diff --git a/tests/data/bt1.bed b/tests/data/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..1ae9665dd3b4c86d819700d7d9b1df37146baa94
--- /dev/null
+++ b/tests/data/bt1.bed
@@ -0,0 +1,10 @@
+I 0 5 a(I:0-5:+) . +
+I 0 5 b(I:0-5:-) . -
+I 0 10 c(I:0-10:+) . +
+I 0 10 d(I:0-10:-) . -
+I 5 10 e(I:5-10:+) . +
+I 5 10 f(I:5-10:-) . -
+I 5 20 g(I:5-20:+) . +
+I 5 20 h(I:5-20:-) . -
+I 10 15 i(I:10-15:+) . +
+I 10 15 j(I:10-15:-) . -
diff --git a/tests/data/shifted/m0/bt1.bed b/tests/data/shifted/m0/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..1ae9665dd3b4c86d819700d7d9b1df37146baa94
--- /dev/null
+++ b/tests/data/shifted/m0/bt1.bed
@@ -0,0 +1,10 @@
+I 0 5 a(I:0-5:+) . +
+I 0 5 b(I:0-5:-) . -
+I 0 10 c(I:0-10:+) . +
+I 0 10 d(I:0-10:-) . -
+I 5 10 e(I:5-10:+) . +
+I 5 10 f(I:5-10:-) . -
+I 5 20 g(I:5-20:+) . +
+I 5 20 h(I:5-20:-) . -
+I 10 15 i(I:10-15:+) . +
+I 10 15 j(I:10-15:-) . -
diff --git a/tests/data/shifted/m1/bt1.bed b/tests/data/shifted/m1/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..9e73706ca2fffde9a0e7e1d95dc7e0e3d0502055
--- /dev/null
+++ b/tests/data/shifted/m1/bt1.bed
@@ -0,0 +1,10 @@
+#I -1 4 a(I:0-5:+) . +
+I 1 6 b(I:0-5:-) . -
+#I -1 9 c(I:0-10:+) . +
+I 1 11 d(I:0-10:-) . -
+I 4 9 e(I:5-10:+) . +
+I 6 11 f(I:5-10:-) . -
+I 4 19 g(I:5-20:+) . +
+I 6 21 h(I:5-20:-) . -
+I 9 14 i(I:10-15:+) . +
+I 11 16 j(I:10-15:-) . -
diff --git a/tests/data/shifted/m10/bt1.bed b/tests/data/shifted/m10/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..30fc82fe85b6b346f7d1eebd457c7180da01ab32
--- /dev/null
+++ b/tests/data/shifted/m10/bt1.bed
@@ -0,0 +1,10 @@
+#I -10 -5 a(I:0-5:+) . +
+I 10 15 b(I:0-5:-) . -
+#I -10 0 c(I:0-10:+) . +
+I 10 20 d(I:0-10:-) . -
+#I -5 0 e(I:5-10:+) . +
+I 15 20 f(I:5-10:-) . -
+#I -5 10 g(I:5-20:+) . +
+I 15 30 h(I:5-20:-) . -
+I 0 5 i(I:10-15:+) . +
+I 20 25 j(I:10-15:-) . -
diff --git a/tests/data/shifted/m11/bt1.bed b/tests/data/shifted/m11/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..6279924b29adfd2a6eb01c8cc56b6ac095d2ea31
--- /dev/null
+++ b/tests/data/shifted/m11/bt1.bed
@@ -0,0 +1,10 @@
+#I -11 -6 a(I:0-5:+) . +
+I 11 16 b(I:0-5:-) . -
+#I -11 -1 c(I:0-10:+) . +
+I 11 21 d(I:0-10:-) . -
+#I -6 -1 e(I:5-10:+) . +
+I 16 21 f(I:5-10:-) . -
+#I -6 9 g(I:5-20:+) . +
+I 16 31 h(I:5-20:-) . -
+#I -1 4 i(I:10-15:+) . +
+I 21 26 j(I:10-15:-) . -
