup.py test does not take options
In-Reply-To: <bug-2266-42@http.bugzilla.open-bio.org/>
Message-ID: <200704110434.l3B4YM1g007209@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2266


chris.lasher at gmail.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |ASSIGNED




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From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 04:55:30 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 00:55:30 -0400
Subject: [Biopython-dev] [Bug 2266] setup.py test does not take options
In-Reply-To: <bug-2266-42@http.bugzilla.open-bio.org/>
Message-ID: <200704110455.l3B4tUWo007910@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2266





------- Comment #2 from chris.lasher at gmail.com  2007-04-11 00:55 EST -------
I have committed the changes in this patch to the CVS repository.


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From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 04:56:52 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 00:56:52 -0400
Subject: [Biopython-dev] [Bug 2266] setup.py test does not take options
In-Reply-To: <bug-2266-42@http.bugzilla.open-bio.org/>
Message-ID: <200704110456.l3B4uqa3007970@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2266


chris.lasher at gmail.com changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|ASSIGNED                    |RESOLVED
         Resolution|                            |FIXED




------- Comment #3 from chris.lasher at gmail.com  2007-04-11 00:56 EST -------
Closing bug.


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From chris.lasher at gmail.com  Wed Apr 11 05:04:51 2007
From: chris.lasher at gmail.com (Chris Lasher)
Date: Wed, 11 Apr 2007 01:04:51 -0400
Subject: [Biopython-dev] Bugzilla Version Numbers
Message-ID: <128a885f0704102204p2872f42fh685919bb8b4656c3@mail.gmail.com>

Hi all,

Does anybody active with Biopython have administrative capabilities
for the project's Bugzilla tracker? The version numbers are a wee bit
out of date.

Chris


From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 15:56:39 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 11:56:39 -0400
Subject: [Biopython-dev] [Bug 2268] New: Cluster unit test suite runs
	indefinitely
Message-ID: <bug-2268-42@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2268

           Summary: Cluster unit test suite runs indefinitely
           Product: Biopython
           Version: Not Applicable
          Platform: PC
        OS/Version: All
            Status: NEW
          Severity: critical
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: chris.lasher at gmail.com


The tests contained in Tests/test_Cluster.py seem to run indefinitely. This
prevents running all unit tests in the Biopython test suite to completion. I am
marking this bug as critical. The only workaround I have found has been to
disable these tests from being run by Tests/run_tests.py. This is not an
acceptable permanent solution.


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From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 16:04:07 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 12:04:07 -0400
Subject: [Biopython-dev] [Bug 2268] Cluster unit test suite runs indefinitely
In-Reply-To: <bug-2268-42@http.bugzilla.open-bio.org/>
Message-ID: <200704111604.l3BG47O0016964@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2268





------- Comment #1 from chris.lasher at gmail.com  2007-04-11 12:04 EST -------
Created an attachment (id=622)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=622&action=view)
run_tests_cluster.patch

This patch prevents the tests in test_Cluster.py from being run by default in
run_tests.py. This is not a permanent solution, it is a workaround.


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From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 16:17:42 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 12:17:42 -0400
Subject: [Biopython-dev] [Bug 2269] New: Shebang (hashbang) lines need
	cleanup
Message-ID: <bug-2269-42@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2269

           Summary: Shebang (hashbang) lines need cleanup
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: chris.lasher at gmail.com


The shebang/hashbang (i.e., "#!/usr/bin...") lines in the Biopython scripts
need to be tidied up. Currently there are 8 different shebang variations in the
Biopython library:

#! /usr/bin/env python
#!/usr/bin/env python
#!/usr/bin/env python2.3
#! /usr/bin/python
#!/usr/bin/python
#!/usr/bin/python 
#!/usr/bin/python -i
#!/usr/bin/python -OO

I propose to move these all to the following standard Python form:
#!/usr/bin/env python


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From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 16:26:22 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 12:26:22 -0400
Subject: [Biopython-dev] [Bug 2268] Cluster unit test suite runs indefinitely
In-Reply-To: <bug-2268-42@http.bugzilla.open-bio.org/>
Message-ID: <200704111626.l3BGQMEr018888@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2268





------- Comment #2 from mdehoon at ims.u-tokyo.ac.jp  2007-04-11 12:26 EST -------
Can you check which of the tests hangs?
You can run python test_Cluster.py to get more information.


