metapredict from the command-line

Using the original metapredict network

We have recently updated the network that makes predictions for metapredict to massively improve accuracy. However, if you need to use the original metapredict predictor as opposed to our new, updated predictor, use the -l or --legacy flag!

Predicting disorder scores from fasta files

The metapredict-predict-disorder command from the command line takes a .fasta file as input and returns disorder scores for the sequences in the FASTA file.

Once metapredict is installed, the user can run metapredict-predict-disorder from the command line:

$ metapredict-predict-disorder <Path to .fasta file>

Example:

$ metapredict-predict-disorder /Users/thisUser/Desktop/interestingProteins.fasta

Note that as of metapredict V2-FF this will automatically parallelize on a GPU or CPU if available. A progress bar will also be generated in the terminal.

Additional Usage:

Specifying where to save the output - If you would like to specify where to save the output, simply use the -o or --output-file flag and then specify the file path and file name. By default this command will save the output file as disorder_scores.csv to your current working directory. However, you can specify the file name in the output path.

Example:

$ metapredict-predict-disorder /Users/thisUser/Desktop/interestingProteins.fasta -o /Users/thisUser/Desktop/disorder_predictions/my_disorder_predictions.csv

Using the original metapredict network- To use the original metapredict network, simply use the -l or --legacy flag.

Example:

$ metapredict-predict-disorder /Users/thisUser/Desktop/interestingProteins.fasta -o /Users/thisUser/Desktop/disorder_predictions/my_disorder_predictions.csv -l

Predicting IDRs from a fasta file

The metapredict-predict-idrs command from the command line takes a .fasta file as input and returns a .fasta file containing the IDRs for every sequence from the input .fasta file.

$ metapredict-predict-idrs <Path to .fasta file>

Example

$ metapredict-predict-idrs /Users/thisUser/Desktop/interestingProteins.fasta

Note that as of metapredict V2-FF this will automatically parallelize on a GPU or CPU if available. A progress bar will also be generated in the terminal.

Additional Usage

specifying where to save the output - If you would like to specify where to save the output, simply use the -o or --output-file flag and then specify the file path and file name.

Example

$ metapredict-predict-idrs /Users/thisUser/Desktop/interestingProteins.fasta -o /Users/thisUser/Desktop/disorder_predictions/my_idrs.fasta

Using the original metapredict predictor To use the original metapredict predictor as opposed to our new, updated predictor, use the -l or --legacy flag! Note that if legacy mode is requested no parallelization is possible.

Example

$ metapredict-predict-idrs /Users/thisUser/Desktop/interestingProteins.fasta -o /Users/thisUser/Desktop/disorder_predictions/my_idrs.fasta -l

Changing output threshold for disorder- To change the cutoff value for something to be considered disordered, simply use the --threshold flag and then specify your value. For legacy, the default is 0.42. For the new version of metapredict, the value is 0.5.

Example

$ metapredict-predict-idrs /Users/thisUser/Desktop/interestingProteins.fasta -o /Users/thisUser/Desktop/disorder_predictions/my_idrs.fasta --threshold 0.3

Predicting disorder scores from sequence

metapredict-quick-predict is a command that will let you input a sequence and get disorder values immediately printed to the terminal. The only argument that can be input is the sequence.

Example:

$ metapredict-quick-predict ISQQMQAQPAMVKSQQQQQQQQQQHQHQQQQLQQQQQLQMSQQQVQQQGIYNNGTIAVAN

Using the original metapredict network- To use the original metapredict network, simply use the -l or --legacy flag.

Example:

$ metapredict-quick-predict ISQQMQAQPAMVKSQQQQQQQQQQHQHQQQQLQQQQQLQMSQQQVQQQGIYNNGTIAVA -l

Predicting AlphaFold2 confidence scores from a fasta file

The metapredict-predict-pLDDT command from the command line takes a .fasta file as input and returns predicted AlphaFold2 pLDDT confidence scores for the sequences in the FASTA file.

$ metapredict-predict-pLDDT <Path to .fasta file>

Example

$ metapredict-predict-pLDDT /Users/thisUser/Desktop/interestingProteins.fasta

Additional Usage

Specify where to save the output - If you would like to specify where to save the output, simply use the -o or --output-file flag and then specify the file path. By default this command will save the output file as pLDDT_scores.csv to your current working directory. However, you can specify the file name in the output path.

Example

$ metapredict-predict-pLDDT /Users/thisUser/Desktop/interestingProteins.fasta -o /Users/thisUser/Desktop/disorder_predictions/my_pLDDT_predictions.csv

Plotting disorder profiles from a fasta file

The metapredict-graph-disorder command from the command line takes a .fasta file as input and returns a graph for every sequence within the .fasta file. Warning This will return a graph for every sequence in the FASTA file.

