202602 2007-12-17 18:08 0000 >=sci-biology/biopython-1.43 require a patch to Bio.SeqUtils 2008-01-30 03:34:34 0000 1 1 1 Unclassified Gentoo Linux Applications 2007.0 All Linux RESOLVED FIXED P2 normal --- 1 justin.t.riley@gmail.com ribosome@gentoo.org sci-biology@gentoo.org justin.t.riley@gmail.com 2007-12-17 18:08:42 0000 In Biopython 1.43 and 1.44 if you try to use six_frame_translations function from the Bio.SeqUtils module, you'll get an error: "global name 'complement' is not defined". I submitted a bug (http://bugzilla.open-bio.org/show_bug.cgi?id=2419) upstream and they responded with a fix from cvs. I've created a patch for Biopython 1.43 in portage as well as bumped the ebuild (and kdtree patch) to 1.44. Ebuilds/patches are attached. I can verify that the patch works for both 1.43 and 1.44 ebuilds on amd64 and ~amd64. ~jtriley justin.t.riley@gmail.com 2007-12-17 18:10:04 0000 Created an attachment (id=138748) Bio.SeqUtils patch for biopython 1.44 justin.t.riley@gmail.com 2007-12-17 18:18:30 0000 Created an attachment (id=138754) ebuild for biopython-1.44 using the patch copy biopython-1.43-kdtree.patch to biopython-1.44-kdtree.patch in the files directory. you also need to have biopython-1.44-sequtils-complement.patch in the files directory for this build to work. justin.t.riley@gmail.com 2007-12-17 18:31:20 0000 Created an attachment (id=138757) biopython 1.43 Bio.SeqUtils patch This patch uses the solution I mention about pasting a complement function here: http://bugzilla.open-bio.org/show_bug.cgi?id=2419 This is NOT the preferred solution but the patch from cvs only works with the latest 1.44 version (or at least I can't get it to work with 1.43 :D ribosome@gentoo.org 2008-01-30 03:34:34 0000 BioPython 1.44 (and patch) in CVS. I removed version 1.43. Thanks for your work. 138748 2007-12-17 18:10 0000 Bio.SeqUtils patch for biopython 1.44 biopython-1.44-sequtils-complement.patch text/plain LS0tIGJpb3B5dGhvbi0xLjQ0L0Jpby9TZXFVdGlscy9fX2luaXRfXy5weS5vbGQJMjAwNy0wOS0x