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clarify add results
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@remkv6
remkv6 committed Nov 18, 2024
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50 changes: 32 additions & 18 deletions dataAnalysis/GenomeAnnotation/DeepGoPlus_AI_Functional_Prediction_of_Proteins.md
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Expand Up @@ -113,30 +113,16 @@ to
if last_release_version != new_release_version:
```

And Updated uniprot address

```python
response = requests.get('https://www.uniprot.org')
```

to

```python
response = requests.get('https://rest.uniprot.org/uniprotkb/search')
```

Once these have been updated we can run
Once this has been updated we can run

```python
python update.py
```




## Run DeepGoPlus analysis

* Download some fun data from a plant parasitic nematode
* Download some fun data from a plant parasitic nematode (Ditylenchus dipsaci)
* Format the data
* Run DeepGoPlus
* Format the output
Expand All @@ -154,7 +140,35 @@ ml miniconda3; conda activate deepgoplus_env; source bin/activate ; deepgoplus -
# format the output
awk 'NF>3' results_DDipsaci |sed 's/\t/#/1' |sed 's/\t/,/g' |sed 's/#/\t/g' >DeepGoPlusResults.tab
```


|Gene_name GoTerms|
|:----|
|jg20583 GO:0110165#0.355 GO:0005575#0.361|
|jg20588 GO:0110165#0.349 GO:0005575#0.357|
|jg16733 GO:0003674#0.567 GO:0005488#0.500 GO:0005515#0.377 GO:0005575#0.725 GO:0005622#0.613 GO:0005737#0.575 GO:0005886#0.331 GO:0007154#0.330 GO:0008150#0.727 GO:0009987#0.583 GO:0016020#0.499 GO:0023052#0.332 GO:0043226#0.400 GO:0043227#0.329 GO:0043229#0.359 GO:0043231#0.311 GO:0050789#0.481 GO:0050794#0.450 GO:0050896#0.393 GO:0051716#0.344 GO:0065007#0.494 GO:0071944#0.352 GO:0110165#0.720|
|jg20471 GO:0110165#0.387 GO:0005575#0.396|
|jg2136 GO:0003674#0.503 GO:0005488#0.369 GO:0005515#0.349 GO:0005575#0.788 GO:0005622#0.688 GO:0005737#0.635 GO:0005886#0.434 GO:0008104#0.443 GO:0008150#0.742 GO:0009987#0.687 GO:0016020#0.654 GO:0016043#0.382 GO:0032991#0.303 GO:0033036#0.444 GO:0033365#0.308 GO:0043226#0.566 GO:0043227#0.528 GO:0043229#0.555 GO:0043231#0.503 GO:0045184#0.435 GO:0051179#0.510 GO:0051234#0.500 GO:0051641#0.465 GO:0051668#0.362 GO:0070727#0.443 GO:0071840#0.387 GO:0071944#0.435 GO:0072657#0.359 GO:0090150#0.353 GO:0110165#0.783|
|jg12535 GO:0110165#0.345 GO:0005575#0.345|
|jg2135 GO:0110165#0.395 GO:0005575#0.397 GO:0005622#0.365 GO:0016020#0.309 GO:0043229#0.329 GO:0043226#0.337|
|jg2134 GO:0110165#0.369 GO:0005575#0.370 GO:0005622#0.343|