$ metapredict-graph-disorder <Path to .fasta file>

Example

$ metapredict-graph-disorder /Users/thisUser/Desktop/interestingProteins.fasta

If no output directory is specified, this function will make an output directory in the current working directory called disorder_out. This directory will hold all generated graphs.

Additional Usage

Adding AlphaFold2 Confidence Scores - To add predicted AlphaFold2 pLDDT confidence scores, simply use the -p or --pLDDT flag.

Example

$ metapredict-graph-disorder /Users/thisUser/Desktop/interestingProteins.fasta p

Specifying where to save the output - To specify where to dave the output, simply use the -o or --output-directory flag.

Example

$ metapredict-graph-disorder /Users/thisUser/Desktop/interestingProteins.fasta -o /Users/thisUser/Desktop/FolderForCoolPredictions

Changing resolution of saved graphs - By default, the output graphs have a DPI of 150. However, the user can change the DPI of the output (higher values have greater resolution but take up more space). To change the DPI simply add the flag -D or --dpi followed by the wanted DPI value.

Example

$ metapredict-graph-disorder /Users/thisUser/Desktop/interestingProteins.fasta -o /Users/thisUser/Desktop/DisorderGraphsFolder/ -D 300

Changing the file type - By default the graphs will save as .png files. However, you can specify the file type by calling --filetype and then specifying the file type. Any matplotlib compatible file extension should work (for example, pdf).

Example

$ metapredict-graph-disorder /Users/thisUser/Desktop/interestingProteins.fasta -o /Users/thisUser/Desktop/DisorderGraphsFolder/ --filetype pdf

Indexing file names - If you would like to index the file names with a leading unique integer starting at 1, use the --indexed-filenames flag.

Example

$ metapredict-graph-disorder /Users/thisUser/Desktop/interestingProteins.fasta -o /Users/thisUser/Desktop/DisorderGraphsFolder/ --indexed-filenames

Changing the disorder threshold line on the graph - If you would like to change the disorder threshold line plotted on the graph, use the --disorder-threshold flag followed by some value between 0 and 1. Default is 0.3.

Example

$ metapredict-graph-disorder /Users/thisUser/Desktop/interestingProteins.fasta -o /Users/thisUser/Desktop/DisorderGraphsFolder/ --disorder-threshold 0.5

Using the original metapredict network- To use the original metapredict network, simply use the -l or --legacy flag.

Example:

$ metapredict-graph-disorder /Users/thisUser/Desktop/interestingProteins.fasta -o /Users/thisUser/Desktop/DisorderGraphsFolder/ --disorder-threshold 0.5 -l

Quick graphing of disorder scores

metapredict-quick-graph is a command that will let you input a sequence and get a plot of the disorder back immediately. You cannot input fasta files for this command. The command only takes three arguments, 1. the sequence 2. optional DPI -D or --dpi of the output graph which defaults to 150 DPI, and 3. optional to include predicted AlphaFold2 confidence scores, use the p or --pLDDT flag.

Example:

$ metapredict-quick-graph ISQQMQAQPAMVKSQQQQQQQQQQHQHQQQQLQQQQQLQMSQQQVQQQGIYNNGTIAVAN

Example:

$ metapredict-quick-graph ISQQMQAQPAMVKSQQQQQQQQQQHQHQQQQLQQQQQLQMSQQQVQQQGIYNNGTIAVAN -p

Example:

$ metapredict-quick-graph ISQQMQAQPAMVKSQQQQQQQQQQHQHQQQQLQQQQQLQMSQQQVQQQGIYNNGTIAVAN -D 200

Using the original metapredict network- To use the original metapredict network, simply use the -l or --legacy flag.

Example:

$ metapredict-quick-graph ISQQMQAQPAMVKSQQQQQQQQQQHQHQQQQLQQQQQLQMSQQQVQQQGIYNNGTIAVAN -l

Graphing disorder scores using UniProt ID

metapredict-uniprot is a command that will let you input any UniProt ID and get a plot of the disorder for the corresponding protein. The default behavior is to have a plot automatically appear. Apart from the UniProt ID which is required for this command, the command has four possible additional optional arguments, 1. To include predicted AlphaFold2 pLDDT confidence scores, use the -p or --pLDDT flag. DPI can be changed with the -D or --dpi flags, default is 150 DPI, 3. Using -o or --output-file will save the plot to a specified directory (default is current directory) - filenames and file extensions (pdf, jpg, png, etc) can be specified here. If there is no file name specified, it will save as the UniProt ID and as a .png, 4. -t or --title will let you specify the title of the plot. By default the title will be Disorder for followed by the UniProt ID.