diff --git a/tests/data/shifted/m19/bt1.bed b/tests/data/shifted/m19/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..ea3b92285bc57333f7a2c97d31573556e0890ec1
--- /dev/null
+++ b/tests/data/shifted/m19/bt1.bed
@@ -0,0 +1,10 @@
+#I -19 -14 a(I:0-5:+) . +
+I 19 24 b(I:0-5:-) . -
+#I -19 -9 c(I:0-10:+) . +
+I 19 29 d(I:0-10:-) . -
+#I -14 -9 e(I:5-10:+) . +
+I 24 29 f(I:5-10:-) . -
+#I -14 1 g(I:5-20:+) . +
+I 24 39 h(I:5-20:-) . -
+#I -9 -4 i(I:10-15:+) . +
+I 29 34 j(I:10-15:-) . -
diff --git a/tests/data/shifted/m20/bt1.bed b/tests/data/shifted/m20/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..4ad9d02fd94631e7516033660e16f23656d781a7
--- /dev/null
+++ b/tests/data/shifted/m20/bt1.bed
@@ -0,0 +1,10 @@
+#I -20 -15 a(I:0-5:+) . +
+I 20 25 b(I:0-5:-) . -
+#I -20 -10 c(I:0-10:+) . +
+I 20 30 d(I:0-10:-) . -
+#I -15 -10 e(I:5-10:+) . +
+I 25 30 f(I:5-10:-) . -
+#I -15 0 g(I:5-20:+) . +
+I 25 40 h(I:5-20:-) . -
+#I -10 -5 i(I:10-15:+) . +
+I 30 35 j(I:10-15:-) . -
diff --git a/tests/data/shifted/m21/bt1.bed b/tests/data/shifted/m21/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..a0a67540684e33dad2ab50dcd8e44b8a5ff34c2d
--- /dev/null
+++ b/tests/data/shifted/m21/bt1.bed
@@ -0,0 +1,10 @@
+#I -21 -16 a(I:0-5:+) . +
+I 21 26 b(I:0-5:-) . -
+#I -21 -11 c(I:0-10:+) . +
+I 21 31 d(I:0-10:-) . -
+#I -16 -11 e(I:5-10:+) . +
+I 26 31 f(I:5-10:-) . -
+#I -16 -1 g(I:5-20:+) . +
+I 26 41 h(I:5-20:-) . -
+#I -11 -6 i(I:10-15:+) . +
+I 31 36 j(I:10-15:-) . -
diff --git a/tests/data/shifted/m4/bt1.bed b/tests/data/shifted/m4/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..d96672e82c4c8fc70e01e013d5b539597782eb6b
--- /dev/null
+++ b/tests/data/shifted/m4/bt1.bed
@@ -0,0 +1,10 @@
+#I -4 1 a(I:0-5:+) . +
+I 4 9 b(I:0-5:-) . -
+#I -4 6 c(I:0-10:+) . +
+I 4 14 d(I:0-10:-) . -
+I 1 6 e(I:5-10:+) . +
+I 9 14 f(I:5-10:-) . -
+I 1 16 g(I:5-20:+) . +
+I 9 24 h(I:5-20:-) . -
+I 6 11 i(I:10-15:+) . +
+I 14 19 j(I:10-15:-) . -
diff --git a/tests/data/shifted/m5/bt1.bed b/tests/data/shifted/m5/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..b7c40949ee5e73fad4c5bc0688593c2e432f1067
--- /dev/null
+++ b/tests/data/shifted/m5/bt1.bed
@@ -0,0 +1,10 @@
+#I -5 0 a(I:0-5:+) . +
+I 5 10 b(I:0-5:-) . -
+#I -5 5 c(I:0-10:+) . +
+I 5 15 d(I:0-10:-) . -
+I 0 5 e(I:5-10:+) . +
+I 10 15 f(I:5-10:-) . -
+I 0 15 g(I:5-20:+) . +
+I 10 25 h(I:5-20:-) . -
+I 5 10 i(I:10-15:+) . +
