-
Notifications
You must be signed in to change notification settings - Fork 1
Expand file tree
/
Copy pathMakefile
More file actions
179 lines (136 loc) · 5.39 KB
/
Makefile
File metadata and controls
179 lines (136 loc) · 5.39 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
WORK=work
SOURCES=src/report.py src/alignment.py src/articulation.py src/relation.py \
src/checklist.py src/changes.py src/merge.py src/report.py src/eulerx.py \
src/intension.py src/table.py src/dribble.py src/property.py src/diff.py
all: $(WORK)/primates-ncbi-2015-2020.csv
diff: $(WORK)/primates-ncbi-2015-2020-diff.csv
# N15 (NCBI 2015)
N15=$(WORK)/ncbi/2015-05-01
$(N15)/dump.zip:
mkdir -p $(N15)/dump
wget -O $@ ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2015-05-01.zip
$(N15)/dump/names.dmp: $(N15)/dump.zip
mkdir -p $(N15)/dump
unzip -d $(N15)/dump $(N15)/dump.zip
touch $(N15)/dump/*
# Convert to DwC form
$(N15)/converted.csv: src/ncbi_to_dwc.py $(N15)/dump/names.dmp
python3 src/ncbi_to_dwc.py $(N15)/dump --out $@
# N20 (NCBI 2020)
N20=$(WORK)/ncbi/2020-08-01
$(N20)/dump.zip:
mkdir -p $(N20)/dump
wget -O $@ ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump_archive/taxdmp_2020-08-01.zip
$(N20)/dump/names.dmp: $(N20)/dump.zip
mkdir -p $(N20)/dump
unzip -d $(N20)/dump $(N20)/dump.zip
touch $(N20)/dump/*
# Convert to DwC form
$(N20)/converted.csv: src/ncbi_to_dwc.py $(N20)/dump/names.dmp
python3 src/ncbi_to_dwc.py $(N20)/dump --out $@
# C (GBIF)
C=$(WORK)/gbif/2019-09-16
$(C)/backbone.zip:
mkdir -p $(C)/dump
wget -O $@ http://rs.gbif.org/datasets/backbone/2019-09-06/backbone.zip
$(C)/dump/Taxon.tsv: $(C)/backbone.zip
mkdir -p $(C)/dump
unzip -d $(C)/dump $<
touch $(C)/dump/*
# No conversion needed
# --------------------
# Extract Primates from each, and compare
$(N15)/primates.csv: src/subset_dwc.py $(N15)/converted.csv
python3 src/subset_dwc.py $(N15)/converted.csv 9443 --out $@
$(N20)/primates.csv: src/subset_dwc.py $(N20)/converted.csv
python3 src/subset_dwc.py $(N20)/converted.csv 9443 --out $@
$(C)/primates.csv: src/subset_dwc.py $(C)/dump/Taxon.tsv
python3 src/subset_dwc.py $(C)/dump/Taxon.tsv 798 --out $@.new
mv $@.new $@
p: $(C)/primates.csv
$(WORK)/primates-ncbi-2015-2020.csv: $(SOURCES) $(N15)/primates.csv $(N20)/primates.csv
python3 src/report.py $(N15)/primates.csv \
$(N20)/primates.csv \
--out $@.new
mv $@.new $@
mv $@.new.log $@.log
# --low-tag=N15 --high-tag=N20
$(WORK)/primates-ncbi-2015-2020-diff.csv: $(SOURCES) $(N15)/primates.csv $(N20)/primates.csv
python3 src/report.py $(N15)/primates.csv \
$(N20)/primates.csv \
--format diff --out $@.new
mv $@.new $@
mv $@.new.log $@.log
$(WORK)/primates-ncbi-2015-2020.ex: $(SOURCES) $(N15)/primates.csv $(N20)/primates.csv
python3 src/report.py $(N15)/primates.csv \
$(N20)/primates.csv \
