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Adding script files
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@mish-su
mish-su authored Jun 15, 2023
1 parent e7abe4e commit fe6419f
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33 changes: 33 additions & 0 deletions Scripts/compareLineages.py
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#!/usr/bin/env python

import os
import csv
import itertools

from pango_aliasor.aliasor import Aliasor

aliasor = Aliasor()

print("\t".join(["maple", "pangolin", "isAncestral", "distance"]))
with open('unique_mismatches_maple_vs_pangolin.tsv', 'r') as f:
reader = csv.DictReader(f, delimiter="\t")
for row in reader:
mUnc = aliasor.uncompress(row["maple"])
pUnc = aliasor.uncompress(row["pangolin"])
if mUnc.startswith(pUnc) or pUnc.startswith(mUnc):
isAnc = "1"
else:
isAnc = "0"
mUncL = mUnc.split('.')
pUncL = pUnc.split('.')
distance = 0
for pair in itertools.zip_longest(mUncL, pUncL, fillvalue=None):
if pair[0] != pair[1]:
distance += 1
if pair[0] and pair[1]:
distance += 1
if mUnc.startswith("X") or pUnc.startswith("X"):
distS = "R"
else:
distS = str(distance)
print("\t".join([row["maple"], row["pangolin"], isAnc, distS]))
10 changes: 10 additions & 0 deletions Scripts/expected.13.14.tsv
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source target reason
AY.4 AY.4.1 new .78
B.1.351 B.1.351.5 new .77
B.1.617.2 AY.33 new .77
B.1.617.2 AY.34 new .78
B.1.617.2 AY.35 new .78
B.1.617.2 AY.36 new .80
B.1.617.2 AY.37 new .80
B.1.617.2 AY.38 new .80
P.1 P.1.12 new .77
44 changes: 44 additions & 0 deletions Scripts/expected.14.15.tsv
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AY.23 AY.23.1 new .86
AY.29 AY.29.1 new .84
AY.4 AY.4.2 new .82
AY.4 AY.4.3 new .83
AY.4 AY.4.4 new .86
AY.4 AY.4.5 new .86
B.1.617.2 AY.39 new .84
B.1.617.2 AY.39.1 new .84
B.1.617.2 AY.39.1.1 new .84
B.1.617.2 AY.40 new .86
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B.1.617.2 AY.46.5 new .88
B.1.617.2 AY.46.6 new .88
B.1.617.2 AY.47 new .88
P.1 P.1.1 updated .82
P.1 P.1.2 updated .82
P.1 P.1.3 updated .82
P.1 P.1.4 updated .82
P.1 P.1.5 updated .82
P.1 P.1.6 updated .82
P.1 P.1.7 updated .82
P.1 P.1.8 updated .85
P.1 P.1.9 updated .85
P.1 P.1.10 updated .85
P.1 P.1.11 updated .85
P.1 P.1.12 updated .85
P.1 P.1.13 new .85
P.1 P.1.14 new .85
P.1 P.1.15 new .85
P.1 P.1.16 new .85
P.1 P.1.17 new .85
P.1 P.1.17.1 new .85
P.1.10 P.1.10.1 updated .85
P.1.10 P.1.10.2 updated .85
92 changes: 92 additions & 0 deletions Scripts/expected.15.16.tsv
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source target reason
AY.16 AY.16.1 new .89
AY.34 AY.34.1 new .92
AY.39 AY.39.2 new .91
AY.4.2 AY.4.2.1 new .93
AY.9 AY.9.1 new .90
AY.9 AY.9.2 new .90
AY.9 AY.9.2.1 new .90
B.1 B.1.639 new .93
B.1.617.2 AY.48 new .89
B.1.617.2 AY.49 new .89
B.1.617.2 AY.50 new .89
B.1.617.2 AY.51 new .89
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B.1.617.2 AY.102 new .90
B.1.617.2 AY.103 new .92
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106 changes: 106 additions & 0 deletions Scripts/expected.2021-11-09_v1.2.133.tsv
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AY.102 AY.102.1
AY.102 AY.102.2
AY.103 AY.103.1
AY.103 AY.103.2
AY.112 AY.112.1
AY.115 AY.116
AY.119 AY.119.1
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AY.12 AY.121.1
AY.122 AY.122.2
AY.122 AY.122.3
AY.122 AY.122.4
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AY.124 AY.124.1
AY.20 AY.20.1
AY.23 AY.23.2
AY.24 AY.24.1
AY.25 AY.25.1
AY.25 AY.25.1.1
AY.25 AY.25.1.2
AY.25 AY.25.2
AY.25 AY.25.3
AY.26 AY.26.1
AY.3 AY.3.2
AY.3 AY.3.3
AY.3 AY.3.4
AY.33 AY.33.1
AY.34 AY.34.1
AY.34 AY.34.2
AY.36 AY.36.1
AY.39 AY.39.3
AY.39.1 AY.39.1.2
AY.39.1 AY.39.1.3
AY.4 AY.4.10
AY.4 AY.4.11
AY.4 AY.4.12
AY.4 AY.4.13
AY.4 AY.4.14
AY.4 AY.4.15
AY.4 AY.4.16
AY.4 AY.4.17
AY.4 AY.4.6
AY.4 AY.4.7
AY.4 AY.4.8
AY.4 AY.4.9
AY.4.2 AY.4.2.1
AY.4.2 AY.4.2.2
AY.4.2 AY.4.2.3
AY.4.2 AY.4.2.4
AY.42 AY.42.1
AY.43 AY.43.1
AY.43 AY.43.2
AY.43 AY.43.3
AY.43 AY.43.4
AY.43 AY.43.5
AY.43 AY.43.6
AY.43 AY.43.7
AY.43 AY.43.8
AY.46.6 AY.46.6.1
AY.5 AY.5.6
AY.75 AY.75.2
AY.75 AY.75.3
AY.75.1 AY.75
AY.75.1 AY.75.2
AY.75.1 AY.75.3
AY.89 AY.4
AY.9.1 AY.9.2
AY.9.2 AY.9.2.2
AY.96 AY.46
AY.96 AY.46.2
AY.96 AY.46.6
AY.96 B.1.617.2
AY.97 AY.5.5
B.1 B.1.639
B.1 B.1.640
B.1 B.1.640.1
B.1 B.1.640.2
B.1.177.79 B.1.177.60
B.1.617.2 AY.112
B.1.617.2 AY.121
B.1.617.2 AY.121.1
B.1.617.2 AY.122
B.1.617.2 AY.123
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B.1.617.2 AY.124.1
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B.1.617.2 AY.133
B.1.621 B.1.621.2
B.1.621.1 BB.2
B.1.628 XB
B.1.637 B.1.637.1
P.1.12 P.1.12.1
P.1.7 P.1.7.1
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