NCAwOTozODozNS4wMDAwMDAwMDAgLTA0MDAKKysrIGJpb3B5dGhvbi0xLjQ0L0Jpby9TZXFVdGls cy9fX2luaXRfXy5weQkyMDA3LTEyLTE3IDExOjA3OjI3LjAwMDAwMDAwMCAtMDUwMApAQCAtNyw4 ICs3LDcgQEAKICMgbGljZW5zZS4gIFBsZWFzZSBzZWUgdGhlIExJQ0VOU0UgZmlsZSB0aGF0IHNo b3VsZCBoYXZlIGJlZW4gaW5jbHVkZWQKICMgYXMgcGFydCBvZiB0aGlzIHBhY2thZ2UuCiAKLWlt cG9ydCBvcywgc3lzLCBnZXRvcHQsIHJlLCB0aW1lCi1mcm9tIHN0cmluZyBpbXBvcnQgbWFrZXRy YW5zCitpbXBvcnQgcmUsIHRpbWUKIGZyb20gQmlvIGltcG9ydCBTZXFJTwogZnJvbSBCaW8gaW1w b3J0IFRyYW5zbGF0ZQogZnJvbSBCaW8uU2VxIGltcG9ydCBTZXEKQEAgLTI3Nyw4ICsyNzYsOSBA QAogICAgbmljZSBsb29raW5nIDYgZnJhbWUgdHJhbnNsYXRpb24gd2l0aCBHQyBjb250ZW50IC0g Y29kZSBmcm9tIHhiYnRvb2xzCiAgICBzaW1pbGFyIHRvIEROQSBTdHJpZGVycyBzaXgtZnJhbWUg dHJhbnNsYXRpb24KICAgICIiIgotICAgY29tcCA9IGNvbXBsZW1lbnQoc2VxKQotICAgYW50aSA9 IHJldmVyc2UoY29tcCkKKyAgIGZyb20gQmlvLlNlcSBpbXBvcnQgcmV2ZXJzZV9jb21wbGVtZW50 CisgICBhbnRpID0gcmV2ZXJzZV9jb21wbGVtZW50KHNlcSkKKyAgIGNvbXAgPSBhbnRpWzo6LTFd CiAgICBsZW5ndGggPSBsZW4oc2VxKQogICAgZnJhbWVzID0ge30KICAgIGZvciBpIGluIHJhbmdl KDAsMyk6CkBAIC0zOTksNiArMzk5LDcgQEAKICMge3t7IAogCiBpZiBfX25hbWVfXyA9PSAnX19t YWluX18nOgorICAgaW1wb3J0IHN5cywgZ2V0b3B0CiAgICAjIGNydWRlIGNvbW1hbmQgbGluZSBv cHRpb25zIHRvIHVzZSBtb3N0IGZ1bmN0aW9ucyBkaXJlY3RseSBvbiBhIEZBU1RBIGZpbGUKICAg IG9wdGlvbnMgPSB7J2FwcGx5X29uX211bHRpX2Zhc3RhJzowLAogICAgICAgICAgICAgICAncXVp Y2snOjAsCg== 138754 2007-12-17 18:18 0000 ebuild for biopython-1.44 using the patch biopython-1.44.ebuild text/plain IyBDb3B5cmlnaHQgMTk5OS0yMDA3IEdlbnRvbyBGb3VuZGF0aW9uCiMgRGlzdHJpYnV0ZWQgdW5k ZXIgdGhlIHRlcm1zIG9mIHRoZSBHTlUgR2VuZXJhbCBQdWJsaWMgTGljZW5zZSB2MgojICRIZWFk ZXI6IC92YXIvY3Zzcm9vdC9nZW50b28teDg2L3NjaS1iaW9sb2d5L2Jpb3B5dGhvbi9iaW9weXRo b24tMS40My5lYnVpbGQsdiAxLjEgMjAwNy8wNS8xNyAxODo0NzozMCByaWJvc29tZSBFeHAgJAoK aW5oZXJpdCBkaXN0dXRpbHMgZXV0aWxzCgpERVNDUklQVElPTj0iQmlvcHl0aG9uIC0gUHl0aG9u IG1vZHVsZXMgZm9yIGNvbXB1dGF0aW9uYWwgbW9sZWN1bGFyIGJpb2xvZ3kiCkxJQ0VOU0U9ImFz LWlzIgpIT01FUEFHRT0iaHR0cDovL3d3dy5iaW9weXRob24ub3JnIgpTUkNfVVJJPSJodHRwOi8v d3d3LmJpb3B5dGhvbi5vcmcvRElTVC8ke1B9LnRhci5neiIKClNMT1Q9IjAiCklVU0U9ImtkdHJl