BioParser is a tool used to process C-terminal decameric sequences, with the evaluation of PDZ binding domains as is primary goal. BioParser will filter and analyze the proteomes of as many organisms as are supplied to it, and will filter based off as many motifs as are supplied to it.
Motifs refers to specifying specific amino acids at certain positions. For example, if you wanted to analyze the enrichment of the amino acids S and T at position 2, you could supply the -motifs argument with P2:ST
BioParser also creates detailed data on the proteomes that is stored in the CSV folder that is created during the programs execution. The -c argument combines all CSV's for one organism, which can be usefull when large numbers of positions are being processed.
Python3
main.py [-h] -refOrganism REFORGANISM -sequenceFolder SEQUENCEFOLDER
-numResidues NUMRESIDUES -inputValues INPUTVALUES
[INPUTVALUES ...] -out OUT -significance SIGNIFICANCE
Arguments:
-refOrganism REFORGANISM
Provide the file name of the organism that the other
organisms will be compared with. Usage:
/path/folder/organism.tsv
-sequenceFolder SEQUENCEFOLDER
The path of the folder that contains tsv files that
contain the last N many residues of all the proteins
in the proteomes in question. Usage: /path/folder
-numResidues NUMRESIDUES
The number of residues to provide statistics on.
Usage: 6
-inputValues INPUTVALUES [INPUTVALUES ...]
The matching positions with desired amino acids.
Usage: P0:ILVF P2:ST ... PX:X
-out OUT Output file directory and name. Do not include file
extensions. Usage: /path/folder/fileName_motif_example
-significance SIGNIFICANCE
significance cut off value example 0.9999 corresponds
to P<0.0001 or 0.1 percent chance the item was flagged
in error
-decouple If a xml file has all ready been generated use this
flag to skip xml generation
-pyth force the use of motifFileMaker over makeXML. Using
this flag will slowdown exicution.
-GUI Launch GUI automatically after program exicution.
Example Usage:
Linux
python3 main.py -refOrganism homo_sapiens_TaxID_9606_R_reviewed.tsv -sequenceFolder rawTSV/ -numResidues 6 -inputValues P0:WYIAFLVM P2:ST -out motif_2_human -significance 0.9999
Windows
main.py -refOrganism homo_sapiens_TaxID_9606_R_reviewed.tsv -sequenceFolder rawTSV/ -numResidues 6 -inputValues P0:WYIAFLVM P2:ST -out motif_2_human -significance 0.9999