From 09133b4f9e5862066d1582552c99ff7312e52742 Mon Sep 17 00:00:00 2001
From: Robert Bossy <Robert.Bossy@inra.fr>
Date: Wed, 20 Oct 2021 13:57:31 +0200
Subject: [PATCH] moved microorganisms roots in a single file
---
cut-root.py | 39 +++++++++++++++++--------
microorganisms-roots.txt | 28 ++++++++++++++++++
microorganisms-roots/Alveolata | 1 -
microorganisms-roots/Amoebozoa | 1 -
microorganisms-roots/Archaea | 1 -
microorganisms-roots/Bacteria | 1 -
microorganisms-roots/Chlamydomonadales | 1 -
microorganisms-roots/Chlorella | 1 -
microorganisms-roots/Choanoflagellida | 1 -
microorganisms-roots/Cryptophyta | 1 -
microorganisms-roots/Desmidiales | 1 -
microorganisms-roots/Diplomonadida | 1 -
microorganisms-roots/Euglenozoa | 1 -
microorganisms-roots/Fungi | 1 -
microorganisms-roots/Glaucocystophyceae | 1 -
microorganisms-roots/Haptophyta | 1 -
microorganisms-roots/Ichthyosporea | 1 -
microorganisms-roots/Nematoda | 1 -
microorganisms-roots/Oxymonadida | 1 -
microorganisms-roots/Parabasalia | 1 -
microorganisms-roots/Prototheca | 1 -
microorganisms-roots/Retortamonadidae | 1 -
microorganisms-roots/Rhizaria | 1 -
microorganisms-roots/Stramenopiles | 1 -
microorganisms-roots/Viruses | 1 -
microorganisms-roots/_Crenarchaeota | 1 -
microorganisms-roots/_Euryarchaeota | 1 -
microorganisms-roots/_Korarchaeota | 1 -
microorganisms-roots/_Nanoarchaeota | 1 -
microorganisms-roots/_Volvox | 1 -
rewrite-taxonomy.snakefile | 8 ++---
31 files changed, 59 insertions(+), 44 deletions(-)
create mode 100644 microorganisms-roots.txt
delete mode 100644 microorganisms-roots/Alveolata
delete mode 100644 microorganisms-roots/Amoebozoa
delete mode 100644 microorganisms-roots/Archaea
delete mode 100644 microorganisms-roots/Bacteria
delete mode 100644 microorganisms-roots/Chlamydomonadales
delete mode 100644 microorganisms-roots/Chlorella
delete mode 100644 microorganisms-roots/Choanoflagellida
delete mode 100644 microorganisms-roots/Cryptophyta
delete mode 100644 microorganisms-roots/Desmidiales
delete mode 100644 microorganisms-roots/Diplomonadida
delete mode 100644 microorganisms-roots/Euglenozoa
delete mode 100644 microorganisms-roots/Fungi
delete mode 100644 microorganisms-roots/Glaucocystophyceae
delete mode 100644 microorganisms-roots/Haptophyta
delete mode 100644 microorganisms-roots/Ichthyosporea
delete mode 100644 microorganisms-roots/Nematoda
delete mode 100644 microorganisms-roots/Oxymonadida
delete mode 100644 microorganisms-roots/Parabasalia
delete mode 100644 microorganisms-roots/Prototheca
delete mode 100644 microorganisms-roots/Retortamonadidae
delete mode 100644 microorganisms-roots/Rhizaria
delete mode 100644 microorganisms-roots/Stramenopiles
delete mode 100644 microorganisms-roots/Viruses
delete mode 100644 microorganisms-roots/_Crenarchaeota
delete mode 100644 microorganisms-roots/_Euryarchaeota
delete mode 100644 microorganisms-roots/_Korarchaeota
delete mode 100644 microorganisms-roots/_Nanoarchaeota
delete mode 100644 microorganisms-roots/_Volvox
diff --git a/cut-root.py b/cut-root.py
index 4c11584..928aeda 100755
--- a/cut-root.py
+++ b/cut-root.py
@@ -4,27 +4,42 @@
import sys
import re
-ROOT_FILES = sys.argv[1:]
+ROOT_FILE = sys.argv[1]
ROOT_CANDIDATES = []
-for rf in ROOT_FILES:
- with open(rf) as f:
- r = f.read().strip()
- ROOT_CANDIDATES.append((rf, r))
+with open(ROOT_FILE) as f:
+ headers = None
+ for line in f:
+ cols = list(c.strip() for c in line.split('\t'))
+ if headers is None:
+ headers = cols
+ continue
+ record = dict(zip(headers, cols))
+ if record['Taxonomy ID'] == '':
+ sys.stderr.write('ignoring %s, not a taxon root\n' % (record['Name'],))
+ else:
+ ROOT_CANDIDATES.append((record['Name'], record['Taxonomy path']))
ROOTS = []
-for rf1, r1 in ROOT_CANDIDATES:
+for name1, path1 in ROOT_CANDIDATES:
accept = True
- for rf2, r2 in ROOT_CANDIDATES:
- if r1 == r2 and rf1 == rf2:
+ for name2, path2 in ROOT_CANDIDATES:
+ if path1 == path2 and name1 == path2:
continue
- if r1.startswith(r2 + '/'):
