Package: compbiolab-CLI
Table Of ContentsTable of ContentsSoftware InfoOverviewInstallationUsageComparing protein sequencesComparing ArgumentsSearchingSearching ArgumentsOptional FlagsAvailable MetricsExamplesSoftware Info:Software Name: compbiolab-CLILatest Software Version: v0.4.0PyPI:https://pypi.org/project/compbiolab-CLI/Documentation:https://cfogel.github.io/compbiolab-CLI-docs/OverviewOur goal for this project is to read a new input sequence and find the protein family which it belongs in by comparing it with existing sequences in the database. In addition to finding the closest family for a new sequence, our search application can also accept an autoencoded fingerprint and see which family is the best match using a variety of different metrics.Our compare application allows different protein families to be compared directly using different distance functions.  It accepts the names of families already in the database, but it can also accept files containing data from new latent spaces.The program can be downloaded from PyPI (the Python Package Index), and it has a Command Line Interface.InstallationInstallPython 3.7 or aboveOpen a terminal. (On Windows, Windows Key + R → Type cmd → Enter)Typepip install compbiolab-CLIUsageComparing protein sequencesFind the distance between fingerprints of two protein familiescompare [-h] <protein_family> <protein_family> [distance_options] [output_options]
             list namesComparing Argumentsprotein_familyProtein family's name. Provide an existing protein family's name or the file name of a new latent space. Files should contain 30 floats, each float in a separate line.distance optionsOptional distance flagsoutput_optionsOptional output flagslist namesShow available protein family namesSearchingFind the closest family to a new protein sequence or familysearch [-h] lat <latent space> [distance_options] [output_options]
            seq <sequence> [output_options]
            list namesSearching Argumentslat <filename> [distance_options] [output_options]Provide the file name of one or more new protein family latent spaces. The closest protein family to these new latent spaces will be shown.distance_optionsOptional distance flagsoutput_optionsOptional output flagsseq <filename> [output_options](Requires 64-bit Python 3.7.x)Provide the name of one or more files containing a protein sequence to get the closest protein families for those sequences.output_optionsOptional output flagslist namesShow available protein family namesOptional FlagsOutput Options-outOutput filename-ofOutput format, text or csv. Default: text-omOutput mode, a[ppend] or w[rite]. Default: aDistance Options-mDistance metric. Default: euclidean-pScalar. The p-norm to apply for Minkowski, weighted and unweighted. Default: 2Available metricseuclidean (default), minkowski, cityblock, sqeuclidean, cosine, correlation, hamming, jaccard, chebyshev, canberra, braycurtis, yule, dice, kulsinski, rogerstanimoto, russellrao, sokalmichener, sokalsneathExamplesYou can find the Euclidean distance between two families ATKA_ATKC and CDSA_RSEP by running the command:compare ATKA_ATKC CDSA_RSEPIf you want to find the Cityblock distance between ATKA_ATKC and a new latent space stored at second_new_latent_example.txt, you can run the command:compare ATKA_ATKC second_new_latent_example.txt -m cityblockIf you want to find the cosine distance between two new latent spaces stored at first_new_latent_example.txt and second_new_latent_example.txt, you can run the command:compare first_new_latent_example.txt second_new_latent_example.txt -m cosineYou can find the closest protein family to first_new_latent_example.txt in cosine distance by running the command:search lat first_new_latent_example.txt -m cosineYou can find the closest family to a new protein sequence (for example new_sequence_example.txt) by running:search seq new_sequence_example.txt