ZSIKS0VZV09SRFM9In5hbHBoYSB+YW1kNjQgfnBwYyB+c3BhcmMgfng4NiIKCkRFUEVORD0iPj1k ZXYtbGFuZy9weXRob24tMi4yCgkJPj1kZXYtcHl0aG9uL2VnZW5peC1teC1iYXNlLTIuMC4zCgkJ Pj1kZXYtcHl0aG9uL251bWVyaWMtMTkuMAoJCT49ZGV2LXB5dGhvbi9yZXBvcnRsYWItMS4xMSIK CnNyY191bnBhY2soKSB7Cgl1bnBhY2sgJHtBfQoJY2QgIiR7U30iCgllcGF0Y2ggIiR7RklMRVNE SVJ9LyR7UH0tYnVpbGRrZHRyZWUucGF0Y2giCgllcGF0Y2ggIiR7RklMRVNESVJ9LyR7UH0tc2Vx dXRpbHMtY29tcGxlbWVudC5wYXRjaCIKCWlmIHVzZSBrZHRyZWU7IHRoZW4KCQlzZWQgLWkgLWUg J3MvVVNFX0tEVFJFRSA9IEZhbHNlL1VTRV9LRFRSRUUgPSBUcnVlLycgXAoJCQkJc2V0dXAucHkg fHwgZGllICJDb3VsZCBub3QgYXBwbHkgcGF0Y2ggZm9yIEtEVHJlZSBzdXBwb3J0LiIKCWZpCn0K CnNyY19jb21waWxlKCkgewoJZGlzdHV0aWxzX3NyY19jb21waWxlCn0KCnNyY19pbnN0YWxsKCkg ewoJRE9DUz0iRG9jLyoudHh0IERvYy8qLnRleCBEb2MvaW5zdGFsbC8qLnR4dCIKCWRpc3R1dGls c19zcmNfaW5zdGFsbAoKCWRvaHRtbCBEb2MvaW5zdGFsbC8qLmh0bWwgfHwgZGllICJGYWlsZWQg dG8gaW5zdGFsbCBIVE1MIGluc3RhbGwgZG9jcy4iCglkb2h0bWwgRG9jLyouaHRtbCB8fCBkaWUg IkZhaWxlZCB0byBpbnN0YWxsIEhUTUwgZG9jcy4iCgljcCAtciBEb2MvZXhhbXBsZXMvIERvYy8q LnBkZiAke0R9L3Vzci9zaGFyZS9kb2MvJHtQRn0vIHx8IFwKCQkJZGllICJGYWlsZWQgdG8gaW5z dGFsbCBkb2N1bWVudGF0aW9uLiIKfQo= 138757 2007-12-17 18:31 0000 biopython 1.43 Bio.SeqUtils patch biopython-1.43-sequtils-complement.patch text/plain LS0tIGJpb3B5dGhvbi0xLjQzL0Jpby9TZXFVdGlscy9fX2luaXRfXy5weS5vbGQJMjAwNy0xMi0x NyAxMzoyMTo0My4wMDAwMDAwMDAgLTA1MDAKKysrIGJpb3B5dGhvbi0xLjQzL0Jpby9TZXFVdGls cy9fX2luaXRfXy5weQkyMDA3LTEyLTE3IDEzOjIyOjMxLjAwMDAwMDAwMCAtMDUwMApAQCAtMjcy LDYgKzI3MiwxMSBAQAogICAgIiBqdXN0IGFuIGFsaWFzIGZvciBzaXhfZnJhbWVfdHJhbnNsYXRp b25zICIKICAgIHJldHVybiBzaXhfZnJhbWVfdHJhbnNsYXRpb25zKHNlcSwgZ2VuZXRpY19jb2Rl KQogCitkZWYgY29tcGxlbWVudChzZXEpOgorICAgIiByZXR1cm5zIHRoZSBjb21wbGVtZW50YXJ5 IHNlcXVlbmNlIChOT1QgYW50aXBhcmFsbGVsKSAiCisgICByZXR1cm4gJycuam9pbihbSVVQQUNE YXRhLmFtYmlndW91c19kbmFfY29tcGxlbWVudFt4XSBmb3IgeCBpbiBzZXFdKQorCisKIGRlZiBz aXhfZnJhbWVfdHJhbnNsYXRpb25zKHNlcSwgZ2VuZXRpY19jb2RlID0gMSk6CiAgICAiIiIKICAg IG5pY2UgbG9va2luZyA2IGZyYW1lIHRyYW5zbGF0aW9uIHdpdGggR0MgY29udGVudCAtIGNvZGUg ZnJvbSB4YmJ0b29scwo=