- sys.stderr.write('%s excluded since it is subsumed by %s\n' % (rf1, rf2))
+ if path1.startswith(path2 + '/'):
+ sys.stderr.write('%s excluded since it is subsumed by %s\n' % (name1, name2))
accept = False
if accept:
- ROOTS.append(r1)
+ sys.stderr.write('Root %s (%s)\n' % (name1, path1))
+ ROOTS.append((name1, path1))
-PATTERN = re.compile(r'\t(?:' + '|'.join(ROOTS) + r')[/\t]')
+PATTERN = re.compile(r'\t(?:' + '|'.join(path for (name, path) in ROOTS) + r')[/\t]')
+REMAIN = list(ROOTS)
for line in sys.stdin:
m = PATTERN.search(line)
if m is not None:
sys.stdout.write(line)
+ for name, path in REMAIN:
+ if path in line:
+ REMAIN.remove((name, path))
+for name, path in REMAIN:
+ sys.stderr.write('%s not seen' % (name,))
diff --git a/microorganisms-roots.txt b/microorganisms-roots.txt
new file mode 100644
index 0000000..e938833
--- /dev/null
+++ b/microorganisms-roots.txt
@@ -0,0 +1,28 @@
+Name MeSH ID MeSH Tree Taxonomy ID Taxonomy path
+Alveolata D056893 B01.043 ncbi:33630 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:2698737/ncbi:33630
+Amoebozoa D056894 B01.046 ncbi:554915 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:554915
+Archaea D001105 B02 ncbi:2157 /ncbi:1/ncbi:131567/ncbi:2157
+Bacteria D001419 B03 ncbi:2 /ncbi:1/ncbi:131567/ncbi:2
+Chlamydomonadales D000077105 B01.650.940.150.511 ncbi:3042 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:33090/ncbi:3041/ncbi:2692248/ncbi:3166/ncbi:2812636/ncbi:3042
+Chlorella D002708 B01.650.940.150.469 ncbi:3071 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:33090/ncbi:3041/ncbi:2692248/ncbi:75966/ncbi:35460/ncbi:35461/ncbi:2511126/ncbi:3071
+Choanoflagellida D056897 B01.175 ncbi:28009 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:33154/ncbi:28009
+Cryptophyta D044785 B01.206 ncbi:3027 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:3027
+Desmidiales D058114 B01.650.940.800.150.200 ncbi:131210 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:33090/ncbi:35493/ncbi:131221/ncbi:131209/ncbi:2684882/ncbi:131210
+Diplomonadida D016828 B01.237 ncbi:5738 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:2611341/ncbi:207245/ncbi:5738
+Euglenozoa D056898 B01.268 ncbi:33682 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:2611352/ncbi:33682
+Fungi D005658 B01.300 ncbi:4751 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:33154/ncbi:4751
+Glaucocystophyceae D058108 B01.650.232 ncbi:38254 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:38254
+Haptophyta D058087 B01.400 ncbi:2830 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:2608109/ncbi:2830
+Ichthyosporea D050298 B01.500 ncbi:127916 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:33154/ncbi:127916
+Nematoda D009348 B01.050.500.500.294 ncbi:6231 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:33154/ncbi:33208/ncbi:6072/ncbi:33213/ncbi:33317/ncbi:1206794/ncbi:6231
+Oxymonadida D056899 B01.625 ncbi:66288 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:2611341/ncbi:2662611/ncbi:66288
+Parabasalia D056900 B01.630 ncbi:5719 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:2611341/ncbi:5719
+Prototheca D011525 B01.650.940.150.634 ncbi:3110 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:33090/ncbi:3041/ncbi:2692248/ncbi:75966/ncbi:35460/ncbi:35461/ncbi:3110
+Retortamonadidae D056919 B01.675 ncbi:193075 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:2611341/ncbi:207245/ncbi:193075
+Rhizaria D056901 B01.680 ncbi:543769 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:2698737/ncbi:543769
+Stramenopiles D058009 B01.750 ncbi:33634 /ncbi:1/ncbi:131567/ncbi:2759/ncbi:2698737/ncbi:33634
+Viruses D014780 B04 ncbi:10239 /ncbi:1/ncbi:10239
+Microbiological Phenomena D008827 G06
+Microbiology D008829 H01.158.273.540
+Microbiological Techniques D008828 E05.200.875,E01.370.225.875
+Attachment Sites, Microbiological D001287 G05.360.340.024.079
diff --git a/microorganisms-roots/Alveolata b/microorganisms-roots/Alveolata