+I 15 20 j(I:10-15:-) . -
diff --git a/tests/data/shifted/m6/bt1.bed b/tests/data/shifted/m6/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..da19eec0a9e10af8a1e291123ddab385c07c7bef
--- /dev/null
+++ b/tests/data/shifted/m6/bt1.bed
@@ -0,0 +1,10 @@
+#I -6 -1 a(I:0-5:+) . +
+I 6 11 b(I:0-5:-) . -
+#I -6 4 c(I:0-10:+) . +
+I 6 16 d(I:0-10:-) . -
+#I -1 4 e(I:5-10:+) . +
+I 11 16 f(I:5-10:-) . -
+#I -1 14 g(I:5-20:+) . +
+I 11 26 h(I:5-20:-) . -
+I 4 9 i(I:10-15:+) . +
+I 16 21 j(I:10-15:-) . -
diff --git a/tests/data/shifted/m9/bt1.bed b/tests/data/shifted/m9/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..9d7fecbee559c15023ad412787e84e805831b9e5
--- /dev/null
+++ b/tests/data/shifted/m9/bt1.bed
@@ -0,0 +1,10 @@
+#I -9 -4 a(I:0-5:+) . +
+I 9 14 b(I:0-5:-) . -
+#I -9 1 c(I:0-10:+) . +
+I 9 19 d(I:0-10:-) . -
+#I -4 1 e(I:5-10:+) . +
+I 14 19 f(I:5-10:-) . -
+#I -4 11 g(I:5-20:+) . +
+I 14 29 h(I:5-20:-) . -
+I 1 6 i(I:10-15:+) . +
+I 19 24 j(I:10-15:-) . -
diff --git a/tests/data/shifted/p0/bt1.bed b/tests/data/shifted/p0/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..1ae9665dd3b4c86d819700d7d9b1df37146baa94
--- /dev/null
+++ b/tests/data/shifted/p0/bt1.bed
@@ -0,0 +1,10 @@
+I 0 5 a(I:0-5:+) . +
+I 0 5 b(I:0-5:-) . -
+I 0 10 c(I:0-10:+) . +
+I 0 10 d(I:0-10:-) . -
+I 5 10 e(I:5-10:+) . +
+I 5 10 f(I:5-10:-) . -
+I 5 20 g(I:5-20:+) . +
+I 5 20 h(I:5-20:-) . -
+I 10 15 i(I:10-15:+) . +
+I 10 15 j(I:10-15:-) . -
diff --git a/tests/data/shifted/p1/bt1.bed b/tests/data/shifted/p1/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..4371a2cbd8a3e766aff42bf1195e2da089cfeb3f
--- /dev/null
+++ b/tests/data/shifted/p1/bt1.bed
@@ -0,0 +1,10 @@
+I 1 6 a(I:0-5:+) . +
+#I -1 4 b(I:0-5:-) . -
+I 1 11 c(I:0-10:+) . +
+#I -1 9 d(I:0-10:-) . -
+I 6 11 e(I:5-10:+) . +
+I 4 9 f(I:5-10:-) . -
+I 6 21 g(I:5-20:+) . +
+I 4 19 h(I:5-20:-) . -
+I 11 16 i(I:10-15:+) . +
+I 9 14 j(I:10-15:-) . -
diff --git a/tests/data/shifted/p10/bt1.bed b/tests/data/shifted/p10/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..5e85143dbb8aae4c97607f37cacf7f075d3853ea
--- /dev/null
+++ b/tests/data/shifted/p10/bt1.bed
@@ -0,0 +1,10 @@
+I 10 15 a(I:0-5:+) . +
+#I -10 -5 b(I:0-5:-) . -
+I 10 20 c(I:0-10:+) . +
+#I -10 0 d(I:0-10:-) . -
+I 15 20 e(I:5-10:+) . +
+#I -5 0 f(I:5-10:-) . -
+I 15 30 g(I:5-20:+) . +
+#I -5 10 h(I:5-20:-) . -