--out $@.new --format eulerx
mv $@.new $@
mv $@.new.log $@.log
$(WORK)/primates-ncbi-gbif.csv: $(SOURCES) $(N20)/primates.csv $(C)/primates.csv
python3 src/report.py $(N20)/primates.csv \
$(C)/primates.csv --out $@.new
mv $@.new $@
mv $@.new.log $@.log
pri: $(WORK)/primates-ncbi-2015-2020.csv
# ----------------------------------------------------------------------
# Mammalia = NCBI 40674
$(N15)/mammalia.csv: src/subset_dwc.py $(N15)/converted.csv
python3 src/subset_dwc.py $(N15)/converted.csv 40674 --out $@
$(N20)/mammalia.csv: src/subset_dwc.py $(N20)/converted.csv
python3 src/subset_dwc.py $(N20)/converted.csv 40674 --out $@
$(WORK)/mammalia-ncbi-2015-2020.csv: $(SOURCES) $(N15)/mammalia.csv $(N20)/mammalia.csv
python3 src/report.py $(N15)/mammalia.csv $(N20)/mammalia.csv \
--out $@.new
mv $@.new $@
mv $@.new.log $@.log
mam: $(WORK)/mammalia-ncbi-2015-2020.csv
# --------------------
publish: doc/primates-ncbi-2015-2020.csv \
doc/primates-ncbi-2015-2020.ex \
doc/mammalia-ncbi-2015-2020.csv \
doc/primates-ncbi-gbif.csv
doc/primates-ncbi-2015-2020.csv: $(WORK)/primates-ncbi-2015-2020.csv
cp -p $< $@
cp -p $<.log $@.log
doc/primates-ncbi-2015-2020.ex: $(WORK)/primates-ncbi-2015-2020.ex
cp -p $< $@
doc/mammalia-ncbi-2015-2020.csv: $(WORK)/mammalia-ncbi-2015-2020.csv
cp -p $< $@
cp -p $<.log $@.log
doc/primates-ncbi-gbif.csv: $(WORK)/primates-ncbi-gbif.csv
cp -p $< $@
cp -p $<.log $@.log
gbif: $(WORK)/primates-ncbi-gbif.csv
test:
python3 src/report.py "(l(pab)c)" "(l(qab)c)" --out -
# ----------------------------------------------------------------------
# Other groups to play with
# Trillium
$(N15)/trillium.csv: src/subset_dwc.py $(N15)/converted.csv
python3 src/subset_dwc.py $(N15)/converted.csv 49674 --out $@
$(N20)/trillium.csv: src/subset_dwc.py $(N20)/converted.csv
python3 src/subset_dwc.py $(N20)/converted.csv 49674 --out $@
$(C)/trillium.csv: src/subset_dwc.py $(C)/dump/Taxon.tsv
python3 src/subset_dwc.py $(C)/dump/Taxon.tsv 2742182 --out $@
$(WORK)/trillium-ncbi-2015-2020.csv: $(SOURCES) $(N15)/trillium.csv $(N20)/trillium.csv
python3 src/report.py $(N15)/trillium.csv $(N20)/trillium.csv \
--out $@.new
mv $@.new $@
t: $(WORK)/trillium-ncbi-2015-2020.csv
$(N15)/mag.csv: src/subset_dwc.py $(N15)/converted.csv
python3 src/subset_dwc.py $(N15)/converted.csv 3401 --out $@
$(N20)/mag.csv: src/subset_dwc.py $(N20)/converted.csv
python3 src/subset_dwc.py $(N20)/converted.csv 3401 --out $@
$(C)/mag.csv: src/subset_dwc.py $(C)/dump/Taxon.tsv
python3 src/subset_dwc.py $(C)/dump/Taxon.tsv 4690 --out $@
$(WORK)/mag-ncbi-2015-2020.csv: $(SOURCES) $(N15)/mag.csv $(N20)/mag.csv
python3 src/report.py $(N15)/mag.csv $(N20)/mag.csv \
--out $@.new
mv $@.new $@
mag: $(WORK)/mag-ncbi-2015-2020.csv
clean:
rm -rf $(WORK)
tags: TAGS
TAGS: $(SOURCES)
etags src/*.py