Command Line Options for DEX programs

 

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Here are the command line options for program in DEX that use the getopt function. 

If the argument is in capital letters, then you must choose a value.  If the argument is in quotes “”, then you need to type in one of the options exactly to have the program identify the proper mode. Those options with no argument are simply run by typing the --option and do not require another value. 

 

Program:  View-many-HD-spectra-script

 

Option (ARGUMENT)                        Specified action                                                                                   

--help (no argument)                             Will print out a list of command line options for the user

--sequence (SEQUENCE)                   Select this sequence in a file for selection

--mass (MASS)                                   Select this monoisotopic mass in the file for selection

--number (NUMBER)                          Select this spectra number in a file, if one_file, will start at this number.  Default is --number 1 if no spectrum identifier is chosen.

--filelist (FILELIST)                             Required tag if using select-spectra and want to read the filenames from a list.  It is the name of the filelist of files you want to open and scan.  Optional when using View-many-HD-spectra-script.

--prefix-for-files (PREFIX)                   Optional tag that will specify the location of the files that are in the           --filelist option.  It is generally required if you use the --filelist option.

--graph (“BOTH”,”OBS”,”DECON”)  Optional tag to display only original OBServed mass spectrum, only DECONvoluted results or BOTH.  Default is BOTH if option is not used.

--overlay (no argument)                        Optional tag to have all the chosen spectra be displayed on one graph, instead of separated out one for each spectra.

--one_file (no argument)                       Optional tag to take all the chosen spectra from the same file.  If using the --filelist option, only the first file that passes the selection criterion will be used for all values.  When using the option the --number option will specify which spectra number to start with the calculation, just like the --rl option behaves.  Thus if you want to start with the first spectra in a file, you must type “--number 1” with the --one_file option. 

--legend (LEGEND,”NO”,”FILE”,”TIME”,”DESC”,”SEQ”,”NUM”)            Optional tag specifies where the user wants the filename (FILE), timepoint (TIME), description (DESC), sequence (SEQ), spectrum number (NUM) or no legend at all (NO).  The default is the filename unless there is a description. 

--short_graph (“yes”,”no”)                     Optional tag to make the xaxis range for the viewing area 30% less.  This will cause the xaxis maximum to be shorter, so the window more fully shows any slightly deuterated result. 

--title (TITLE)                                      Optional tag to rename the title to something other than the standard, which is the sequence of the first spectra chosen (must not have any spaces in the title).

--subtitle (SUBTITLE)                         Optional tag to rename the subtitle to something other than the standard, which is the location of the first spectra chosen (must not have any spaces in the subtitle).

--hardcopy (no argument)                     Optional tag to have a hardcopy of the result saved to the file graph_multi.ps.  You can print from UNIX by typing: lpr -Pprintername graph_multi.ps

--file_num (F1,F2,F3,etc.)                    Optional tag that will specify which files to use of the ones selected on the command line or in the filelist.  It will put them in the order that you specify here, if it is the only high priority option chosen.  The files are integer numbers, separated by a comma and no spaces.  For example, to choose only the 4th, 2nd and 5th files from a list, type: --file_num  4,2,5.  This is a high priority option when using the --filelist option, meaning it will not use any low priority options if this is used.  Repeated numbers will be shown more than once.

--line_num (L1,L2,etc.)                        Optional tag used only if using the --filelist option.  It is similar to --file_num option of choosing line numbers from those specified in the filelist.  It is integer numbers with commas separating them (no spaces). If you do no have a Line_num column in the filelist, then no files will be displayed and you should remove this option and try the program again.  This is a high priority option when using the --filelist option, meaning it will not use any low priority options if this is used.  It will put them in the order that you specify here, if it is the only high priority option chosen.  Do not repeat any line_num more than once.

--file_id (FILE_ID)                               Optional tag used only if using the --filelist option.  It will search the filenames in the filelist and print only ones that match all the search criteria.  The search pattern is similar to the * search in UNIX, but the wild character is a comma instead.  For example, to choose all the timepoints that start with “time” and have a “0min” in the filename, type:  --file_id time,0min.  The results will be for files “time-0min.dat” and “time-10min.dat”.  You can have any number of commas as search separators.  This is a low priority option when using the --filelist option, meaning it is only used if no high priority search options are used. 

--identifier (IDENTIFIER)                    Optional tag used only if using the --filelist option.  It is very similar to the --file_id option except it will search the “Description” column instead of the filenames.  The search strings are also separated by commas.  For example, to search for all files that begin with an “F” and have the number “1” in them, type:  --identifier F,1.  This will result in files “F_1m” and “F_10m” being selected from the filelist.  If you do not have a description column in the filelist, then no files will be displayed and you should remove this option and try the program again.  You can have any number of commas as search separators.  This is a low priority option when using the --filelist option, meaning it is only used if no high priority search options are used. 

--timepoints (TIMEPOINTS)               Optional tag used only if using the --filelist option.  It is similar in operation to the --file_num option, except that you can use floating point numbers.  Timepoints are separated by commas, with no spaces.  For example, if you want to just choose the timepoints that have the time values of 0, 1, and 10 minutes, type:  --timepoints 0,1,10.  The resulting files selected are “time-0min.dat”, “time-1min.dat”, and time-10min.dat”.  It will put them in the order that you specify here, if it is the only high priority option chosen.  This is a high priority option when using the         --filelist option, meaning it will not use any low priority options if this is used.  Do not repeat any timepoint more than once.

--num_files (NUMBER)                       Optional tag that specifies the number of files you want to display (must be an integer).  If more than that number is given, only the number will be displayed. 