|jg12533 GO:0110165#0.360 GO:0005575#0.364 GO:0016020#0.329|
|jg14715 GO:0110165#0.370 GO:0005575#0.383 GO:0005622#0.305|
|jg21581 GO:0110165#0.380 GO:0005575#0.380|
|jg2133 GO:0003674#0.732 GO:0005215#0.637 GO:0005575#0.637 GO:0005622#0.327 GO:0005737#0.327 GO:0005886#0.602 GO:0006810#0.737 GO:0006811#0.616 GO:0006812#0.598 GO:0008150#0.948 GO:0008324#0.354 GO:0009987#0.771 GO:0015075#0.362 GO:0015095#0.319 GO:0015318#0.575 GO:0015693#0.555 GO:0016020#0.603 GO:0022857#0.637 GO:0022890#0.566 GO:0030001#0.589 GO:0034220#0.616 GO:0046873#0.340 GO:0050896#0.334 GO:0051179#0.737 GO:0051234#0.737 GO:0051716#0.307 GO:0055085#0.679 GO:0071944#0.602 GO:0098655#0.596 GO:0098660#0.607 GO:0098662#0.595 GO:0110165#0.637 GO:1903830#0.445|
|jg12534 GO:0110165#0.394 GO:0005575#0.396 GO:0005622#0.314|
|jg24909 GO:0000902#0.352 GO:0003674#0.510 GO:0005488#0.356 GO:0005515#0.326 GO:0005575#0.791 GO:0005622#0.389 GO:0005886#0.490 GO:0007154#0.433 GO:0007165#0.395 GO:0007166#0.343 GO:0007275#0.622 GO:0007399#0.531 GO:0007409#0.345 GO:0007411#0.325 GO:0008150#0.946 GO:0009653#0.424 GO:0009987#0.768 GO:0016020#0.579 GO:0016043#0.472 GO:0022008#0.405 GO:0023052#0.432 GO:0030030#0.360 GO:0030154#0.441 GO:0030182#0.384 GO:0031175#0.360 GO:0032501#0.665 GO:0032502#0.645 GO:0048468#0.419 GO:0048518#0.435 GO:0048522#0.377 GO:0048583#0.318 GO:0048666#0.372 GO:0048667#0.347 GO:0048699#0.391 GO:0048731#0.606 GO:0048812#0.348 GO:0048856#0.645 GO:0048858#0.348 GO:0048869#0.441 GO:0050789#0.629 GO:0050794#0.563 GO:0050896#0.579 GO:0051716#0.428 GO:0061564#0.345 GO:0065007#0.646 GO:0071840#0.472 GO:0071944#0.562 GO:0097485#0.341 GO:0110165#0.791 GO:0120036#0.360 GO:0120039#0.348|
|jg14716 GO:0110165#0.373 GO:0005575#0.379|
|jg21582 GO:0110165#0.382 GO:0005575#0.389 GO:0005622#0.307|
|jg2132 GO:0003674#0.662 GO:0005215#0.547 GO:0005575#0.643 GO:0005886#0.483 GO:0006810#0.656 GO:0006811#0.580 GO:0006812#0.566 GO:0008150#0.934 GO:0008324#0.327 GO:0009987#0.734 GO:0015075#0.328 GO:0015095#0.319 GO:0015318#0.541 GO:0015693#0.550 GO:0016020#0.534 GO:0022857#0.547 GO:0022890#0.539 GO:0030001#0.561 GO:0034220#0.575 GO:0046873#0.319 GO:0050896#0.411 GO:0051179#0.661 GO:0051234#0.656 GO:0051716#0.341 GO:0055085#0.587 GO:0071944#0.490 GO:0098655#0.565 GO:0098660#0.568 GO:0098662#0.565 GO:0110165#0.640 GO:1903830#0.448|
|jg12531 GO:0110165#0.364 GO:0005575#0.374|
|jg14717 GO:0110165#0.370 GO:0005575#0.371 GO:0005622#0.305|
