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peterjc / thapbi-pict

Tree Health and Plant Biosecurity Initiative - Phytophthora ITS1 Classifier Tool
https://thapbi-pict.readthedocs.io/
MIT License
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Worked example change from v1.0.0 to v1.0.1 #567

Closed peterjc closed 1 year ago

peterjc commented 1 year ago

In local testing on our cluster, the changes in v1.0.0 to v1.0.1 seem to have altered the soil nematode output slightly - spotted via scripts/rst_doc_test.py which is not run on CI due to the size of the raw data and the run time.

Expected:

============= ====== ========= ======= ======== ========= ========
#marker       sample Raw FASTQ Flash   Cutadapt Threshold Accepted
============= ====== ========= ======= ======== ========= ========
D3Af-D3Br     Blank  1193593   1039205 0        25        0
D3Af-D3Br     MC1    3897994   3317661 0        25        0
D3Af-D3Br     MC2    4228233   3685150 0        25        0
D3Af-D3Br     MC3    4309817   3864130 0        25        0
JB3-JB5GED    Blank  69641     62060   0        25        0
JB3-JB5GED    MC1    1236201   1157824 0        25        0
JB3-JB5GED    MC2    2160885   2058441 1        25        0
JB3-JB5GED    MC3    1204900   1139777 0        25        0
NF1-18Sr2b    Blank  260778    218813  187776   25        140063
NF1-18Sr2b    MC1    2483453   2126062 2109488  25        1394752
NF1-18Sr2b    MC2    2349364   1985981 1972923  25        1359807
NF1-18Sr2b    MC3    2435278   2088185 2070379  25        1409756
SSUF04-SSUR22 Blank  57199     46879   0        25        0
SSUF04-SSUR22 MC1    3162379   2633321 77       25        0
SSUF04-SSUR22 MC2    2790363   2370732 280      25        0
SSUF04-SSUR22 MC3    1953138   1640045 52       25        0
============= ====== ========= ======= ======== ========= ========

Now:

============= ====== ========= ======= ======== ========= ========
#marker       sample Raw FASTQ Flash   Cutadapt Threshold Accepted
============= ====== ========= ======= ======== ========= ========
D3Af-D3Br     Blank  1193593   1039205 0        25        0
D3Af-D3Br     MC1    3897994   3317661 0        25        0
D3Af-D3Br     MC2    4228233   3685150 0        25        0
D3Af-D3Br     MC3    4309817   3864130 0        25        0
JB3-JB5GED    Blank  69641     62060   0        25        0
JB3-JB5GED    MC1    1236201   1157824 0        25        0
JB3-JB5GED    MC2    2160885   2058441 1        25        0
JB3-JB5GED    MC3    1204900   1139777 0        25        0
NF1-18Sr2b    Blank  260778    218813  187776   25        140063
NF1-18Sr2b    MC1    2483453   2126062 2109488  25        1394883
NF1-18Sr2b    MC2    2349364   1985981 1972923  25        1359884
NF1-18Sr2b    MC3    2435278   2088185 2070379  25        1409844
SSUF04-SSUR22 Blank  57199     46879   0        25        0
SSUF04-SSUR22 MC1    3162379   2633321 77       25        0
SSUF04-SSUR22 MC2    2790363   2370732 280      25        0
SSUF04-SSUR22 MC3    1953138   1640045 52       25        0
============= ====== ========= ======= ======== ========= ========

This example does run our UNOISE Levenstein implementation, so given https://github.com/peterjc/thapbi-pict/commit/8fb51438f1e927571c7b6ab39b0a7691f7b693da fixing a corner case in the implementation was one of the main changes in v1.0.1, this makese sense. As can be seen above, the change in this example is neglibigle.