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nickp60nickp60
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Merge pull request #7 from Stikus/main
Update patterns and tests
2 parents f608163 + e4242c7 commit 2b7ad27

3 files changed

Lines changed: 36 additions & 68 deletions

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‎fcid/run.py‎

Lines changed: 32 additions & 64 deletions
Original file line numberDiff line numberDiff line change
@@ -6,21 +6,16 @@
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["HWI-M[0-9]{4}", [["MiSeq"]]],
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["HWUSI", [["Genome Analyzer IIx"]]],
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["M[0-9]{5}", [["MiSeq"]]],
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["HWI-C[0-9]{5}", [["HiSeq 1500"]]],
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["C[0-9]{5}", [["HiSeq 1500"]]],
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["HWI-D[0-9]{5}", [["HiSeq 2500"]]],
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["D[0-9]{5}", [["HiSeq 2500"]]],
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["(HWI-)?C[0-9]{5}", [["HiSeq 1500"]]],
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["(HWI-)?D[0-9]{5}", [["HiSeq 2500"]]],
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["J[0-9]{5}", [["HiSeq 3000"]]],
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["K[0-9]{5}", [["HiSeq 3000", "HiSeq 4000"]]],
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["E[0-9]{5}", [["HiSeq X"]]],
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["NB[0-9]{6}", [["NextSeq"]]],
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["NS[0-9]{6}", [["NextSeq"]]],
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["N[BS][0-9]{6}", [["NextSeq 500", "NextSeq 550"]]],
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["VH[0-9]{5}", [["NextSeq 2000"]]],
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["MN[0-9]{5}", [["MiniSeq"]]],
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["A[0-9]{5}", [["NovaSeq"]]],
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["NA[0-9]{5}", [["NovaSeq"]]],
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["SN[0-9]{3}", [["HiSeq2000", "HiSeq2500"]]],
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["SN[0-9]{3}", [["HiSeq2000", "HiSeq2500"]]],
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["N?A[0-9]{5}", [["NovaSeq 6000"]]],
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["SN[0-9]{3}", [["HiSeq 2000", "HiSeq 2500"]]],
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[".*", [["Unknown Machine"]]],
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]
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# Below are the relevant texts from the 3 emails with tech support
@@ -64,62 +59,35 @@
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# Three emails: 12/7/2022, 9/19/2023, and 2/29/2024
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FCIDs = [
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["BNT[A-Z,0-9]{5}-[A-Z,0-9]{4}", [["iSeq 100"], "Standard Output flow cell"]],
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["BRB[A-Z,0-9]{5}-[A-Z,0-9]{4}", [["iSeq 100"], "Standard Output flow cell"]],
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["BPC[A-Z,0-9]{5}-[A-Z,0-9]{4}", [["iSeq 100"], "Standard Output flow cell"]],
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["BPG[A-Z,0-9]{5}-[A-Z,0-9]{4}", [["iSeq 100"], "Standard Output flow cell"]],
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["BPA[A-Z,0-9]{5}-[A-Z,0-9]{4}", [["iSeq 100"], "Standard Output flow cell"]],
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["BPL[A-Z,0-9]{5}-[A-Z,0-9]{4}", [["iSeq 100"], "Standard Output flow cell"]],
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["BNT[A-Z,0-9]{5}-[A-Z,0-9]{4}", [["iSeq 100"], "Standard Output flow cell"]],
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["BTR[A-Z,0-9]{5}-[A-Z,0-9]{4}", [["iSeq 100"], "Standard Output flow cell"]],
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["000H[A-Z,0-9]{5}", [["MiniSeq"], "Mid or High Output flow cell"]],