|jg2131 GO:0003674#0.693 GO:0003824#0.533 GO:0004596#0.302 GO:0005575#0.794 GO:0005622#0.767 GO:0005634#0.345 GO:0005737#0.700 GO:0005829#0.433 GO:0008080#0.452 GO:0008150#0.728 GO:0008152#0.422 GO:0009058#0.373 GO:0009059#0.340 GO:0009987#0.509 GO:0010467#0.331 GO:0016020#0.550 GO:0016407#0.452 GO:0016410#0.452 GO:0016740#0.486 GO:0016746#0.464 GO:0016747#0.456 GO:0019538#0.347 GO:0031248#0.356 GO:0031414#0.356 GO:0032991#0.465 GO:0034212#0.302 GO:0043170#0.374 GO:0043226#0.548 GO:0043227#0.501 GO:0043229#0.538 GO:0043231#0.478 GO:0044237#0.378 GO:0044238#0.405 GO:0044249#0.349 GO:0110165#0.791 GO:0140535#0.376 GO:1902493#0.356 GO:1902494#0.387 GO:1990234#0.366|
|jg12532 GO:0003674#0.493 GO:0005488#0.322 GO:0005575#0.874 GO:0005622#0.810 GO:0005737#0.716 GO:0005773#0.331 GO:0005886#0.503 GO:0006810#0.393 GO:0006811#0.343 GO:0008150#0.874 GO:0009987#0.794 GO:0016020#0.788 GO:0030154#0.353 GO:0032502#0.434 GO:0034220#0.314 GO:0043226#0.772 GO:0043227#0.719 GO:0043229#0.728 GO:0043231#0.677 GO:0048856#0.412 GO:0048869#0.353 GO:0050789#0.322 GO:0050896#0.322 GO:0051179#0.440 GO:0051234#0.397 GO:0055085#0.316 GO:0065007#0.537 GO:0071944#0.534 GO:0098590#0.305 GO:0110165#0.872|
|jg14718 GO:0110165#0.401 GO:0005575#0.405 GO:0005622#0.352 GO:0016020#0.338 GO:0043226#0.308|
|jg21580 GO:0110165#0.351 GO:0005575#0.367|
|jg2130 GO:0003674#0.357 GO:0005575#0.859 GO:0005622#0.811 GO:0005737#0.680 GO:0005773#0.408 GO:0005794#0.341 GO:0005886#0.440 GO:0008150#0.580 GO:0009987#0.440 GO:0012505#0.384 GO:0016020#0.702 GO:0032991#0.306 GO:0043226#0.693 GO:0043227#0.667 GO:0043229#0.669 GO:0043231#0.652 GO:0051179#0.309 GO:0071944#0.457 GO:0110165#0.851|
|jg20474 GO:0110165#0.349 GO:0005575#0.353|
|jg14711 GO:0003674#0.429 GO:0005488#0.396 GO:0005515#0.376 GO:0005575#0.836 GO:0005622#0.775 GO:0005737#0.724 GO:0005886#0.353 GO:0006810#0.537 GO:0008104#0.304 GO:0008150#0.843 GO:0009987#0.787 GO:0016020#0.694 GO:0016192#0.307 GO:0031090#0.352 GO:0032501#0.486 GO:0032502#0.308 GO:0032991#0.384 GO:0033036#0.307 GO:0043226#0.649 GO:0043227#0.625 GO:0043229#0.623 GO:0043231#0.597 GO:0046907#0.423 GO:0048856#0.308 GO:0051179#0.648 GO:0051234#0.642 GO:0051641#0.557 GO:0051649#0.438 GO:0070727#0.305 GO:0071944#0.370 GO:0110165#0.830|
|jg12530 GO:0000785#0.355 GO:0000976#0.566 GO:0000977#0.496 GO:0000978#0.441 GO:0000981#0.346 GO:0000987#0.449 GO:0001067#0.566 GO:0003674#0.785 GO:0003676#0.663 GO:0003677#0.625 GO:0003690#0.615 GO:0003700#0.453 GO:0005488#0.785 GO:0005515#0.674 GO:0005575#0.820 GO:0005622#0.682 GO:0005634#0.515 GO:0005667#0.380 GO:0005694#0.356 GO:0005737#0.324 GO:0006139#0.749 GO:0006351#0.725 GO:0006355#0.720 GO:0006357#0.494 