peterjc (Peter Cock)

Name
Peter Cock
Website/Blog
http://www.warwick.ac.uk/go/peter_cock/
Location
Scotland, UK
Member Since
Mar 16, 2009 (9 months)

Following 8 githubbers and watching 6 repositories view all →

Public Repositories (1)

  • biopython

    My fork of the official git mirror of the Biopython CVS repository

    legend

    Forked from biopython/biopython Mon Mar 23 04:43:06 -0700 2009

    Last updated Tue Dec 22 09:19:03 -0800 2009

Public Activity feed

peterjc pushed to master at biopython/biopython Wed Dec 23 04:04:35 -0800 2009
HEAD is 3a150f8c1d01de6272a8681bc1c00cbc799694b5
  • peterjc committed 3a150f8c:
    Adding a few more NCBI Entrez DTD files, in particular eLink_090910.dtd which is currently in use, plus a selection of others found browsing their website which may also still be current
peterjc created branch master at peterjc/biopython Tue Dec 22 09:19:05 -0800 2009
New branch is at peterjc/biopython/tree/master
peterjc deleted branch master at peterjc/biopython Tue Dec 22 09:04:38 -0800 2009
Deleted branch was at peterjc/biopython/tree/master
peterjc pushed to master at peterjc/biopython Tue Dec 22 08:52:20 -0800 2009
HEAD is 3de284c98cb074baf2d749a8bc83836a547ce082
  • peterjc committed 3de284c9:
    Revert "Basic Bio.SeqIO.index() support for gzipped files."
peterjc pushed to master at biopython/biopython Tue Dec 22 08:48:21 -0800 2009
HEAD is 1a09129bdc91f872a32d66ac783f4cceec2fbf25
  • peterjc committed 1a09129b:
    Don't use failUnless in unittests (avoids a PendingDeprecationWarning in Python 2.7)
peterjc pushed to master at peterjc/biopython Tue Dec 22 08:45:28 -0800 2009
HEAD is 5a085664b386e892f431425811efc8b460dbc8d1
  • peterjc committed 5a085664:
    Basic Bio.SeqIO.index() support for gzipped files, based on discussion on the mailing list with Renato Alves and Eric Talevich, with doctest and unit tests. This has only been tested on Mac OS, but should be fine on Linux too. I have concerns about Windows, and DOS vs Unix newlines within a gzipped plain text file (the Python gzip.open does not seem to support mode='rU'). Binary files may also be an issue, e.g. SFF files, although these are less likely to be gzipped.
peterjc created branch index-zip at peterjc/biopython Tue Dec 22 07:26:06 -0800 2009
New branch is at peterjc/biopython/tree/index-zip
peterjc pushed to master at peterjc/biopython Tue Dec 22 06:35:42 -0800 2009
HEAD is d2bd86cb4e6e128f54d24f90164b10109d8e06ed

2 commits »

peterjc pushed to master at biopython/biopython Tue Dec 22 05:11:36 -0800 2009
HEAD is d2bd86cb4e6e128f54d24f90164b10109d8e06ed
  • peterjc committed d2bd86cb:
    Fixed sorting of recently added names, I hadn't noticed de Hoon and de Vries had been filed under 'D' (USA style - we may want to change that).
peterjc pushed to master at biopython/biopython Tue Dec 22 04:11:31 -0800 2009
HEAD is 86d8d99aab894ab5f32a0e7a0c45d63a441da645
  • peterjc committed 86d8d99a:
    Updating CONTRIB and NEWS for Biopython 1.53 contributors as discussed on the mailing list (trying to follow the more inclusive style of the Sage project)
peterjc pushed to master at peterjc/biopython Mon Dec 21 08:51:22 -0800 2009
HEAD is 21b4ff3214ef5651ffd9f9fe07e6e4f09568aac7

110 commits »

peterjc pushed to master at biopython/biopython Fri Dec 18 07:26:19 -0800 2009
HEAD is 21b4ff3214ef5651ffd9f9fe07e6e4f09568aac7

2 commits »

peterjc pushed to master at biopython/biopython Thu Dec 17 04:40:35 -0800 2009
HEAD is 9be131d717d28ed411299ce9aee198d19e79c742
  • peterjc committed 9be131d7:
    Minor docstring improvements to BioSQL/DBUtils.py
peterjc pushed to master at biopython/biopython Wed Dec 16 06:49:10 -0800 2009
HEAD is d14f3cf2b48517e0e06569c60878850f1b16a2eb
  • peterjc committed d14f3cf2:
    Bumping version number to 1.53+ now that the 1.52 release is done
peterjc pushed to master at biopython/biopython Tue Dec 15 09:23:53 -0800 2009
HEAD is ad9e9314bfea852f08273de26cc75365d2697c0e

