From 08df6f3317342158e70bbbd62e9a049ac106573d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?= <ak4@sanger.ac.uk> Date: Fri, 28 Jan 2011 11:35:59 +0000 Subject: [PATCH] Updating ensembl-dev@ebi.ac.uk --> dev@ensembl.org --- docs/tutorial/ensembl_tutorial.txt | 9 ++++-- misc-scripts/CreateFile4CopyDBoverServer.pl | 2 +- .../alternative_splicing/Fetch_gff.pl | 2 +- misc-scripts/anopheles_scripts/format_bacs.pl | 2 +- misc-scripts/anopheles_scripts/format_blat.pl | 2 +- .../anopheles_scripts/load_karyotype.pl | 2 +- .../assembly/AssemblyMapper/BlastzAligner.pm | 2 +- misc-scripts/assembly/EXAMPLE.use_mapping.pl | 2 +- misc-scripts/assembly/README | 2 +- .../assembly/align_by_clone_identity.pl | 2 +- .../assembly/align_nonident_regions.pl | 2 +- .../align_nonident_regions_wrapper.pl | 2 +- misc-scripts/assembly/check_mapping.pl | 2 +- misc-scripts/assembly/compare_assemblies.pl | 2 +- misc-scripts/assembly/find_overlaps.pl | 2 +- misc-scripts/assembly/fix_overlaps.pl | 2 +- .../assembly/load_alternative_assembly.pl | 2 +- misc-scripts/assembly/mapping_stats.pl | 2 +- misc-scripts/db/cleanup_tmp_tables.pl | 2 +- .../density_feature/glovar_snp_density.pl | 2 +- misc-scripts/id_mapping/README | 30 ++++++++++++++----- misc-scripts/id_mapping/dump_by_seq_region.pl | 2 +- misc-scripts/id_mapping/dump_cache.pl | 2 +- .../id_mapping/fake_stable_id_mapping.pl | 2 +- misc-scripts/id_mapping/id_mapping.pl | 2 +- misc-scripts/id_mapping/run.pl | 2 +- misc-scripts/id_mapping/synteny_rescore.pl | 2 +- .../id_mapping/utils/batch_id_history.pl | 2 +- .../id_mapping/utils/compare_results.pl | 2 +- .../id_mapping/utils/compare_scores.pl | 2 +- misc-scripts/id_mapping/utils/dump_scores.pl | 2 +- .../utils/manage_id_mapping_tables.pl | 2 +- misc-scripts/overlapping_regions.pl | 2 +- misc-scripts/repeats/vega_repeat_libraries.pl | 2 +- misc-scripts/schema_patch.pl | 2 +- misc-scripts/utilities/show_method_status.pl | 2 +- 36 files changed, 63 insertions(+), 44 deletions(-) diff --git a/docs/tutorial/ensembl_tutorial.txt b/docs/tutorial/ensembl_tutorial.txt index a065b5a3c8..97cdde79e9 100644 --- a/docs/tutorial/ensembl_tutorial.txt +++ b/docs/tutorial/ensembl_tutorial.txt @@ -1,8 +1,10 @@ Ensembl Perl API Tutorial -By Michele Clamp. Updated, revised, and rewritten by Michele Clamp, Ewan Birney, Graham McVicker and Dan Andrews. +By Michele Clamp. Updated, revised, and rewritten by Michele Clamp, +Ewan Birney, Graham McVicker and Dan Andrews. -Revisions: EB Oct 01, MC Jan 02, MC Mar 02, DA Jul 02, DA Oct 02, GM Oct 02, DA Feb 03, GM Feb 04, GM Aug 04 +Revisions: EB Oct 01, MC Jan 02, MC Mar 02, DA Jul 02, DA Oct 02, GM Oct +02, DA Feb 03, GM Feb 04, GM Aug 04 Introduction @@ -22,7 +24,8 @@ If you have your PERL5LIB environment variable set correctly (see the section on perldoc Bio::EnsEMBL::Slice -For additional information you can contact ensembl-dev, the Ensembl development mailing list (see www.ensembl.org/Docs/Lists/). +For additional information you can contact the Ensembl development +mailing list (see www.ensembl.org/Docs/Lists/). Perl diff --git a/misc-scripts/CreateFile4CopyDBoverServer.pl b/misc-scripts/CreateFile4CopyDBoverServer.pl index 2ae83fa38b..819fcfbb7f 100755 --- a/misc-scripts/CreateFile4CopyDBoverServer.pl +++ b/misc-scripts/CreateFile4CopyDBoverServer.pl @@ -7,7 +7,7 @@ # Benoit Ballester <benoit@ebi.ac.uk> # # Please post comments/questions to the Ensembl development list -# <ensembl-dev@ebi.ac.uk> +# <dev@ensembl.org> # ######################################### use strict; diff --git a/misc-scripts/alternative_splicing/Fetch_gff.pl b/misc-scripts/alternative_splicing/Fetch_gff.pl index bdbdf3a04f..8b28547675 100644 --- a/misc-scripts/alternative_splicing/Fetch_gff.pl +++ b/misc-scripts/alternative_splicing/Fetch_gff.pl @@ -13,7 +13,7 @@ =head1 CONTACT Please email comments or questions to the public Ensembl - developers