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From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 16:32:33 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 12:32:33 -0400
Subject: [Biopython-dev] [Bug 2251] [PATCH] NumPy support for BioPython
In-Reply-To: <bug-2251-42@http.bugzilla.open-bio.org/>
Message-ID: <200704111632.l3BGWXs6019455@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2251





------- Comment #9 from mdehoon at ims.u-tokyo.ac.jp  2007-04-11 12:32 EST -------
In this patch, do you still need to define NPY_GENERIC_DIMENSION_FMT in
python/clustermodule.c? Since you don't seem to be using it.


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From bugzilla-daemon at portal.open-bio.org  Wed Apr 11 17:02:55 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Wed, 11 Apr 2007 13:02:55 -0400
Subject: [Biopython-dev] [Bug 2251] [PATCH] NumPy support for BioPython
In-Reply-To: <bug-2251-42@http.bugzilla.open-bio.org/>
Message-ID: <200704111702.l3BH2tFh022804@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2251





------- Comment #10 from edschofield at gmail.com  2007-04-11 13:02 EST -------
(In reply to comment #9)
> In this patch, do you still need to define NPY_GENERIC_DIMENSION_FMT in
> python/clustermodule.c? Since you don't seem to be using it.

Yeah, I realized that as soon as I mailed off the last patch. Do you want me to
create a new patch just for this change? I figure such small changes can be
made more easily in-tree.


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From bugzilla-daemon at portal.open-bio.org  Fri Apr 13 21:55:10 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Fri, 13 Apr 2007 17:55:10 -0400
Subject: [Biopython-dev] [Bug 2268] Cluster unit test suite runs indefinitely
In-Reply-To: <bug-2268-42@http.bugzilla.open-bio.org/>
Message-ID: <200704132155.l3DLtAUB011430@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2268





------- Comment #3 from chris.lasher at gmail.com  2007-04-13 17:55 EST -------
It hangs on line 181 in "def test_kcluster"
clusterid, error, nfound = kcluster (data1, nclusters=nclusters, mask=mask1,
weight=weight1, transpose=0, npass=100, method='a', dist='e')


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From biopython-dev at maubp.freeserve.co.uk  Thu Apr 19 10:08:52 2007
From: biopython-dev at maubp.freeserve.co.uk (Peter)
Date: Thu, 19 Apr 2007 11:08:52 +0100
Subject: [Biopython-dev] Bugzilla Version Numbers
In-Reply-To: <128a885f0704102204p2872f42fh685919bb8b4656c3@mail.gmail.com>
References: <128a885f0704102204p2872f42fh685919bb8b4656c3@mail.gmail.com>
Message-ID: <46273FB4.4030805@maubp.freeserve.co.uk>

Chris Lasher wrote:
> Hi all,
> 
> Does anybody active with Biopython have administrative capabilities
> for the project's Bugzilla tracker? The version numbers are a wee bit
> out of date.

They are, aren't they!  I asked on the list last month about this, and 
updating the component fields too:

http://lists.open-bio.org/pipermail/biopython-dev/2007-March/002652.html

As no-one on the list has come forward, I guess one of us should get in 
touch with the relevant Open Bio people, probably by emailing "support" 
at the domain helpdesk.open-bio.org

Who needs/wants bugzilla admin rights?

