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CYAPA added
authorcmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Wed, 9 Jul 2014 18:35:23 +0000 (18:35 +0000)
committercmzmasek@gmail.com <cmzmasek@gmail.com@ca865154-3058-d1c3-3e42-d8f55a55bdbd>
Wed, 9 Jul 2014 18:35:23 +0000 (18:35 +0000)
forester/data/surfacing/genome_locations.txt patch | blob | history
forester/data/surfacing/genome_locations_eos.txt patch | blob | history
forester/data/surfacing/genomes_all.txt patch | blob | history
forester/data/surfacing/genomes_eos_all.txt patch | blob | history
forester/data/tol_156.xml patch | blob | history

diff --git a/forester/data/surfacing/genome_locations.txt b/forester/data/surfacing/genome_locations.txt
index 93df656..9faab1d 100644 (file)
--- a/forester/data/surfacing/genome_locations.txt
+++ b/forester/data/surfacing/genome_locations.txt
@@ -1,4 +1,4 @@
-# Last updated: 140708
+# Last updated: 140709
 #
 # Ophistokonta::Animals (mammals)
 BOVIN   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/BOVIN.fasta
@@ -208,7 +208,7 @@ ENTBH   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/E
 ENTDS   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/ENTDS.fasta
 ENTHI   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/ENTHI.fasta
 POLPA   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/POLPA.fasta
-# Archaeplastida::Viridaeplantae::Streptophyta
+# Viridaeplantae::Streptophyta
 AMBTC   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/AMBTC.fasta
 AQUCA   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/AQUCA.fasta
 ARALY   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/ARALY.fasta
@@ -240,7 +240,7 @@ SORBI   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/S
 SOYBN   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/SOYBN.fasta
 THEHA   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/THEHA.fasta
 VITVI   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/VITVI.fasta
-# Archaeplastida::Viridaeplantae::Chlorophyta
+# Viridaeplantae::Chlorophyta
 ASCXX   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/ASCXX.fasta
 CHLRE   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/CHLRE.fasta
 CHLVA   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/CHLVA.fasta
@@ -251,8 +251,10 @@ ORCXX   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/O
 OSTLU   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/OSTLU.fasta
 OSTTA   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/OSTTA.fasta
 VOLCA   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/VOLCA.fasta
-# Archaeplastida::Rhodophyta
+# Rhodophyta
 CYAME   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/CYAME.fasta
+# Glaucophyta
+CYAPA   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/CYAPA.fasta
 # Chromalveolates
 AKEXX   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/AKEXX.fasta
 ALIXX   /home/czmasek/DATA/SEQUENCES/GENOMES/PROTEIN_PREDICTIONS_CDHIT_095/ALL/ALIXX.fasta
diff --git a/forester/data/surfacing/genome_locations_eos.txt b/forester/data/surfacing/genome_locations_eos.txt
index 7eb9f45..cc3bf20 100644 (file)
--- a/forester/data/surfacing/genome_locations_eos.txt
+++ b/forester/data/surfacing/genome_locations_eos.txt
@@ -1,4 +1,4 @@
-# Last updated: 140708
+# Last updated: 140709
 #
 # Ophistokonta::Animals (mammals)
 BOVIN   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/BOVIN.fasta
@@ -208,7 +208,7 @@ ENTBH   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/ENTBH.fasta
 ENTDS   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/ENTDS.fasta
 ENTHI   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/ENTHI.fasta
 POLPA   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/POLPA.fasta
-# Archaeplastida::Viridaeplantae::Streptophyta
+# Viridaeplantae::Streptophyta
 AMBTC   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/AMBTC.fasta
 AQUCA   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/AQUCA.fasta
 ARALY   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/ARALY.fasta
@@ -240,7 +240,7 @@ SORBI   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/SORBI.fasta
 SOYBN   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/SOYBN.fasta
 THEHA   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/THEHA.fasta
 VITVI   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/VITVI.fasta
-# Archaeplastida::Viridaeplantae::Chlorophyta
+# Viridaeplantae::Chlorophyta
 ASCXX   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/ASCXX.fasta
 CHLRE   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/CHLRE.fasta
 CHLVA   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/CHLVA.fasta
@@ -251,8 +251,10 @@ ORCXX   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/ORCXX.fasta
 OSTLU   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/OSTLU.fasta
 OSTTA   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/OSTTA.fasta
 VOLCA   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/VOLCA.fasta
-# Archaeplastida::Rhodophyta
+# Rhodophyta
 CYAME   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/CYAME.fasta
+# Glaucophyta
+CYAPA   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/CYAPA.fasta
 # Chromalveolates
 AKEXX   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/AKEXX.fasta
 ALIXX   /home/czmasek/PUBLIC/DATA/PROTEIN_PREDICTIONS_CDHIT_095/ALIXX.fasta
diff --git a/forester/data/surfacing/genomes_all.txt b/forester/data/surfacing/genomes_all.txt