+I 20 25 i(I:10-15:+) . +
+I 0 5 j(I:10-15:-) . -
diff --git a/tests/data/shifted/p11/bt1.bed b/tests/data/shifted/p11/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..761e6858251ec76de7635e8fb5e405fa5d6c6e40
--- /dev/null
+++ b/tests/data/shifted/p11/bt1.bed
@@ -0,0 +1,10 @@
+I 11 16 a(I:0-5:+) . +
+#I -11 -6 b(I:0-5:-) . -
+I 11 21 c(I:0-10:+) . +
+#I -11 -1 d(I:0-10:-) . -
+I 16 21 e(I:5-10:+) . +
+#I -6 1 f(I:5-10:-) . -
+I 16 31 g(I:5-20:+) . +
+#I -6 9 h(I:5-20:-) . -
+I 21 26 i(I:10-15:+) . +
+#I -1 4 j(I:10-15:-) . -
diff --git a/tests/data/shifted/p19/bt1.bed b/tests/data/shifted/p19/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..d80bd8b715f91de9c739358ec032cc6a68546c52
--- /dev/null
+++ b/tests/data/shifted/p19/bt1.bed
@@ -0,0 +1,10 @@
+I 19 24 a(I:0-5:+) . +
+#I -19 -14 b(I:0-5:-) . -
+I 19 29 c(I:0-10:+) . +
+#I -19 -9 d(I:0-10:-) . -
+I 24 29 e(I:5-10:+) . +
+#I -14 -9 f(I:5-10:-) . -
+I 24 39 g(I:5-20:+) . +
+#I -14 1 h(I:5-20:-) . -
+I 29 34 i(I:10-15:+) . +
+#I -9 -4 j(I:10-15:-) . -
diff --git a/tests/data/shifted/p20/bt1.bed b/tests/data/shifted/p20/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..d72aaaef7f5ae13d700e0fe934941c8b992e3733
--- /dev/null
+++ b/tests/data/shifted/p20/bt1.bed
@@ -0,0 +1,10 @@
+I 20 25 a(I:0-5:+) . +
+#I -20 -15 b(I:0-5:-) . -
+I 20 30 c(I:0-10:+) . +
+#I -20 -10 d(I:0-10:-) . -
+I 25 30 e(I:5-10:+) . +
+#I -15 -10 f(I:5-10:-) . -
+I 25 40 g(I:5-20:+) . +
+#I -15 0 h(I:5-20:-) . -
+I 30 35 i(I:10-15:+) . +
+#I -10 -5 j(I:10-15:-) . -
diff --git a/tests/data/shifted/p21/bt1.bed b/tests/data/shifted/p21/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..6cafac3606188d36411e238b53456f69b59eca3b
--- /dev/null
+++ b/tests/data/shifted/p21/bt1.bed
@@ -0,0 +1,10 @@
+I 21 26 a(I:0-5:+) . +
+#I -21 -16 b(I:0-5:-) . -
+I 21 31 c(I:0-10:+) . +
+#I -21 -11 d(I:0-10:-) . -
+I 26 31 e(I:5-10:+) . +
+#I -16 -11 f(I:5-10:-) . -
+I 26 41 g(I:5-20:+) . +
+#I -16 -1 h(I:5-20:-) . -
+I 31 36 i(I:10-15:+) . +
+#I -11 -6 j(I:10-15:-) . -
diff --git a/tests/data/shifted/p4/bt1.bed b/tests/data/shifted/p4/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..6c26b2390615fc6ae96ff3de478e53b9aef3f168
--- /dev/null
+++ b/tests/data/shifted/p4/bt1.bed
@@ -0,0 +1,10 @@
+I 4 9 a(I:0-5:+) . +
+#I -4 1 b(I:0-5:-) . -
+I 4 14 c(I:0-10:+) . +
+#I -4 6 d(I:0-10:-) . -
+I 9 14 e(I:5-10:+) . +