Peter



From biopython-dev at maubp.freeserve.co.uk  Fri Apr 27 18:29:13 2007
From: biopython-dev at maubp.freeserve.co.uk (Peter)
Date: Fri, 27 Apr 2007 19:29:13 +0100
Subject: [Biopython-dev] Unified aligmment input/output, Bio.AlignIO?
Message-ID: <463240F9.8010907@maubp.freeserve.co.uk>

Following the release of Biopython 1.43 with Bio.SeqIO, I would like to 
do a better job for multiple sequence alignment file formats - creating 
a new module Bio.AlignIO

While most multiple sequence alignment files usually contain a single 
alignment (made up of multiple sequences), this is not the general case.

In the PHYLIP suite, concatenated alignments in phylip format are 
produced by the seqboot program for tasks like bootstrapping of a 
phylogenetic tree.  Currently SeqIO chokes on these!

Another example is the output of some the EMBOSS programs can contain 
many multiple sequences alignments, for example the water and needle 
tools can produce many pairwise alignments.

In such cases, being able to write code like the following seems to be 
the logical extension of the Bio.SeqIO style we have agreed on:

from Bio import AlignIO
for alignment in AlignIO.parse("many.phy", "phylip") :
     print "Alignment with %i sequences of length %i" \
         % (len(alignment.get_all_seqs()),
            alignment.get_alignment_length())
     ...

i.e. The AlignIO.parse() function would be an iterator returning 
alignment objects. Does this sound reasonable so far?

As part of this work, I would also like to introduce a "RichAlignment" 
or "AnnotatedAlignment" as a subclass of the generic Alignment class 
which would be able to hold all the alignment annotation found in 
pfam/stockholm files such as alignment ID, description, comments etc 
plus all the per column annotation.

Assuming the existence of this AnnotatedAlignment class, the existing 
PFAM/Stockholm parser in Bio.SeqIO would be turned into a Bio.AlignIO 
parser to take advantage of the rich annotation.

Note - I would intend to still allow Bio.SeqIO to be used on multiple 
sequence alignment files, however the implementation may well do this 
internally via Bio.AlignIO

---------------------------------------------------------------------

This also raises the related (but separate) issue of improving the 
generic Alignment object, raised in bug 1944:

http://bugzilla.open-bio.org/show_bug.cgi?id=1944

I personally would prefer the alignment class to act more like an 
array/matrix of residues/characters.

I would also like to be able to splice an alignment (both by the 
columns, or by the sequence numbers) to get a sub-alignment.  The 
suggested AnnotatedAlignment class would have to take care of also 
splicing any per sequence or per column annotation.

Peter



From mdehoon at c2b2.columbia.edu  Sun Apr 29 05:33:33 2007
From: mdehoon at c2b2.columbia.edu (Michiel de Hoon)
Date: Sun, 29 Apr 2007 14:33:33 +0900
Subject: [Biopython-dev] Problem compiling Biopython 1.43 in Ubuntu
In-Reply-To: <b43bf2080704100811m1dd67174u6a51b3d0275e4c6a@mail.gmail.com>
References: <b43bf2080704100811m1dd67174u6a51b3d0275e4c6a@mail.gmail.com>
Message-ID: <46342E2D.6000806@c2b2.columbia.edu>

Sorry for my late reply.

Sebastian Bassi wrote:
> I tried to build biopython 1.43 in Ubuntu 6.10 (Edgy Eft). First I met
> all dependencies and then I did:
> python setup.py build and it failed. So the second try was with N in
> the question about compiling Bio.KDTree and I got the same:

 From your output, Bio.KDTree does not seem to be the problem.

> sbassi at inet2BALC:~/bioinfo/biopython-1.43$ python setup.py build
> running build
> running build_py
 > ...
> running build_ext
> building 'Bio.clistfns' extension
> gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O2 -Wall
> -Wstrict-prototypes -fPIC -I/usr/include/python2.4 -c
> Bio/clistfnsmodule.c -o build/temp.linux-i686-2.4/Bio/clistfnsmodule.o
> In file included from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/syslimits.h:7,
>                  from /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:11,
>                  from /usr/include/python2.4/Python.h:18,
>                  from Bio/clistfnsmodule.c:10:
> /usr/lib/gcc/i486-linux-gnu/4.1.2/include/limits.h:122:61: error:
> limits.h: No such file or directory
> In file included from Bio/clistfnsmodule.c:10:
> /usr/include/python2.4/Python.h:32:19: error: stdio.h: No such file or directory
...