2 commits »

peterjc created tag biopython-153 at biopython/biopython Tue Dec 15 07:20:13 -0800 2009
New tag is at biopython/biopython/tree/biopython-153
peterjc pushed to master at biopython/biopython Tue Dec 15 06:25:31 -0800 2009
HEAD is 67dad42bb7ee4badb166493799c5cf61593f4649
peterjc pushed to master at biopython/biopython Tue Dec 15 06:01:45 -0800 2009
HEAD is 4285556c0b26a330fc66a7f499ebfc379d5496b0
  • peterjc committed 4285556c:
    Minor correction to reference to Bio.Emboss module
peterjc pushed to master at biopython/biopython Tue Dec 15 05:02:12 -0800 2009
HEAD is 8b90c5d631ceaad04d9f2e7d163470b127a75538
peterjc pushed to master at biopython/biopython Tue Dec 15 03:14:25 -0800 2009
HEAD is 57df2db987723a71f0dd4baaf5caa7616dd15170
  • peterjc committed 57df2db9:
    Bumping version number ready for release this afternoon
peterjc pushed to master at biopython/biopython Mon Dec 14 09:42:22 -0800 2009
HEAD is 57bf8c8dc5542006466fa829d652449dd69d60f2
  • pcock committed 57bf8c8d:
    Use a filename starting temp_* for the BioSQL SQLite database, to make it clearer this is a temp file. TODO - Deleting it after the tests?
peterjc pushed to master at biopython/biopython Mon Dec 14 09:26:32 -0800 2009
HEAD is 22c74123da8022e04543fcded9e4ae9439d982b8
  • peterjc committed 22c74123:
    Better solution to cross platform variations in test_ProtParam.py output
peterjc pushed to master at biopython/biopython Mon Dec 14 09:09:03 -0800 2009
HEAD is 103b73edf93262ecf8daedd6d6f85c643c997d0d
  • pcock committed 103b73ed:
    Testing BLAST+ detection on Windows works
peterjc pushed to master at biopython/biopython Mon Dec 14 09:06:23 -0800 2009
HEAD is 79dcbec419ac219e14d3bbd2cfc87ecc9041b0e2
peterjc pushed to master at biopython/biopython Fri Dec 11 13:34:07 -0800 2009
HEAD is dc933b6d5265fc41b3db82ab853107564f189c63
  • peterjc committed dc933b6d:
    Tweak to tutorial in case MedLine results lack fields (see mailing list discussion)
peterjc pushed to master at biopython/biopython Thu Dec 10 09:09:48 -0800 2009
HEAD is c0e1e642e7781fbaab4839b7b6f8fc5321e092cc
peterjc pushed to master at biopython/biopython Thu Dec 10 08:45:44 -0800 2009
HEAD is dc5c326a520c9ff67ead19f83d127b7540b3f9db
  • peterjc committed dc5c326a:
    Deprecating Bio.GFF as discussed on the mailing list
peterjc pushed to master at biopython/biopython Thu Dec 10 06:30:45 -0800 2009
HEAD is 3e3e15fe8a817e1527871947556713b2e69ad7c5
  • peterjc committed 3e3e15fe:
    Mention ATOM/HETATM element support in Bio.PDB in the NEWS file
peterjc pushed to master at biopython/biopython Thu Dec 10 06:25:11 -0800 2009
HEAD is 2b025ba07f6298d7ecb242bdba28c545167b5cc3
  • peterjc committed 2b025ba0:
    Removing C implementations of deprecated modules listfns, mathfns and stringfns
peterjc pushed to master at biopython/biopython Thu Dec 10 06:13:14 -0800 2009
HEAD is dec0ef78482e04b4587ad5c24a0f50d8d0c6ac50
  • peterjc committed dec0ef78:
    Include the new seqmatchall wrapper in test_Emboss.py (see Bug 2969)
peterjc pushed to master at biopython/biopython Thu Dec 10 05:12:40 -0800 2009
HEAD is 453118cbde77c05eb4e4913f8621e61155da0ccb
  • peterjc committed 453118cb:
    Record element in PDB ouput (see Bug 2495), based on a patch from Frederik Gwinner
peterjc pushed to master at biopython/biopython Thu Dec 10 04:41:17 -0800 2009
HEAD is 7277a67defd4cb7ae4354003bd0d9353c93918ab
  • peterjc committed 7277a67d:
    Adding seqmatchall wrapper to Bio.Emboss.Applications with simple doctest (based on patch from Leighton Pritchard, Bug 2969)
peterjc pushed to master at biopython/biopython Thu Dec 10 04:23:48 -0800 2009
HEAD is 65ff92587f11d5f349c9f5288019ac32c97c1450
  • peterjc committed 65ff9258:
    Minor bug in date handling in GenBank output (fix from Brad on github)
peterjc pushed to master at biopython/biopython Thu Dec 10 04:16:27 -0800 2009
HEAD is e8fc8b4ad26b41d85fb2ef6d658610304c860aa3

2 commits »