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Author: Nilesh Patra <npatra974@gmail.com>
Description: Remove python-2 relevant code, use python3 support.
Last Changed: August 20, 2020
--- a/make_expterm.py
+++ b/make_expterm.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
import sys
@@ -73,11 +73,11 @@
j = int((tail - min_tail[at])/dy)
if i == 0 or j == 0:
- print >> sys.stderr, at, i, j, hp, tail, min_hp[at], min_tail[at], dx, dy
+ print(at, i, j, hp, tail, min_hp[at], min_tail[at], dx, dy, file=sys.stderr)
if not (0 <= i < num_bins and 0 <= j < num_bins):
- print >> sys.stderr, "WARNING: out of range values:", i, j, at, hp, tail
- print >> sys.stderr, "Ranges=", min_hp[at], max_hp[at], min_tail[at], max_tail[at]
+ print("WARNING: out of range values:", i, j, at, hp, tail, file=sys.stderr)
+ print("Ranges=", min_hp[at], max_hp[at], min_tail[at], max_tail[at], file=sys.stderr)
continue
D[at][i][j] += 1
@@ -90,12 +90,12 @@
def warn_if_out_of_range(value, rng, title):
if value <= rng[0] or value >= rng[1]:
if title not in warned:
- print >> sys.stderr, "@" * 60
- print >> sys.stderr, """WARNING: random %s generated with energy lower than supplied range.
+ print("@" * 60, file=sys.stderr)
+ print("""WARNING: random %s generated with energy lower than supplied range.
Such examples are ignored. I suggest you re-run calibrate.sh after changing
- the lowerbound in the range variable therein.""" % (title)
- print >> sys.stderr, "Range = ", rng, "Seen = ", value
- print >> sys.stderr, "@" * 60
+ the lowerbound in the range variable therein.""" % (title), file=sys.stderr)
+ print("Range = ", rng, "Seen = ", value, file=sys.stderr)
+ print("@" * 60, file=sys.stderr)
warned[title] = True
return True
return False
@@ -105,8 +105,8 @@
"""Write out the matrix (transposed)"""
for j in range(len(A)):
for i in range(len(A)):
- print A[i][j],
- print
+ print(A[i][j], end=' ')
+ print()
def main():
@@ -118,14 +118,14 @@
#tail_range = (float(sys.argv[6]), float(sys.argv[7]))
# print the header
- print seqlen, num_bins # hp_range[0], hp_range[1], tail_range[0], tail_range[1]
+ print(seqlen, num_bins) # hp_range[0], hp_range[1], tail_range[0], tail_range[1]
set_ranges_from_file(infile, num_bins)
D = hist2d_from_file(infile, num_bins) #, hp_range, tail_range)
# for every at value, compute and print the matrix
for at in sorted(D):
- print at, min_hp[at], max_hp[at], min_tail[at], max_tail[at]
+ print(at, min_hp[at], max_hp[at], min_tail[at], max_tail[at])
print_matrix(D[at])
if __name__ == '__main__': main()
--- a/random_fasta.py
+++ b/random_fasta.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
# generate a FASTA file with length random characters
import random, sys
@@ -11,7 +11,7 @@
def random_fasta(fasta, length, at):
fasta = open(fasta, 'w')
- print >> fasta, ">random uniform length=", length
+ print(">random uniform length=", length, file=fasta)
for i in range(1,length+1):
fasta.write(random_base(at))
@@ -26,7 +26,7 @@
i += random.randint(5, 500)
j = i + random.randint(200, 2000)
if(j < length):
- print >> coords, "UNK", i, j, "random"
+ print("UNK", i, j, "random", file=coords)
i = j
coords.close()
--- a/calibrate.sh
+++ b/calibrate.sh
@@ -52,11 +52,11 @@
MAKE_EXPTERM=`findprog make_expterm.py`
#==============================
-# Ensure python is avialable
+# Ensure python3 is avialable
#==============================
-if [ ! -x "`which python`" ] ; then
- echo "`basename $0`: python must be installed to run calibration scripts" > /dev/stderr
+if [ ! -x "`which python3`" ] ; then
+ echo "`basename $0`: python3 must be installed to run calibration scripts" > /dev/stderr
exit 3
fi
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