If gcc cannot find standard headers such as limits.h or stdio.h, there 
seems to be a real problem with your installation. Can you compile a 
simple program with gcc if it #includes stdio.h? If not, try to solve 
that problem first. If so, try to find out why "gcc yourtestprogram.c" 
compiles, but "gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O2 -Wall 
-Wstrict-prototypes -fPIC -I/usr/include/python2.4 -c 
Bio/clistfnsmodule.c -o build/temp.linux-i686-2.4/Bio/clistfnsmodule.o" 
doesn't. It may be that you have C_INCLUDE_PATH #defined somewhere, 
messing up the search paths.

--Michiel.


From sbassi at gmail.com  Sun Apr 29 05:58:44 2007
From: sbassi at gmail.com (Sebastian Bassi)
Date: Sun, 29 Apr 2007 02:58:44 -0300
Subject: [Biopython-dev] Problem compiling Biopython 1.43 in Ubuntu
In-Reply-To: <46342E2D.6000806@c2b2.columbia.edu>
References: <b43bf2080704100811m1dd67174u6a51b3d0275e4c6a@mail.gmail.com>
	<46342E2D.6000806@c2b2.columbia.edu>
Message-ID: <b43bf2080704282258r410bae75tb958c3e01a9e993@mail.gmail.com>

On 4/29/07, Michiel de Hoon <mdehoon at c2b2.columbia.edu> wrote:
>  From your output, Bio.KDTree does not seem to be the problem.
...
> If gcc cannot find standard headers such as limits.h or stdio.h, there
> seems to be a real problem with your installation. Can you compile a
....

I already fixed. Build-essential was missing (this was in a brand new
Ubuntu install). Then I updated the biopython wiki with the list of
packages that must be installed before installing BioPython in Ubuntu
on 13th April.
Thank you anyway for your help!
Best,
SB


From bugzilla-daemon at portal.open-bio.org  Sun Apr 29 10:18:22 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 29 Apr 2007 06:18:22 -0400
Subject: [Biopython-dev] [Bug 2268] Cluster unit test suite runs indefinitely
In-Reply-To: <bug-2268-42@http.bugzilla.open-bio.org/>
Message-ID: <200704291018.l3TAIMDP009802@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2268





------- Comment #4 from mdehoon at ims.u-tokyo.ac.jp  2007-04-29 06:18 EST -------
Which platform are you on (Windows/MacOSX/Unix/Linux)? I would like to
reproduce this bug.


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From bugzilla-daemon at portal.open-bio.org  Sun Apr 29 10:57:44 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 29 Apr 2007 06:57:44 -0400
Subject: [Biopython-dev] [Bug 2251] [PATCH] NumPy support for BioPython
In-Reply-To: <bug-2251-42@http.bugzilla.open-bio.org/>
Message-ID: <200704291057.l3TAvixC011222@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2251





------- Comment #11 from mdehoon at ims.u-tokyo.ac.jp  2007-04-29 06:57 EST -------
Looking at this patch again, it seems that it is still broken for 64-bits
platforms.

In NumPy, the struct PyArrayObject has a member npy_intp *dimensions. In
parse_array, we set nrows and ncols equal to dimensions[0] and dimensions[1],
respectively. The variables nrows and ncols are both int. What if npy_intp* is
not equal to int*?

By the way, I don't quite understand why the dimensions member is declared
npy_intp* in NumPy. In Numeric, the same member is int*, so in NumPy I would
expect to find npy_intp without the *.