index 2539986..d479c76 100644 (file)
--- a/forester/data/surfacing/genomes_all.txt
+++ b/forester/data/surfacing/genomes_all.txt
@@ -1,4 +1,4 @@
-# Last updated: 140708
+# Last updated: 140709
 #
 # Ophistokonta::Animals (mammals)
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/BOVIN.hmmscan    BOVIN
@@ -204,7 +204,7 @@
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ENTDS.hmmscan    ENTDS
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ENTHI.hmmscan    ENTHI
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/POLPA.hmmscan    POLPA
-# Archaeplastida::Viridaeplantae::Streptophyta
+# Viridaeplantae::Streptophyta
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/AMBTC.hmmscan    AMBTC
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/AQUCA.hmmscan    AQUCA
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ARALY.hmmscan    ARALY
@@ -236,7 +236,7 @@
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/SOYBN.hmmscan    SOYBN
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/THEHA.hmmscan    THEHA
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/VITVI.hmmscan    VITVI
-# Archaeplastida::Viridaeplantae::Chlorophyta
+# Viridaeplantae::Chlorophyta
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ASCXX.hmmscan    ASCXX
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CHLRE.hmmscan    CHLRE
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CHLVA.hmmscan    CHLVA
@@ -247,8 +247,10 @@
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/OSTLU.hmmscan    OSTLU
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/OSTTA.hmmscan    OSTTA
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/VOLCA.hmmscan    VOLCA
-# Archaeplastida::Rhodophyta
+# Rhodophyta
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CYAME.hmmscan    CYAME
+# Glaucophyta
+/home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CYAPA.hmmscan    CYAPA
 # Chromalveolates
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/AKEXX.hmmscan    AKEXX
 /home/czmasek/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ALIXX.hmmscan    ALIXX
diff --git a/forester/data/surfacing/genomes_eos_all.txt b/forester/data/surfacing/genomes_eos_all.txt
index 9cad5d5..e9ef1dd 100644 (file)
--- a/forester/data/surfacing/genomes_eos_all.txt
+++ b/forester/data/surfacing/genomes_eos_all.txt
@@ -1,4 +1,4 @@
-# Last updated: 140708
+# Last updated: 140709
 #
 # Ophistokonta::Animals (mammals)
 /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/BOVIN.hmmscan    BOVIN
@@ -204,7 +204,7 @@
 /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ENTDS.hmmscan    ENTDS
 /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ENTHI.hmmscan    ENTHI
 /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/POLPA.hmmscan    POLPA
-# Archaeplastida::Viridaeplantae::Streptophyta
+# Viridaeplantae::Streptophyta
 /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/AMBTC.hmmscan    AMBTC
 /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/AQUCA.hmmscan    AQUCA
 /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ARALY.hmmscan    ARALY
@@ -236,7 +236,7 @@
 /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/SOYBN.hmmscan    SOYBN
 /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/THEHA.hmmscan    THEHA
 /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/VITVI.hmmscan    VITVI
-# Archaeplastida::Viridaeplantae::Chlorophyta
+# Viridaeplantae::Chlorophyta
 /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ASCXX.hmmscan    ASCXX
 /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CHLRE.hmmscan    CHLRE
 /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CHLVA.hmmscan    CHLVA
@@ -247,8 +247,10 @@
 /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/OSTLU.hmmscan    OSTLU
 /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/OSTTA.hmmscan    OSTTA
 /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/VOLCA.hmmscan    VOLCA
-# Archaeplastida::Rhodophyta
+# Rhodophyta
 /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CYAME.hmmscan    CYAME
+# Glaucophyta
+/home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/CYAPA.hmmscan    CYAPA
 # Chromalveolates
 /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/AKEXX.hmmscan    AKEXX
 /home/czmasek/PUBLIC/DATA/GENOME_HMMSCAN/CDHIT_095_PFAM270X/ALIXX.hmmscan    ALIXX
diff --git a/forester/data/tol_156.xml b/forester/data/tol_156.xml
index 8768717..80141c2 100644 (file)
--- a/forester/data/tol_156.xml
+++ b/forester/data/tol_156.xml
@@ -5153,7 +5153,6 @@
                   <taxonomy>\r
                     <id provider="uniprot">38254</id>\r
                     <scientific_name>Glaucocystophyceae</scientific_name>\r
-                    <synonym>Glaucophyta</synonym>\r
                     <rank>class</rank>\r
                   </taxonomy>\r
                   <clade>\r
@@ -5184,7 +5183,8 @@
                     <scientific_name>Emiliania huxleyi</scientific_name>\r
                     <synonym>Pontosphaera huxleyi</synonym>\r
                     <rank>species</rank>\r
-                    <uri>http://research.kahaku.go.jp/zoology/kaisei/hp-2/images/hapto.jpg</uri>\r
+                    <uri>http://www.nhm.ac.uk/resources-rx/images/1049/emiliania-huxleyi-light-microscope-image_68318_1.jpg</uri>\r
+                    <uri>http://cmore.soest.hawaii.edu/education/kidskorner/images/emiliania_600px.jpg</uri>\r
                   </taxonomy>\r
                 </clade>\r
                 <clade>\r