saier_lab

Python Program

• Program that runs mmseqs search, mmseqs convertalis, and hmmtop on designated files; also pulls substrate data from tcdb.org.
• Result files from convertalis,hmmtop, and substrate data will be organized and stored into three dictionary objects (see Sample Run for example)
• Using the said dictionary from convertalis, program automatically generates a fasta file with accessions from both target and query and corresponding sequences.
• Program asks for 3 input files (2 for both search and convertalis and 1 for hmmtop), and 3 names for output files (1 for search, convertalis, and .faa file, 1 for hmmtop, and 1 for substrate data)

Sample Run

• 3 lines were the output when print() is called on 3 dictionaries, in which results of convertalis, hmmtop, and substrate data were stored
• Files and file names used in the run that produces these results: 1. QueryDB: proteomeDB 2. TargetDB: tcdbDB 3. Result Name: pyDB 4. Fasta file: sample.faa (from first 100 lines of tcdbDB) 5. hmmtop Result Name: sample_hmm.hmmtop 6. Substrate data file Name: substrate.tsv