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From bugzilla-daemon at portal.open-bio.org  Sun Apr 29 16:01:43 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 29 Apr 2007 12:01:43 -0400
Subject: [Biopython-dev] [Bug 2268] Cluster unit test suite runs indefinitely
In-Reply-To: <bug-2268-42@http.bugzilla.open-bio.org/>
Message-ID: <200704291601.l3TG1hgA021031@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2268





------- Comment #5 from chris.lasher at gmail.com  2007-04-29 12:01 EST -------
I experience this bug in Linux (Ubuntu 6.10 Edgy Eft) on 32-bit Intel boxes. Is
this bug not reproducible across all platforms?


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From bugzilla-daemon at portal.open-bio.org  Sun Apr 29 19:06:51 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 29 Apr 2007 15:06:51 -0400
Subject: [Biopython-dev] [Bug 2268] Cluster unit test suite runs indefinitely
In-Reply-To: <bug-2268-42@http.bugzilla.open-bio.org/>
Message-ID: <200704291906.l3TJ6p9K026799@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2268


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
                 CC|                            |biopython-
                   |                            |bugzilla at maubp.freeserve.co.
                   |                            |uk




------- Comment #6 from biopython-bugzilla at maubp.freeserve.co.uk  2007-04-29 15:06 EST -------
I can't reproduce this here.

I find test_Cluster.py runs very quickly (and passes) on my 64 bit Linux
machine (Ubuntu Linux 6.04 Dapper Drake) using python 2.4.3 and a freshly
downloaded biopython from CVS.

Barring the usual "import errors" for tests which depend on 3rd party resources
I don't have setup (like the SQL stuff) all the tests ran OK taking 2 minutes.


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From bugzilla-daemon at portal.open-bio.org  Sun Apr 29 19:26:18 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 29 Apr 2007 15:26:18 -0400
Subject: [Biopython-dev] [Bug 2284] New: Bio.GFF.easy uses Bio.SeqIO.FASTA
	which is now deprecated
Message-ID: <bug-2284-42@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2284

           Summary: Bio.GFF.easy uses Bio.SeqIO.FASTA which is now
                    deprecated
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


Specifically Bio.SeqIO.FASTA.FastaReader() and Bio.SeqIO.FASTA.FastaWriter()
are used by the following:

function fasta_single()
function fasta_multi()
function fasta_write()
class TempFastaWriter
class TempFastaWriterSingle

I'm not sure about the classes do, the doc-string unit test (and therefore
test_GFF.py) don't cover them.  Maybe we can deprecate/remove them?

Modifiying the functions to use Bio.SeqIO should be trivial.  I'm tempted to
suggest we deprecate/remove the fasta utility functions instead - and
genbank_single() too.


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From bugzilla-daemon at portal.open-bio.org  Sun Apr 29 19:49:44 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Sun, 29 Apr 2007 15:49:44 -0400
Subject: [Biopython-dev] [Bug 2284] Bio.GFF.easy uses Bio.SeqIO.FASTA which
	is now deprecated
In-Reply-To: <bug-2284-42@http.bugzilla.open-bio.org/>
Message-ID: <200704291949.l3TJniBs028138@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2284


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
         AssignedTo|biopython-dev at biopython.org |biopython-
                   |                            |bugzilla at maubp.freeserve.co.
                   |                            |uk
             Status|NEW                         |ASSIGNED




------- Comment #1 from biopython-bugzilla at maubp.freeserve.co.uk  2007-04-29 15:49 EST -------
Created an attachment (id=642)
 --> (http://bugzilla.open-bio.org/attachment.cgi?id=642&action=view)
Patch to Bio/GFF/easy.py

Updates fasta utility functions to use Bio.SeqIO instead of Bio.SeqIO.FASTA
Removes classes TempFastaWriter and TempFastaWriterSingle