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["D[A-Z,0-9]{4}", [["MiSeq"], "MiSeq Nano flow cell"]],
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["G[A-Z,0-9]{4}", [["MiSeq"], "MiSeq Micro flow cell"]],
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["A[A-Z,0-9]{4}", [["MiSeq"], "MiSeq Standard v2 flow cell"]],
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["B[A-Z,0-9]{4}", [["MiSeq"], "MiSeq Standard flow cell"]],
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["C[A-Z,0-9]{4}", [["MiSeq"], "MiSeq Standard flow cell"]],
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["J[A-Z,0-9]{4}", [["MiSeq"], "MiSeq Standard flow cell"]],
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["K[A-Z,0-9]{4}", [["MiSeq"], "MiSeq Standard flow cell"]],
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["L[A-Z,0-9]{4}", [["MiSeq"], "MiSeq Standard flow cell"]],
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[
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"[A-Z,0-9]{5}AF[A-Z,0-9]{2}",
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[["NextSeq 500", "NextSeq 550"], "Mid Output flow cell"],
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],
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[
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"[A-Z,0-9]{5}AG[A-Z,0-9]{2}",
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[["NextSeq 500", "NextSeq 550"], "High Output flow cell"],
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],
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[
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"[A-Z,0-9]{5}BG[A-Z,0-9]{2}",
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[["NextSeq 500", "NextSeq 550"], "High Output flow cell"],
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],
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["[A-Z,0-9]{7}M5", [["NextSeq 1000", "NextSeq 2000"], "P1 or P2 flow cell"]],
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["[A-Z,0-9]{7}HV", [["NextSeq 1000", "NextSeq 2000"], "P3 flow cell"]],
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["H[A-Z,0-9]{4}BGXX", [["NextSeq"], "High output flow cell"]],
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["H[A-Z,0-9]{4}BGXY", [["NextSeq"], "High output flow cell"]],
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["[A-Z,0-9]{5}BC[A-Z,0-9]{2}", [["HiSeq 2500"], "Rapid Run (2-lane) v2 flow cell"]],
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["[A-Z,0-9]{5}AC[A-Z,0-9]{2}", [["HiSeq 2500"], "TrueSeq v3 flow cell"]],
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["[A-Z,0-9]{5}AN[A-Z,0-9]{2}", [["HiSeq 2500"], "High Output v3 flow cell"]],
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[
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"[A-Z,0-9]{5}BB[A-Z,0-9]{2}",
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[["HiSeq 3000", "HiSeq 4000"], "(8-lane) v1 flow cell"],
106-
],
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["[A-Z,0-9]{5}AL[A-Z,0-9]{2}", [["HiSeq X"], "(8-lane) flow cell"]],
108-
["[A-Z,0-9]{5}CC[A-Z,0-9]{2}", [["HiSeq X"], "(8-lane) flow cell"]],
109-
["[A-Z,0-9]{5}DR[A-Z,0-9]{2}", [["NovaSeq 6000"], "SP or S1 flow cell"]],
110-
["[A-Z,0-9]{5}DM[A-Z,0-9]{2}", [["NovaSeq 6000"], "S2 flow cell"]],
111-
["[A-Z,0-9]{5}DS[A-Z,0-9]{2}", [["NovaSeq 6000"], "S4 flow cell"]],
62+
["B(NT|RB|PC|PG|PA|PL|TR)[A-Z0-9]{5}-[A-Z0-9]{4}", [["iSeq 100"], "Standard Output flow cell"]],
63+
["000H[A-Z0-9]{5}", [["MiniSeq"], "Mid or High Output flow cell"]],
64+
["D[A-Z0-9]{4}", [["MiSeq"], "MiSeq Nano flow cell"]],
65+
["G[A-Z0-9]{4}", [["MiSeq"], "MiSeq Micro flow cell"]],
66+
["A[A-Z0-9]{4}", [["MiSeq"], "MiSeq Standard v2 flow cell"]],
67+
["[BCJKL][A-Z0-9]{4}", [["MiSeq"], "MiSeq Standard flow cell"]],
68+
["[A-Z0-9]{5}AF[A-Z0-9]{2}", [["NextSeq 500", "NextSeq 550"], "Mid Output flow cell"]],
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["[A-Z0-9]{5}[AB]G[A-Z0-9]{2}", [["NextSeq 500", "NextSeq 550"], "High Output flow cell"]],
70+
["[A-Z0-9]{7}M5", [["NextSeq 1000", "NextSeq 2000"], "P1 or P2 flow cell"]],
71+