+I 1 6 f(I:5-10:-) . -
+I 9 24 g(I:5-20:+) . +
+I 1 16 h(I:5-20:-) . -
+I 14 19 i(I:10-15:+) . +
+I 6 11 j(I:10-15:-) . -
diff --git a/tests/data/shifted/p5/bt1.bed b/tests/data/shifted/p5/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..db85793255a755fffd2039a358e4abdd490d5bc5
--- /dev/null
+++ b/tests/data/shifted/p5/bt1.bed
@@ -0,0 +1,10 @@
+I 5 10 a(I:0-5:+) . +
+#I -5 0 b(I:0-5:-) . -
+I 5 15 c(I:0-10:+) . +
+#I -5 5 d(I:0-10:-) . -
+I 10 15 e(I:5-10:+) . +
+I 0 5 f(I:5-10:-) . -
+I 10 25 g(I:5-20:+) . +
+I 0 15 h(I:5-20:-) . -
+I 15 20 i(I:10-15:+) . +
+I 5 10 j(I:10-15:-) . -
diff --git a/tests/data/shifted/p6/bt1.bed b/tests/data/shifted/p6/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..fce8c22d7525b4838944d52ea74ffa18d2c719fd
--- /dev/null
+++ b/tests/data/shifted/p6/bt1.bed
@@ -0,0 +1,10 @@
+I 6 11 a(I:0-5:+) . +
+#I -6 -1 b(I:0-5:-) . -
+I 6 16 c(I:0-10:+) . +
+#I -6 4 d(I:0-10:-) . -
+I 11 16 e(I:5-10:+) . +
+#I -1 4 f(I:5-10:-) . -
+I 11 26 g(I:5-20:+) . +
+#I -1 14 h(I:5-20:-) . -
+I 16 21 i(I:10-15:+) . +
+I 4 9 j(I:10-15:-) . -
diff --git a/tests/data/shifted/p9/bt1.bed b/tests/data/shifted/p9/bt1.bed
new file mode 100644
index 0000000000000000000000000000000000000000..26dc92518dd9fd55dc8ef715e57fc9c1e98d9887
--- /dev/null
+++ b/tests/data/shifted/p9/bt1.bed
@@ -0,0 +1,10 @@
+I 9 14 a(I:0-5:+) . +
+#I -9 -4 b(I:0-5:-) . -
+I 9 19 c(I:0-10:+) . +
+#I -9 1 d(I:0-10:-) . -
+I 14 19 e(I:5-10:+) . +
+#I -4 1 f(I:5-10:-) . -
+I 14 29 g(I:5-20:+) . +
+#I -4 11 h(I:5-20:-) . -
+I 19 24 i(I:10-15:+) . +
+I 1 6 j(I:10-15:-) . -
diff --git a/tests/test_bam25prime.py b/tests/test_bam25prime.py
new file mode 100755
index 0000000000000000000000000000000000000000..e2c76b33edff4805e8437372e39b3f5402d246ec
--- /dev/null
+++ b/tests/test_bam25prime.py
@@ -0,0 +1,126 @@
+#!/usr/bin/env python3
+"""
+Test cases for bam25prime.
+"""
+
+import unittest
+from collections import namedtuple
+from pathlib import Path
+from bam25prime import (
+ BedTool, make_bed_shifter, make_bed_shift_checker)
+
+
+Interval = namedtuple("Interval", ["chrom", "start", "stop", "strand"])
+
+THIS_DIR = Path("__file__").resolve().parent
+data_dir = THIS_DIR.joinpath("data")
+
+
+def load_interval_dict(bed_path):
+ """
+ Build a dict to store intervals allowing easy comparison between
+ obtained and expected results using bed names (4th column) as keys.