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From biopython-dev at maubp.freeserve.co.uk  Sun Apr 29 22:56:19 2007
From: biopython-dev at maubp.freeserve.co.uk (Peter)
Date: Sun, 29 Apr 2007 23:56:19 +0100
Subject: [Biopython-dev] UniGene flat file parser
In-Reply-To: <4542ED32.8060702@c2b2.columbia.edu>
References: <200610261056.25883.sdavis2@mail.nih.gov>	<4540F7F4.2050003@c2b2.columbia.edu>	<014DBF86B19310419F0DF8910FC56457240CEA@nihcesmlbx10.nih.gov>
	<4542ED32.8060702@c2b2.columbia.edu>
Message-ID: <46352293.8030004@maubp.freeserve.co.uk>

Hello Sean,

Late last year there was a thread talking about adding your UniGene flat 
file parser to Biopython - which you did on Oct 31st 2006 according to CVS.

I've just checked in a very simple unit test - please feel free to 
improve or add to this if needed.

Peter



From bugzilla-daemon at portal.open-bio.org  Mon Apr 30 09:20:37 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 30 Apr 2007 05:20:37 -0400
Subject: [Biopython-dev] [Bug 2285] New: Creating Bio.AlignIO to cope with
	alignments like Bio.SeqIO does sequences
Message-ID: <bug-2285-42@http.bugzilla.open-bio.org/>

http://bugzilla.open-bio.org/show_bug.cgi?id=2285

           Summary: Creating Bio.AlignIO to cope with alignments like
                    Bio.SeqIO does sequences
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


I would like to introduce an alignment equivalent of the SeqRecord based
Bio.SeqIO module, sample usage:

from Bio import AlignIO
for alignment in AlignIO.parse(open("many.phy"), "phylip") :
     print "Alignment with %i sequences of length %i" \
         % (len(alignment.get_all_seqs()),
            alignment.get_alignment_length())

As with Bio.SeqIO, I would have an input function "parse" which returns an
iterator - but giving Alignment objects.  Based on my own experience, most
alignment files usually contain a single alignment, but this is not the general
case.

For example, given a concatenated PHLYIP alignment (e.g. produced by seqboot)
containing five alignments of four sequences, then AlignIO.parse() would return
an interator giving five Alignment objects. Currently Bio.SeqIO won't parse
such PHLYIP files, but I would make it return twenty SeqRecords.

Clustalw and Stockholm files can also be concatenated and can use used to hold
many different multiple sequence alignments.

Another example is the EMBOSS simple/pairs alignment format, which again is
frequently used to hold more than one alignment. I would plan to add support
for this file format in Bio.AlignIO

Details:
I would move and rewrite the existing Bio.SeqIO code for clustal, stockholm and
phylip formats to Bio.AlignIO, and modify the Bio.SeqIO parse and write
functions to offload work to Bio.AlignIO when there is no Bio.SeqIO handler
defined.

Progress:
I have this working for parsing clustal, stockholm and phylip files already -
and converting the writers is underway.

I aim to attach a (big) patch shortly, and would like some feedback/discussion
on the idea.

See also Bug 1944 to enhance the Alignment class - Bio.AlignIO can be
implemented without that work.


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From bugzilla-daemon at portal.open-bio.org  Mon Apr 30 14:51:28 2007
From: bugzilla-daemon at portal.open-bio.org (bugzilla-daemon at portal.open-bio.org)
Date: Mon, 30 Apr 2007 10:51:28 -0400
Subject: [Biopython-dev] [Bug 2268] Cluster unit test suite runs indefinitely
In-Reply-To: <bug-2268-42@http.bugzilla.open-bio.org/>
Message-ID: <200704301451.l3UEpS3I001417@portal.open-bio.org>

http://bugzilla.open-bio.org/show_bug.cgi?id=2268





------- Comment #7 from chris.lasher at gmail.com  2007-04-30 10:51 EST -------
I installed Ubuntu 7.04 (Feisty Fawn) on 32-bit Intel, and this bug persists
with the latest CVS on that distribution.


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