src/figures: Use open() instead of file() in Python scripts

file() is gone in Python 3, and open() was always the prefered method
for opening files.  I just didn't know that when I wrote the original
code ;).

diff --git a/src/figures/cantilever-data/avg_data.py b/src/figures/cantilever-data/avg_data.py
index 73bab0d5f6ffa2cf177daefc960003ac3d8b8aef..c9a3fe1489c9e34cb2d9806f3b43f6dbe40d6635 100755 (executable)
--- a/src/figures/cantilever-data/avg_data.py
+++ b/src/figures/cantilever-data/avg_data.py
@@ -13,7 +13,7 @@ def read_raw(Kcuts=KCUTS, datafile=DATAFILE):
     Ks = []
     for i in range(len(Kcuts)+1):
         Ks.append([])
-    for line in file(datafile, 'r'):
+    for line in open(datafile, 'r'):
         if line[0] == '#':
             continue # ignore comments
         fields = line.strip().split('\t')
@@ -36,7 +36,7 @@ def write_k_file(Ks, kfile=KFILE):
     avgK = [0]*len(Ks)
     stdK = [0]*len(Ks)
     numK = [0]*len(Ks)
-    kf = file(kfile, 'w')
+    kf = open(kfile, 'w')
     for i in range(len(Ks)):
         K = numpy.array(Ks[i])
         avgK[i] = K.mean()
@@ -53,7 +53,7 @@ def write_k_file(Ks, kfile=KFILE):
 def write_average_file(FofV, avgK, avgfile=AVGFILE):
     Vs = FofV.keys()
     Vs.sort()
-    af = file(AVGFILE, 'w')
+    af = open(AVGFILE, 'w')
     print >> af, '#'+'\t'.join(\
         ['Pulling speed (nm/s)','Spring constant (pN/nm)',
          'Mean force (pN)','Std. force (pN)','Events (#)'])

diff --git a/src/figures/cantilever-data/fit_data.py b/src/figures/cantilever-data/fit_data.py
index f87a6e0d16b0cccac355abffd7c63095d2ef8d5e..de03a664ceba28981f5670cc7181c3d42e9c9a6e 100755 (executable)
--- a/src/figures/cantilever-data/fit_data.py
+++ b/src/figures/cantilever-data/fit_data.py
@@ -14,7 +14,7 @@ y = []
 w = [] # weights
 
 print >> sys.stderr, "Fitting data from", fname
-for line in file(fname, 'r'):
+for line in open(fname, 'r'):
     fields = [float(a) for a in line.strip().split()]
     if WEIGHTHACK==True:
         w = int(fields[3])

diff --git a/src/figures/cantilever-data/get_loading_rates.py b/src/figures/cantilever-data/get_loading_rates.py
index efb310cbe34592b8957264459e0728e09d8c01ab..99e6f2417adbcfd110c717f7dd1b09a12afe8c15 100755 (executable)
--- a/src/figures/cantilever-data/get_loading_rates.py
+++ b/src/figures/cantilever-data/get_loading_rates.py
@@ -14,9 +14,9 @@ OFILEs = [None, None, None]
 for i,K in enumerate(Ks):
     if K == None:
         continue
-    OFILEs[i] = file('loading-rate.d/loading_rate_%.2f.dat' % K, 'w')
+    OFILEs[i] = open('loading-rate.d/loading_rate_%.2f.dat' % K, 'w')
 
-for line in file(DATA, 'r'):
+for line in open(DATA, 'r'):
     if line[0] == '#':
         continue
     fields = line.strip().split()

diff --git a/src/figures/fit-space/extract_fit_valley.py b/src/figures/fit-space/extract_fit_valley.py
index 829bbc825ace561ac635a29360bbc912c7b34e2b..386127fb7666a155d5d2759332519a097e5f9984 100644 (file)
--- a/src/figures/fit-space/extract_fit_valley.py
+++ b/src/figures/fit-space/extract_fit_valley.py
@@ -10,7 +10,7 @@ data_filename = sys.argv[1]
 
 data = {}
 header = None
-for line in file(data_filename, 'r'):
+for line in open(data_filename, 'r'):
     if len(line.strip()) == 0:
         continue
     if line.startswith('#'):

diff --git a/src/figures/script/pyfit b/src/figures/script/pyfit
index f0d6cf7f4163daf7ecda40c9602ae027677ef519..69ffa23f52588bc16d486688031e8e4cd5fa7546 100755 (executable)
--- a/src/figures/script/pyfit
+++ b/src/figures/script/pyfit
@@ -155,7 +155,7 @@ ignored.
 
     mod_includes = parse_modules(options.modules)
     fn = parse_function(options.function)
-    data = read_data(file(datafile, 'r'),
+    data = read_data(open(datafile, 'r'),
                      options.xcol, options.ycol, options.wcol)
     initial_ps = [float(x) for x in options.params.split(',')]