deleted file mode 100644
index 68604cd..0000000
--- a/microorganisms-roots/Alveolata
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:2698737/ncbi:33630
diff --git a/microorganisms-roots/Amoebozoa b/microorganisms-roots/Amoebozoa
deleted file mode 100644
index 0d27f58..0000000
--- a/microorganisms-roots/Amoebozoa
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:554915
diff --git a/microorganisms-roots/Archaea b/microorganisms-roots/Archaea
deleted file mode 100644
index 48279c0..0000000
--- a/microorganisms-roots/Archaea
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2157
diff --git a/microorganisms-roots/Bacteria b/microorganisms-roots/Bacteria
deleted file mode 100644
index 7abbde7..0000000
--- a/microorganisms-roots/Bacteria
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2
diff --git a/microorganisms-roots/Chlamydomonadales b/microorganisms-roots/Chlamydomonadales
deleted file mode 100644
index 92eac40..0000000
--- a/microorganisms-roots/Chlamydomonadales
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:33090/ncbi:3041/ncbi:2692248/ncbi:3166/ncbi:2812636/ncbi:3042
diff --git a/microorganisms-roots/Chlorella b/microorganisms-roots/Chlorella
deleted file mode 100644
index 945ed27..0000000
--- a/microorganisms-roots/Chlorella
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:33090/ncbi:3041/ncbi:2692248/ncbi:75966/ncbi:35460/ncbi:35461/ncbi:2511126/ncbi:3071
diff --git a/microorganisms-roots/Choanoflagellida b/microorganisms-roots/Choanoflagellida
deleted file mode 100644
index d6449de..0000000
--- a/microorganisms-roots/Choanoflagellida
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:33154/ncbi:28009
diff --git a/microorganisms-roots/Cryptophyta b/microorganisms-roots/Cryptophyta
deleted file mode 100644
index 1255f03..0000000
--- a/microorganisms-roots/Cryptophyta
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:3027
diff --git a/microorganisms-roots/Desmidiales b/microorganisms-roots/Desmidiales
deleted file mode 100644
index 5a511d1..0000000
--- a/microorganisms-roots/Desmidiales
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:33090/ncbi:35493/ncbi:131221/ncbi:131209/ncbi:2684882/ncbi:131210
diff --git a/microorganisms-roots/Diplomonadida b/microorganisms-roots/Diplomonadida
deleted file mode 100644
index 37583ce..0000000
--- a/microorganisms-roots/Diplomonadida
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:2611341/ncbi:207245/ncbi:5738
diff --git a/microorganisms-roots/Euglenozoa b/microorganisms-roots/Euglenozoa
deleted file mode 100644
index c2a12e9..0000000
--- a/microorganisms-roots/Euglenozoa
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:2611352/ncbi:33682
diff --git a/microorganisms-roots/Fungi b/microorganisms-roots/Fungi
deleted file mode 100644
index 5669838..0000000
--- a/microorganisms-roots/Fungi
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:33154/ncbi:4751
diff --git a/microorganisms-roots/Glaucocystophyceae b/microorganisms-roots/Glaucocystophyceae
deleted file mode 100644
index 3059f6d..0000000
--- a/microorganisms-roots/Glaucocystophyceae
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:38254
diff --git a/microorganisms-roots/Haptophyta b/microorganisms-roots/Haptophyta
deleted file mode 100644
index dac52ab..0000000
--- a/microorganisms-roots/Haptophyta
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:2608109/ncbi:2830
diff --git a/microorganisms-roots/Ichthyosporea b/microorganisms-roots/Ichthyosporea
deleted file mode 100644
index 39bc6b1..0000000
--- a/microorganisms-roots/Ichthyosporea
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:33154/ncbi:127916
diff --git a/microorganisms-roots/Nematoda b/microorganisms-roots/Nematoda
deleted file mode 100644
index e8fdf14..0000000
--- a/microorganisms-roots/Nematoda
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:33154/ncbi:33208/ncbi:6072/ncbi:33213/ncbi:33317/ncbi:1206794/ncbi:6231
diff --git a/microorganisms-roots/Oxymonadida b/microorganisms-roots/Oxymonadida
