Use GNU Make

ecell · Jun 14, 2022 · fce1248 · fce1248
1 parent 21b1aca
commit fce1248
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Showing 6 changed files with 13 additions and 2 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,4 @@
+scripts/bigg_models_metabolites.txt
+scripts/bigg.metabolite.csv
+scripts/bigg_models_reactions.txt
+scripts/reac_xref.tsv
diff --git a/requirements.txt b/requirements.txt
@@ -0,0 +1,2 @@
+pandas
+requests
diff --git a/scripts/Makefile b/scripts/Makefile
@@ -0,0 +1,2 @@
+bigg.metabolite.csv: bigg_models_metabolites.txt
+	python bigg.metabolite.py
diff --git a/scripts/bigg.reaction.py b/scripts/bigg.reaction.py
@@ -1,5 +1,5 @@
 import pandas as pd
-df = pd.read_table("http://bigg.ucsd.edu/static/namespace/bigg_models_reactions.txt")
+df = pd.read_table("bigg_models_reactions.txt")
 df2 = df.drop(columns=['name', 'reaction_string', 'model_list', 'old_bigg_ids'])
 df2['database_links'] = df2['database_links'].str.split('; ')
 df2 = df2.explode('database_links')

diff --git a/scripts/download.sh b/scripts/download.sh
@@ -0,0 +1,3 @@
+wget http://bigg.ucsd.edu/static/namespace/bigg_models_metabolites.txt
+wget http://bigg.ucsd.edu/static/namespace/bigg_models_reactions.txt
+wget https://www.metanetx.org/cgi-bin/mnxget/mnxref/reac_xref.tsv
diff --git a/scripts/metanetx.reaction.py b/scripts/metanetx.reaction.py
@@ -1,7 +1,7 @@
 import pandas as pd
 import requests
 
-df = pd.read_table("https://www.metanetx.org/cgi-bin/mnxget/mnxref/reac_xref.tsv", skiprows=351)
+df = pd.read_table("reac_xref.tsv", skiprows=351)
 df2 = df.drop(columns=['description'])
 df3 = df2['#source'].str.split(':', expand=True)
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		bigg.metabolite.csv: bigg_models_metabolites.txt
		python bigg.metabolite.py