GO:0006366#0.502 GO:0007275#0.460 GO:0007399#0.345 GO:0008134#0.430 GO:0008150#0.945 GO:0008152#0.775 GO:0009058#0.770 GO:0009059#0.770 GO:0009889#0.754 GO:0009891#0.666 GO:0009893#0.679 GO:0009987#0.899 GO:0010467#0.770 GO:0010468#0.748 GO:0010556#0.754 GO:0010557#0.654 GO:0010604#0.674 GO:0016020#0.643 GO:0016043#0.347 GO:0016070#0.749 GO:0019219#0.730 GO:0019222#0.775 GO:0022008#0.336 GO:0030154#0.428 GO:0030182#0.329 GO:0031323#0.770 GO:0031325#0.676 GO:0031326#0.754 GO:0031328#0.662 GO:0032501#0.485 GO:0032502#0.533 GO:0032774#0.749 GO:0032991#0.464 GO:0034654#0.749 GO:0043170#0.770 GO:0043226#0.652 GO:0043227#0.565 GO:0043228#0.450 GO:0043229#0.646 GO:0043231#0.550 GO:0043232#0.448 GO:0043425#0.330 GO:0043565#0.583 GO:0044237#0.770 GO:0044238#0.765 GO:0044249#0.770 GO:0045893#0.640 GO:0045935#0.653 GO:0045944#0.473 GO:0048468#0.316 GO:0048518#0.719 GO:0048522#0.711 GO:0048699#0.331 GO:0048731#0.440 GO:0048856#0.533 GO:0048869#0.430 GO:0050789#0.871 GO:0050794#0.859 GO:0050896#0.346 GO:0051252#0.728 GO:0051254#0.645 GO:0060255#0.763 GO:0065007#0.872 GO:0071840#0.352 GO:0080090#0.765 GO:0090304#0.749 GO:0097159#0.663 GO:0110165#0.738 GO:0140110#0.467 GO:0140297#0.387 GO:0141187#0.749 GO:1902680#0.640 GO:1990837#0.574 GO:2001141#0.721|
|jg14712 GO:0003674#0.487 GO:0005488#0.446 GO:0005575#0.906 GO:0005622#0.864 GO:0005737#0.808 GO:0005739#0.572 GO:0006091#0.344 GO:0006119#0.340 GO:0006120#0.340 GO:0006139#0.390 GO:0006163#0.343 GO:0006164#0.343 GO:0006753#0.345 GO:0006754#0.340 GO:0006793#0.358 GO:0006796#0.358 GO:0008150#0.714 GO:0008152#0.557 GO:0009058#0.540 GO:0009060#0.343 GO:0009117#0.345 GO:0009141#0.340 GO:0009142#0.340 GO:0009144#0.340 GO:0009145#0.340 GO:0009150#0.340 GO:0009152#0.340 GO:0009165#0.344 GO:0009199#0.340 GO:0009201#0.340 GO:0009205#0.340 GO:0009206#0.340 GO:0009259#0.340 GO:0009260#0.340 GO:0009987#0.658 GO:0015980#0.344 GO:0015986#0.340 GO:0016020#0.822 GO:0019637#0.351 GO:0019646#0.340 GO:0019693#0.340 GO:0022900#0.344 GO:0022904#0.340 GO:0031974#0.306 GO:0032991#0.390 GO:0034654#0.382 GO:0042773#0.340 GO:0042775#0.340 GO:0043226#0.809 GO:0043227#0.785 GO:0043229#0.805 GO:0043231#0.780 GO:0043233#0.306 GO:0044237#0.543 GO:0044238#0.542 GO:0044249#0.404 GO:0044281#0.356 GO:0045333#0.343 GO:0046034#0.340 GO:0046390#0.340 GO:0055086#0.346 GO:0070013#0.304 GO:0072521#0.343 GO:0072522#0.343 GO:0090407#0.349 GO:0098796#0.316 GO:0110165#0.903 GO:1901135#0.356 GO:1901137#0.348 GO:1901293#0.344 GO:1902494#0.321|

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