deleted file mode 100644
index a5a82c3..0000000
--- a/microorganisms-roots/Oxymonadida
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:2611341/ncbi:2662611/ncbi:66288
diff --git a/microorganisms-roots/Parabasalia b/microorganisms-roots/Parabasalia
deleted file mode 100644
index f2a90da..0000000
--- a/microorganisms-roots/Parabasalia
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:2611341/ncbi:5719
diff --git a/microorganisms-roots/Prototheca b/microorganisms-roots/Prototheca
deleted file mode 100644
index 8974461..0000000
--- a/microorganisms-roots/Prototheca
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:33090/ncbi:3041/ncbi:2692248/ncbi:75966/ncbi:35460/ncbi:35461/ncbi:3110
diff --git a/microorganisms-roots/Retortamonadidae b/microorganisms-roots/Retortamonadidae
deleted file mode 100644
index 0c9e290..0000000
--- a/microorganisms-roots/Retortamonadidae
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:2611341/ncbi:207245/ncbi:193075
diff --git a/microorganisms-roots/Rhizaria b/microorganisms-roots/Rhizaria
deleted file mode 100644
index b0fe36e..0000000
--- a/microorganisms-roots/Rhizaria
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:2698737/ncbi:543769
diff --git a/microorganisms-roots/Stramenopiles b/microorganisms-roots/Stramenopiles
deleted file mode 100644
index e6f72b6..0000000
--- a/microorganisms-roots/Stramenopiles
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:2698737/ncbi:33634
diff --git a/microorganisms-roots/Viruses b/microorganisms-roots/Viruses
deleted file mode 100644
index e159dd1..0000000
--- a/microorganisms-roots/Viruses
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:10239
diff --git a/microorganisms-roots/_Crenarchaeota b/microorganisms-roots/_Crenarchaeota
deleted file mode 100644
index 4dbf627..0000000
--- a/microorganisms-roots/_Crenarchaeota
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2157/ncbi:1783275/ncbi:28889
diff --git a/microorganisms-roots/_Euryarchaeota b/microorganisms-roots/_Euryarchaeota
deleted file mode 100644
index 8149b0a..0000000
--- a/microorganisms-roots/_Euryarchaeota
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2157/ncbi:28890
diff --git a/microorganisms-roots/_Korarchaeota b/microorganisms-roots/_Korarchaeota
deleted file mode 100644
index 60a5d1a..0000000
--- a/microorganisms-roots/_Korarchaeota
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2157/ncbi:1783275/ncbi:51967
diff --git a/microorganisms-roots/_Nanoarchaeota b/microorganisms-roots/_Nanoarchaeota
deleted file mode 100644
index 4aa9262..0000000
--- a/microorganisms-roots/_Nanoarchaeota
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2157/ncbi:1783276/ncbi:192989
diff --git a/microorganisms-roots/_Volvox b/microorganisms-roots/_Volvox
deleted file mode 100644
index 781fcbd..0000000
--- a/microorganisms-roots/_Volvox
+++ /dev/null
@@ -1 +0,0 @@
-/ncbi:1/ncbi:131567/ncbi:2759/ncbi:33090/ncbi:3041/ncbi:2692248/ncbi:3166/ncbi:2812636/ncbi:3042/ncbi:3065/ncbi:3066
diff --git a/rewrite-taxonomy.snakefile b/rewrite-taxonomy.snakefile
index 87cbf43..d2daf4c 100644
--- a/rewrite-taxonomy.snakefile
+++ b/rewrite-taxonomy.snakefile
@@ -6,10 +6,10 @@ rule all:
config['OUTDIR'] + '/finish.txt',
config['OUTDIR'] + '/taxid_microorganisms.txt',
config['OUTDIR'] + '/taxa+id_microorganisms.txt',
- config['OUTDIR'] + '/taxa+id_microorganisms.trie',
+ # config['OUTDIR'] + '/taxa+id_microorganisms.trie',
config['OUTDIR'] + '/taxid_full.txt',
config['OUTDIR'] + '/taxa+id_full.txt',
- config['OUTDIR'] + '/taxa+id_full.trie'
+ # config['OUTDIR'] + '/taxa+id_full.trie'
rule check:
@@ -30,10 +30,10 @@ rule microorganisms:
input:
full=config['OUTDIR'] + '/{p}_full.txt',
- roots='microorganisms-roots'
+ roots='microorganisms-roots.txt'
shell:
- '''./cut-root.py {input.roots}/* <{input.full} >{output}'''
+ '''./cut-root.py {input.roots} <{input.full} >{output}'''
rule taxaid_full:
--
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