From: cmzmasek@gmail.com Date: Tue, 9 Apr 2013 22:53:55 +0000 (+0000) Subject: taxonomy extraction changed X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=d03d163409fdf356d33177486c78246ad353ae1c;p=jalview.git taxonomy extraction changed --- diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file b/forester/aptx/aptx_configuration_files/_aptx_configuration_file index 27984ce..d0b07d3 100644 --- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file +++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file @@ -107,9 +107,13 @@ native_ui: ? # To replace underscores with spaces during NH/NHX/Nexus file parsing: # 'replace_underscores_in_nh_parsing', possible values are 'yes', 'no' # -# To extract UniProt taxonomy codes (e.g. CAEEL) from node names during NH/NHX/Nexus file parsing: -# 'taxonomy_extraction_in_nh_parsing', -# possible values are 'yes' (for e.g. BCL2_MOUSE), 'pfam' (for e.g. BCL2_MOUSE/23-453), 'no' +# To extract UniProt taxonomy codes (e.g. CAEEL) or UniProt identifiers (or scientific names) +# from node names during NH/NHX/Nexus file parsing: 'taxonomy_extraction_in_nh_parsing' +# possible values are: +# 'no' +# 'pfam_strict' (for e.g. MOUSE from BCL2_MOUSE/23-453, or [uniprot] 10090 from BCL2_10090/23-453) +# 'pfam_relaxed' (for e.g. MOUSE from bax_MOUSE, or [uniprot] 10090 from bax_10090) +# 'aggressive' (for e.g. MOUSE from MOUSE, or [uniprot] 10090 from 10090, or Nematostella vectensis from xyz_Nematostella_vectensis) # # Internal node labels are confidence values during NH/NHX/Nexus file parsing: # 'internal_labels_are_confidence_values', possible values are 'yes', 'no' diff --git a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 index 432efba..4309cc5 100644 --- a/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 +++ b/forester/aptx/aptx_configuration_files/_aptx_configuration_file_1 @@ -107,9 +107,13 @@ native_ui: ? # To replace underscores with spaces during NH/NHX/Nexus file parsing: # 'replace_underscores_in_nh_parsing', possible values are 'yes', 'no' # -# To extract UniProt taxonomy codes (e.g. CAEEL) from node names during NH/NHX/Nexus file parsing: -# 'taxonomy_extraction_in_nh_parsing', -# possible values are 'yes' (for e.g. BCL2_MOUSE), 'pfam' (for e.g. BCL2_MOUSE/23-453), 'no' +# To extract UniProt taxonomy codes (e.g. CAEEL) or UniProt identifiers (or scientific names) +# from node names during NH/NHX/Nexus file parsing: 'taxonomy_extraction_in_nh_parsing' +# possible values are: +# 'no' +# 'pfam_strict' (for e.g. MOUSE from BCL2_MOUSE/23-453, or [uniprot] 10090 from BCL2_10090/23-453) +# 'pfam_relaxed' (for e.g. MOUSE from bax_MOUSE, or [uniprot] 10090 from bax_10090) +# 'aggressive' (for e.g. MOUSE from MOUSE, or [uniprot] 10090 from 10090, or Nematostella vectensis from xyz_Nematostella_vectensis) # # Internal node labels are confidence values during NH/NHX/Nexus file parsing: # 'internal_labels_are_confidence_values', possible values are 'yes', 'no' @@ -151,7 +155,7 @@ ext_descendents_data_to_return: user_selected # NH/NHX/Nexus file parsing: internal_labels_are_confidence_values: no replace_underscores_in_nh_parsing: no -taxonomy_extraction_in_nh_parsing: pfam +taxonomy_extraction_in_nh_parsing: pfam_relaxed