Example:

$ metapredict-uniprot Q8RYC8

Example:

$ metapredict-uniprot Q8RYC8 -p

Example:

$ metapredict-uniprot Q8RYC8 -D 300

Example:

$ metapredict-uniprot Q8RYC8 -o /Users/ThisUser/Desktop/MyFolder/DisorderGraphs

Example:

$ metapredict-uniprot Q8RYC8 -o /Users/ThisUser/Desktop/MyFolder/DisorderGraphs/my_graph.png

Example:

$ metapredict-uniprot Q8RYC8 -t ARF19

Using the original metapredict network- To use the original metapredict network, simply use the -l or --legacy flag.

Example:

$ metapredict-uniprot Q8RYC8 -l

Graphing disorder using the common name of a protein

Sometimes you just don’t know the UniProt ID for your favorite protein, and looking it up can be a pain. With the metapredict-name command, you can input the common name of your favorite protein and get a graph in return. Metapredict will also print the name of the organisms and the UniProt ID it found so you know you’re looking at the correct protein. This is because this functionality queries your input protein name on UniProt and takes the top hit. Sometimes this is the protein you’re looking for, but not always. To increase the likelihood of success, use your protein name and the organism name for this command.

Example

$ metapredict-name p53

will graph the metapredict disorder scores for the Homo sapiens p53 protein. This is because Homo sapiens p53 is the top hit on UniProt when you search p53. However…

$ metapredict-name p53 chicken

will graph the p53 from Gallus gallus!

Additional Usage

Changing the DPI

Changing the DPI will adjust the resolution of the graph. To change the DPI, use the -D or --dpi flag.

Example

$ metapredict-name p53 -D 300

Graphing predicted pLDDT scores

To add predicted pLDDT scores to the graph, use the -p or --pLDDT flag.

Example

$ metapredict-name p53 -p

Changing the title

To change the title, use the -t or --title flag.

Example

$ metapredict-name p53 -t my_cool_graph_of_p53

Using the legacy version of metapredict

To use the legacy version of metapredict for your disorder scores, use the -l or --legacy flag.

Example

$ metapredict-name p53 -l

Printing the full UniProt ID to your terminal

To have your terminal print the entire UniProt ID as well as the full protein sequence from your specified protein upon graphing, use the -v or --verbose flag.

Example

$ metapredict-name p53 -v

Turning off all printing to the terminal

By default, the metapredict-name command prints the UniProt ID as well as other information related to your protein to the terminal. The purpose of this is to make it explicitly clear which protein was graphed because grabbing the top hit from UniProt does not guarantee that it is the protein you want or expected. However, this behavior can be turned off by using the -s or --silent flag.

Example

$ metapredict-name p53 -s

Graphing predicted AlphaFold2 pLDDT scores from a fasta file

The metapredict-graph-pLDDT command from the command line takes a .fasta file as input and returns a graph of the predicted AlphaFold2 pLDDT confidence score for every sequence within the .fasta file. Warning This will return a graph for every sequence in the FASTA file.

$ metapredict-graph-pLDDT <Path to .fasta file>

Example

$ metapredict-graph-pLDDT /Users/thisUser/Desktop/interestingProteins.fasta

If no output directory is specified, this function will make an output directory in the current working directory called pLDDT_out. This directory will hold all generated graphs.

Additional Usage

Specifying where to save the output - To specify where to dave the output, simply use the -o or --output-directory flag.

Example

$ metapredict-graph-pLDDT /Users/thisUser/Desktop/interestingProteins.fasta -o /Users/thisUser/Desktop/FolderForCoolPredictions

Changing resolution of saved graphs - By default, the output graphs have a DPI of 150. However, the user can change the DPI of the output (higher values have greater resolution but take up more space). To change the DPI simply add the flag -D or --dpi followed by the wanted DPI value.

Example

$ metapredict-graph-pLDDT /Users/thisUser/Desktop/interestingProteins.fasta -o /Users/thisUser/Desktop/pLDDTGraphsFolder/ -D 300

Changing the file type - By default the graphs will save as .png files. However, you can specify the file type by calling --filetype and then specifying the file type. Any matplotlib compatible file extension should work (for example, pdf).

Example

$ metapredict-graph-pLDDT /Users/thisUser/Desktop/interestingProteins.fasta -o /Users/thisUser/Desktop/pLDDTGraphsFolder/ --filetype pdf

Indexing file names - If you would like to index the file names with a leading unique integer starting at 1, use the --indexed-filenames flag.

Example

$ metapredict-graph-pLDDT /Users/thisUser/Desktop/interestingProteins.fasta -o /Users/thisUser/Desktop/pLDDTGraphsFolder/ --indexed-filenames