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tmsplit.md

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Documentation for script: tmsplit

Summary

This program cuts protein sequences under 4 different criteria: 1) cut a residue range

Dependencies

The following Python module needs to be available to the script:

  1. tmsFunction
    This module is part of the distribution.

Command line options

The following options are available. You can also run the script without arguments to display the options:

-h, --help            show this help message and exit.  
-if INPUTFILE         The path of the file containing the FASTA sequences 
                      that are to be processed.  
-od OUTPUTDIR         The path to the directory for the output. If the 
                      directory is not present,it will be created.  
-of OUTFILE           Name of the file in which the processed sequence will 
                      be placed. NOTE: Do not add any extensions to the  
                      name. ".faa" will automaticaly be assigned.  
-rangeCut             Extract a segment of variable size from a protein  
                      sequence. Start(-s or --start) and End(-e or --end)  
                      required for range cut.  
-equal                Cut protein(s) into segments of equal length. Parts 
                      (-p or --parts) required for equal cut.  
-tmsCut               Cut multiple sequences between any two TMS's. Start(-s 
                      or --start) and End(-e or --end) required for TMS 
                      cut.The tail argument is optional, but the default is 3.  
-split                Split protein(s) into groups of TMS. Choose  
                      overlapping(-over) or non-overlapping(-non). DEFAULT  
                      is non-overlapping. TMS(-tms) argument required for  
                      TMS split.The tail argument is optional, but the  
                      default is 3.  
-t TAIL, --tail TAIL  The number of residues left before and after the  
                      sequence segments. DEFAULT is 3.  
-p PARTS, --parts PARTS  
                      Argument for equal cut. The number of segments of  
                      equal length the sequence(s) should be cut into.  
-s START, --start START 
                      Argument for TMS cut. The number of the TMS or Residue  
                      that will be the first in the segment.  
-e END, --end END     Argeument for TMS cut. The number of the TMS or  
                      Residue that will be the last in the segment.  
-tms TMS              Argument for TMS Split. The number of TMS per group.  
-over                 Argument for TMS Split. TMS are grouped by overlapping  
                      sections. Ex [1,2,3],[2,3,4] etc...  
-non                  DEFAULT Argument for TMS Split. TMSs are grouped by  
                      non-overlapping sections. Ex [1,2,3],[4,5,6] etc...  
                      Also requires a condition -ignore, -append, or -new  
-ignore               Argument for TMS Split Non-Overlapping. Any TMS that  
                      are not able to be formed into a full group are  
                      ignored.  
-append               DEFAULT Argument for TMS Split Non-Overlapping.Any TMS  
                      that are not able to be formed into a full group are  
                      added to the last possible segment.  
-new                  Argument for TMS Split Non-Overlapping. Any TMS that  
                      are not able to be formed into a full group are added  
                      to another segment