list at <ensembl-dev@ebi.ac.uk>. + developers list at <dev@ensembl.org>. Questions may also be sent to the Ensembl help desk at <helpdesk@ensembl.org>. diff --git a/misc-scripts/anopheles_scripts/format_bacs.pl b/misc-scripts/anopheles_scripts/format_bacs.pl index 61f95b74cc..07828639fa 100644 --- a/misc-scripts/anopheles_scripts/format_bacs.pl +++ b/misc-scripts/anopheles_scripts/format_bacs.pl @@ -17,7 +17,7 @@ =head1 CONTACTS - ensembl-dev@ebi.ac.uk + dev@ensembl.org mongin@ebi.ac.uk =cut diff --git a/misc-scripts/anopheles_scripts/format_blat.pl b/misc-scripts/anopheles_scripts/format_blat.pl index 46342cb500..df70c236f6 100644 --- a/misc-scripts/anopheles_scripts/format_blat.pl +++ b/misc-scripts/anopheles_scripts/format_blat.pl @@ -12,7 +12,7 @@ =head1 CONTACT - ensembl-dev@ebi.ac.uk + dev@ensembl.org mongin@ebi.ac.uk =cut diff --git a/misc-scripts/anopheles_scripts/load_karyotype.pl b/misc-scripts/anopheles_scripts/load_karyotype.pl index c2ad9978c6..1a3ee4877b 100644 --- a/misc-scripts/anopheles_scripts/load_karyotype.pl +++ b/misc-scripts/anopheles_scripts/load_karyotype.pl @@ -14,7 +14,7 @@ =head1 CONTACTS - ensembl-dev@ebi.ac.uk + dev@ensembl.org mongin@ebi.ac.uk =cut diff --git a/misc-scripts/assembly/AssemblyMapper/BlastzAligner.pm b/misc-scripts/assembly/AssemblyMapper/BlastzAligner.pm index 8185da2070..a5806d13cd 100644 --- a/misc-scripts/assembly/AssemblyMapper/BlastzAligner.pm +++ b/misc-scripts/assembly/AssemblyMapper/BlastzAligner.pm @@ -60,7 +60,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/assembly/EXAMPLE.use_mapping.pl b/misc-scripts/assembly/EXAMPLE.use_mapping.pl index 2a716a98e2..3624c4192f 100644 --- a/misc-scripts/assembly/EXAMPLE.use_mapping.pl +++ b/misc-scripts/assembly/EXAMPLE.use_mapping.pl @@ -53,7 +53,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/assembly/README b/misc-scripts/assembly/README index 286033f599..7c0a3b9b5d 100644 --- a/misc-scripts/assembly/README +++ b/misc-scripts/assembly/README @@ -210,7 +210,7 @@ correct. If you find other bugs please report them to the Ensembl development mailing -list <ensembl-dev@ebi.ac.uk> or to Patrick Meidl <meidl@ebi.ac.uk>. +list <dev@ensembl.org> or to Patrick Meidl <meidl@ebi.ac.uk>. ------------------------------------------------------------------------------- diff --git a/misc-scripts/assembly/align_by_clone_identity.pl b/misc-scripts/assembly/align_by_clone_identity.pl index 344edb4e2a..56cde03d01 100755 --- a/misc-scripts/assembly/align_by_clone_identity.pl +++ b/misc-scripts/assembly/align_by_clone_identity.pl @@ -91,7 +91,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/assembly/align_nonident_regions.pl b/misc-scripts/assembly/align_nonident_regions.pl index c513af7d98..865d86b95a 100755 --- a/misc-scripts/assembly/align_nonident_regions.pl +++ b/misc-scripts/assembly/align_nonident_regions.pl @@ -88,7 +88,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/assembly/align_nonident_regions_wrapper.pl b/misc-scripts/assembly/align_nonident_regions_wrapper.pl index a71aeada46..6765f26b2e 100755 --- a/misc-scripts/assembly/align_nonident_regions_wrapper.pl +++ b/misc-scripts/assembly/align_nonident_regions_wrapper.pl @@ -66,7 +66,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/assembly/check_mapping.pl b/misc-scripts/assembly/check_mapping.pl index d5aaea034f..1e56cea2f3 100755 --- a/misc-scripts/assembly/check_mapping.pl +++ b/misc-scripts/assembly/check_mapping.pl @@ -70,7 +70,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/assembly/compare_assemblies.pl b/misc-scripts/assembly/compare_assemblies.pl index 5a42142c27..0841d2a89c 100755 --- a/misc-scripts/assembly/compare_assemblies.pl +++ b/misc-scripts/assembly/compare_assemblies.pl @@ -68,7 +68,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/assembly/find_overlaps.pl b/misc-scripts/assembly/find_overlaps.pl index 4b422f1d32..b438729ff1 100755 --- a/misc-scripts/assembly/find_overlaps.pl +++ b/misc-scripts/assembly/find_overlaps.pl @@ -52,7 +52,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/assembly/fix_overlaps.pl b/misc-scripts/assembly/fix_overlaps.pl index e4764a7ab4..10c95322b1 100755 --- a/misc-scripts/assembly/fix_overlaps.pl +++ b/misc-scripts/assembly/fix_overlaps.pl @@ -68,7 +68,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/assembly/load_alternative_assembly.pl b/misc-scripts/assembly/load_alternative_assembly.pl index 9d8db61f6d..e14deab42c 100755 --- a/misc-scripts/assembly/load_alternative_assembly.pl +++ b/misc-scripts/assembly/load_alternative_assembly.pl @@ -74,7 +74,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/assembly/mapping_stats.pl b/misc-scripts/assembly/mapping_stats.pl index 8c7cb00678..c0dcd8df69 100755 --- a/misc-scripts/assembly/mapping_stats.pl +++ b/misc-scripts/assembly/mapping_stats.pl @@ -69,7 +69,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/db/cleanup_tmp_tables.pl b/misc-scripts/db/cleanup_tmp_tables.pl index 7156823996..d05304d12c 100755 --- a/misc-scripts/db/cleanup_tmp_tables.pl +++ b/misc-scripts/db/cleanup_tmp_tables.pl @@ -45,7 +45,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/density_feature/glovar_snp_density.pl b/misc-scripts/density_feature/glovar_snp_density.pl index 109ca4dce9..38f7e4be36 100755 --- a/misc-scripts/density_feature/glovar_snp_density.pl +++ b/misc-scripts/density_feature/glovar_snp_density.pl @@ -66,7 +66,7 @@ Patrick Meidl <pm2@sanger.ac.uk> =head1 CONTACT -Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk +Post questions to the EnsEMBL development list dev@ensembl.org =cut diff --git a/misc-scripts/id_mapping/README b/misc-scripts/id_mapping/README index d517069433..375a61bac9 100644 --- a/misc-scripts/id_mapping/README +++ b/misc-scripts/id_mapping/README @@ -2,15 +2,31 @@ Ensembl stable ID mapping ------------------------------------------------------------------------------- -Author: Patrick Meidl <meidl@ebi.ac.uk> +Please post questions to the Ensembl developers mailing list +<dev@ensembl.org> -Please post questions to the Ensembl developers mailinglist -<ensembl-dev@ebi.ac.uk> +The scripts in this directory are used in Ensembl production to map +stable IDs between one release and another. -The scripts in this directory are used in Ensembl production to map stable IDs -between one release and another. +Please refer to the documents in ensembl-doc/id_mapping/ for both user +and developer level documentation. -Please refer to the documents in ensembl-docs/id_mapping/ for both user and -developer level documentation. +The following is a quick start with a bare bones description of the +steps we go through when we run the stable ID mapping for an Ensembl +release: + +QUICK START + +1. Empty stable IDs from target database, or back them up using the + utils/myManager.ksh script. + +2. As a sanity check, compare the gene biotypes in source and target + databases. + +3. Create a configuration file. + +4. Run the mapping using the myRun.ksh script. + +5. Study the result. diff --git a/misc-scripts/id_mapping/dump_by_seq_region.pl b/misc-scripts/id_mapping/dump_by_seq_region.pl index 096a7faa36..2315026e1f 100755 --- a/misc-scripts/id_mapping/dump_by_seq_region.pl +++ b/misc-scripts/id_mapping/dump_by_seq_region.pl @@ -45,7 +45,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/id_mapping/dump_cache.pl b/misc-scripts/id_mapping/dump_cache.pl index cb0ad996b0..f953f4888b 100755 --- a/misc-scripts/id_mapping/dump_cache.pl +++ b/misc-scripts/id_mapping/dump_cache.pl @@ -55,7 +55,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/id_mapping/fake_stable_id_mapping.pl b/misc-scripts/id_mapping/fake_stable_id_mapping.pl index 9640bc0827..066f121d41 100755 --- a/misc-scripts/id_mapping/fake_stable_id_mapping.pl +++ b/misc-scripts/id_mapping/fake_stable_id_mapping.pl @@ -73,7 +73,7 @@ Patrick Meidl <pm2@sanger.ac.uk> =head1 CONTACT -Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk +Post questions to the EnsEMBL development list dev@ensembl.org =cut diff --git a/misc-scripts/id_mapping/id_mapping.pl b/misc-scripts/id_mapping/id_mapping.pl index 824f2e1024..4ddb13b6d4 100755 --- a/misc-scripts/id_mapping/id_mapping.pl +++ b/misc-scripts/id_mapping/id_mapping.pl @@ -45,7 +45,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/id_mapping/run.pl b/misc-scripts/id_mapping/run.pl index 48e562355f..8aacd2fe87 100755 --- a/misc-scripts/id_mapping/run.pl +++ b/misc-scripts/id_mapping/run.pl @@ -46,7 +46,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/id_mapping/synteny_rescore.pl b/misc-scripts/id_mapping/synteny_rescore.pl index 0a0344d1cb..15311059c3 100755 --- a/misc-scripts/id_mapping/synteny_rescore.pl +++ b/misc-scripts/id_mapping/synteny_rescore.pl @@ -45,7 +45,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/id_mapping/utils/batch_id_history.pl b/misc-scripts/id_mapping/utils/batch_id_history.pl index 46ecaf1e72..7d338ac941 100755 --- a/misc-scripts/id_mapping/utils/batch_id_history.pl +++ b/misc-scripts/id_mapping/utils/batch_id_history.pl @@ -44,7 +44,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/id_mapping/utils/compare_results.pl b/misc-scripts/id_mapping/utils/compare_results.pl index 0511f7bb28..c368545f67 100755 --- a/misc-scripts/id_mapping/utils/compare_results.pl +++ b/misc-scripts/id_mapping/utils/compare_results.pl @@ -45,7 +45,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/id_mapping/utils/compare_scores.pl b/misc-scripts/id_mapping/utils/compare_scores.pl index 6370fbe787..1408ca22f9 100755 --- a/misc-scripts/id_mapping/utils/compare_scores.pl +++ b/misc-scripts/id_mapping/utils/compare_scores.pl @@ -39,7 +39,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/id_mapping/utils/dump_scores.pl b/misc-scripts/id_mapping/utils/dump_scores.pl index 773acfa72c..506a2489e4 100755 --- a/misc-scripts/id_mapping/utils/dump_scores.pl +++ b/misc-scripts/id_mapping/utils/dump_scores.pl @@ -46,7 +46,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/id_mapping/utils/manage_id_mapping_tables.pl b/misc-scripts/id_mapping/utils/manage_id_mapping_tables.pl index 46c9de7bb0..e34aa32169 100755 --- a/misc-scripts/id_mapping/utils/manage_id_mapping_tables.pl +++ b/misc-scripts/id_mapping/utils/manage_id_mapping_tables.pl @@ -72,7 +72,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/overlapping_regions.pl b/misc-scripts/overlapping_regions.pl index 9157b8764d..79caea50b4 100644 --- a/misc-scripts/overlapping_regions.pl +++ b/misc-scripts/overlapping_regions.pl @@ -54,7 +54,7 @@ Daniel Rios <dani@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/repeats/vega_repeat_libraries.pl b/misc-scripts/repeats/vega_repeat_libraries.pl index 812b1f23ba..46c53cc055 100644 --- a/misc-scripts/repeats/vega_repeat_libraries.pl +++ b/misc-scripts/repeats/vega_repeat_libraries.pl @@ -53,7 +53,7 @@ Based on code by James Smith <js5@sanger.ac.uk> =head1 CONTACT -Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk +Post questions to the EnsEMBL development list dev@ensembl.org =cut diff --git a/misc-scripts/schema_patch.pl b/misc-scripts/schema_patch.pl index d22b94d7a3..578ab217b0 100755 --- a/misc-scripts/schema_patch.pl +++ b/misc-scripts/schema_patch.pl @@ -67,7 +67,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut diff --git a/misc-scripts/utilities/show_method_status.pl b/misc-scripts/utilities/show_method_status.pl index 97cae97528..ad9de0ee8c 100755 --- a/misc-scripts/utilities/show_method_status.pl +++ b/misc-scripts/utilities/show_method_status.pl @@ -55,7 +55,7 @@ Patrick Meidl <meidl@ebi.ac.uk>, Ensembl core API team =head1 CONTACT Please post comments/questions to the Ensembl development list -<ensembl-dev@ebi.ac.uk> +<dev@ensembl.org> =cut -- GitLab