["[A-Z0-9]{7}HV", [["NextSeq 1000", "NextSeq 2000"], "P3 flow cell"]],
72+
["[A-Z0-9]{5}BC[A-Z0-9]{2}", [["HiSeq 2500"], "Rapid Run (2-lane) v2 flow cell"]],
73+
["[A-Z0-9]{5}AC[A-Z0-9]{2}", [["HiSeq 2500"], "TruSeq v3 flow cell"]],
74+
["[A-Z0-9]{5}AN[A-Z0-9]{2}", [["HiSeq 2500"], "High Output v3 flow cell"]],
75+
["[A-Z0-9]{5}BB[A-Z0-9]{2}", [["HiSeq 3000", "HiSeq 4000"], "(8-lane) v1 flow cell"]],
76+
["[A-Z0-9]{5}AL[A-Z0-9]{2}", [["HiSeq X"], "(8-lane) flow cell"]],
77+
["[A-Z0-9]{5}CC[A-Z0-9]{2}", [["HiSeq X"], "(8-lane) flow cell"]],
78+
["[A-Z0-9]{5}DR[A-Z0-9]{2}", [["NovaSeq 6000"], "SP or S1 flow cell"]],
79+
["[A-Z0-9]{5}DM[A-Z0-9]{2}", [["NovaSeq 6000"], "S2 flow cell"]],
80+
["[A-Z0-9]{5}DS[A-Z0-9]{2}", [["NovaSeq 6000"], "S4 flow cell"]],
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["[A-Z0-9]{6}LT3", [["NovaSeq X", "NovaSeq X Plus"], "10B flow cell"]],
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["[A-Z0-9]{6}LT4", [["NovaSeq X", "NovaSeq X Plus"], "25B flow cell"]],
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["[A-Z0-9]{6}LT[A-Z,0-9]", [["NovaSeq X", "NovaSeq X Plus"], "Unknown flow cell"]],
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# ["[A-Z,0-9]{5}ACXX", [["HiSeq 1000", "HiSeq 1500", "HiSeq 2000", "HiSeq 2500"], "High Output (8-lane) v3 flow cell"]],
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# ["H[A-Z,0-9]{4}BCXY", [["HiSeq 1500", "HiSeq 2500"], "Rapid Run (2-lane) v2 flow cell"]],
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# ["C[A-Z,0-9]{4}ANXX", [["HiSeq 1500", "HiSeq 2000", "HiSeq 2500"], "High Output (8-lane) v4 flow cell"]],
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# ["C[A-Z,0-9]{4}AC[A-Z,0-9]{2}", [["HiSeq 2500"], "High Output (8-lane) v4 flow cell"]],
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["H[A-Z,0-9]{4}ADXX", [["HiSeq 1500", "HiSeq 2500"], "Rapid Run (2-lane) v1 flow cell"]],
120-
["H[A-Z,0-9]{4}ADXY", [["HiSeq 1500", "HiSeq 2500"], "Rapid Run (2-lane) v1 flow cell"]],
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# ["H[A-Z,0-9]{4}BC[A-Z,0-9]{2}", [["HiSeq 2500"], "Rapid Run (2-lane) v2 flow cell"]],
122-
# ["H[A-Z,0-9]{4}BBXY[A-Z,0-9]{2}", [["HiSeq 4000"], "(8-lane) v1 flow cell"]],
83+
["[A-Z0-9]{6}LT[A-Z0-9]", [["NovaSeq X", "NovaSeq X Plus"], "Unknown flow cell"]],
84+
# ["[A-Z0-9]{5}ACXX", [["HiSeq 1000", "HiSeq 1500", "HiSeq 2000", "HiSeq 2500"], "High Output (8-lane) v3 flow cell"]],
85+
# ["H[A-Z0-9]{4}BCXY", [["HiSeq 1500", "HiSeq 2500"], "Rapid Run (2-lane) v2 flow cell"]],
86+
# ["C[A-Z0-9]{4}ANXX", [["HiSeq 1500", "HiSeq 2000", "HiSeq 2500"], "High Output (8-lane) v4 flow cell"]],
87+
# ["C[A-Z0-9]{4}AC[A-Z0-9]{2}", [["HiSeq 2500"], "High Output (8-lane) v4 flow cell"]],
88+
["H[A-Z0-9]{4}ADX[XY]", [["HiSeq 1500", "HiSeq 2500"], "Rapid Run (2-lane) v1 flow cell"]],
89+
# ["H[A-Z0-9]{4}BC[A-Z0-9]{2}", [["HiSeq 2500"], "Rapid Run (2-lane) v2 flow cell"]],
90+
# ["H[A-Z0-9]{4}BBXY[A-Z0-9]{2}", [["HiSeq 4000"], "(8-lane) v1 flow cell"]],
12391
[".*", [["Unknown Machine"], "Unknown flow cell"]],
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]
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‎fcid/test_fcid.py‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -110,15 +110,15 @@ def test_integration_bymachine():
110110
shell=True,
111111
)
112112
print(res.decode())
113-
assert res.decode() == "NovaSeq\n"
113+
assert res.decode() == "NovaSeq 6000\n"
114114

115115
def test_integration_bymachine_detailed():
116116
res = subprocess.check_output(
117117
["python fcid/run.py A12345 --by-machine --detailed"],
118118
shell=True,
119119
)
120120
print(res.decode())
121-
assert res.decode() == "NovaSeq\n"
121+
assert res.decode() == "NovaSeq 6000\n"
122122

123123

124124
def test_dubious_patterns():

‎pyproject.toml‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
44

55
[project]
66
name = "fcid"
7-
version = "0.0.11"
7+
version = "0.0.12"
88
authors = [
99
{name = "Nick Waters", email = "nickp60@gmail.com"},
1010
]
@@ -19,4 +19,4 @@ classifiers = [
1919

2020

2121
[project.scripts]
22-
fcid = "fcid.run:main"
22+
fcid = "fcid.run:main"

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