+ """
+ itvl_dict = {}
+ with open(bed_path) as fh:
+ for line in fh:
+ if len(line.strip()) == 0 or line[0] == "#":
+ continue
+ (
+ chrom, start, stop,
+ name, _, strand, *_) = line.strip().split("\t")
+ assert name not in itvl_dict, f"Non unique name: {name}"
+ itvl_dict[name] = Interval(
+ chrom, int(start), int(stop), strand)
+ return itvl_dict
+
+
+def compare_itvl_dicts(observed, expected):
+ """
+ Compute the sets of interval names:
+ * missing in the observed
+ * spurious in the observed
+ * different in the observed
+ Return a (missing, spurious, different) tuple.
+ """
+ obs_names = set(observed.keys())
+ exp_names = set(expected.keys())
+ missing = exp_names - obs_names
+ spurious = obs_names - exp_names
+ common = obs_names & exp_names
+ different = set()
+ for itvl_name in common:
+ if observed[itvl_name] != expected[itvl_name]:
+ different.add(itvl_name)
+ return (missing, spurious, different)
+
+
+def check_shifter(bed_path, s_name, shifter, checker):
+ bt = BedTool(bed_path)
+ bed_name = bed_path.stem
+ msg_base = f"{bed_name} transformed with {s_name}"
+ print(msg_base)
+ expected = load_interval_dict(
+ data_dir.joinpath("shifted", s_name, f"{bed_name}.bed"))
+ #print("bt")
+ #print(bt)
+ #print(bt)
+ #shifted_1 = bt.each(shifter).saveas()
+ #print(" shifted")
+ #print(shifted_1)
+ #print(shifted_1)
+ #shifted_2 = shifted_1.remove_invalid().saveas()
+ shifted_2 = bt.filter(checker).each(shifter).remove_invalid().saveas()
+ #print(" invalid removed")
+ #print(shifted_2)
+ #print(shifted_2)
+ shifted = shifted_2.sort()
+ #print(" sorted")
+ #print(shifted)
+ #print(shifted)
+ observed = load_interval_dict(shifted.fn)
+ #print(observed)
+ (missing, spurious, different) = compare_itvl_dicts(
+ observed, expected)
+ msg = "\n".join([
+ msg_base,
+ f"\tMissing: {missing}",
+ f"\tSpurious: {spurious}",
+ f"\tDifferent: {different}"])
+ return (missing, spurious, different, msg)
+
+
+class TestBam25prime(unittest.TestCase):
+ def test_shift_pos(self):
+ shifters = {
+ f"p{shift}": (
+ make_bed_shifter(shift),
+ make_bed_shift_checker(shift))
+ for shift in [0, 1, 4, 5, 6, 9, 10, 11, 19, 20, 21]
+ }
+ for bed_path in data_dir.glob("*.bed"):
+ for (s_name, (shifter, checker)) in shifters.items():
+ (missing, spurious, different, msg) = check_shifter(
+ bed_path, s_name, shifter, checker)
+ self.assertFalse(
+ missing | spurious | different,
+ msg)
+
+ def test_shift_neg(self):
+ shifters = {
+ f"m{shift}": (
+ make_bed_shifter(-shift),
+ make_bed_shift_checker(-shift))
+ for shift in [0, 1, 4, 5, 6, 9, 10, 11, 19, 20, 21]
+ }
+ for bed_path in data_dir.glob("*.bed"):
+ for (s_name, (shifter, checker)) in shifters.items():
+ (missing, spurious, different, msg) = check_shifter(
+ bed_path, s_name, shifter, checker)
+ self.assertFalse(
+ missing | spurious | different,
+ msg)
+
+
+if __name__ == "__main__":
+ unittest.main()