--current_file (NUMBER)                    Optional tag that specifies to view-many-HD-spectra the current file for graphing.  This is an internal option that will probably not be of much use elsewhere.

--rl (NUMBER)                                   Optional tag that specifies the lower range for the number of files selected.  For example, if you specify 10 files, and you type --rl 4, then the program will start selecting the files starting with the 4th one in alphabetical order.  This is a low priority option when using the --filelist option, meaning it is only used if no high priority search options are used. 

--rh (NUMBER)                                  Optional tag that specifies the upper range for the number of files selected.  It is similar to --rl in operation.  This is a low priority option when using the --filelist option, meaning it is only used if no high priority search options are used. 

--start_offset (NUMBER)                    Optional tag that changes the default offset for each spectra.  The default is 1.5, and there should be little reason to change it. 

 

Examples (with Tutorial data)                                                                                                                           

Click here for an image.

Click here for an image.

Click here for an image.

 

 

Program:  Grab-1-peptide script

 

Option (ARGUMENT)            Specified action                                                                                               

--help (no argument)                             Will print out a list of command line options for the user

--sequence (SEQUENCE)                   Select this sequence in a file for selection

--mass (MASS)                                   Select this monoisotopic mass in the file for selection

--number (NUMBER)                          Select this spectra number in a file, if one_file, will start at this number.  Default is --number 1 if no spectrum identifier is chosen.

--filelist (FILELIST)                             Required tag if you want to read the filenames from a list.  It is the name of the filelist of files you want to open and scan.  Optional when using Grab-1-peptide-script.

--prefix-for-files (PREFIX)                   Optional tag that will specify the location of the files that are in the           --filelist option.  It is generally required if you use the --filelist option.

--file_output (OUTPUTFILE)               Optional tag if you want to output the results to a file name you specify after you type this option.  If you do not use this option or the “>” command with Grab-1-peptide-scritpt, the output will be displayed to stdout (the terminal). 

 

Examples (with Tutorial data)                                                                                                               

 

 

Program:  HD-analysis-script

 

Option (ARGUMENT)                        Specified action                                                                                   

--help (no argument)                           Will print out a list of command line options for the user

--sequence (SEQUENCE)                   Select this sequence in a file for selection

--mass (MASS)                                   Select this monoisotopic mass in the file for selection

--number (NUMBER)                           Select this spectra number in a file, if one_file, will start at this number.  Default is --number 1 if no spectrum identifier is chosen.

--program (”(cent)roid”,”width”,”pop”)    Optional tag to specify which type of program you want to run with the selected files.  Default is “cent” when no option is suggested. 

--filelist (FILELIST)                             Required tag if using select-spectra and want to read the filenames from a list, or if you want more than one set of experiments graphed separately.  It is the name of the filelist of files you want to open and scan.  Optional when using HD-analysis-script.

--prefix-for-files (PREFIX)                  Optional tag that will specify the location of the files that are in the --filelist option.  It is generally required if you use the --filelist option. You can abbreviate this to --prefix in most cases. 

--file_output (OUTPUTFILE)               Optional tag if you want to output the population and centroid (and peak width when specified) results to a file name you specify after you type this option.  If you do not use this option, the text output containing all the data will be in the file “HD_analysis_output”.

--grace (“no”,”yes”)                                Optional tag if you want to have the Grace graph automatically displayed at the end of the program.  Default is “yes” when the option is not specified.  If you did not install Grace, then you should use this option.

--graph (“BOTH”,”OBS”,”DECON”)  Optional tag to display only original OBServed mass spectrum, only DECONvoluted results or BOTH.  Default is BOTH if option is not used.

--overlay (no argument)                        Optional tag to have all the chosen spectra be displayed on the same graph line.  If multiple Line_num values have the same Time, then it is suggested you use the --xaxis_label INDEX option as well to prevent overlap. 

--one_file (no argument)                       Optional tag to take all the chosen spectra from the same file.  If using the --filelist option, only the first file that passes the selection criterion will be used for all values.  When using the option the --number option will specify which spectra number to start with the calculation, just like the --rl option behaves.  Thus if you want to start with the first spectra in a file, you must type “--number 1” with the --one_file option. 

--xaxis_label (“NO”,”FILE”,”INDEX”,”TIME”,”MASS”,”SEQ”)            Optional tag to determine the label for the data points.  Default is FILE to display the filename along the x-axis.  The y-axis will be set to 0.0 if you choose a label, so you can view the label below the graph.  If you do not want to have the label, type NO, and the y-axis will not be set to 0.0.  If you type INDEX, the values will not be displayed based on their Time values but by an index that starts at one.  TIME will show the time (in user units) for each file as the label, while MASS and SEQ will display the spectra respective M(0) or sequence as the label. 

--legend (LEGEND,”NO”)                     Optional tag specifies where the user wants the no legend at all (NO) or some special identifier for the legend of each line.  If the user types in a legend, both the OBS and DECON lines will have this at the beginning of their legend name.  The default is the Line_num where there is a Line_num with the --filelist option, or else it has not identifier at the beginning of the legend. 

--title (TITLE)                                      Optional tag to rename the title to something other than the standard, which is the sequence of the first spectra chosen (must not have any spaces in the title).

--subtitle (SUBTITLE)                         Optional tag to rename the subtitle to something other than the standard, which is the location of the first spectra chosen (must not have any spaces in the subtitle).

--hardcopy (no argument)                     Optional tag to have a hardcopy of the result saved to the file graph_multi.ps.  You can print from UNIX by typing: lpr -Pprintername graph_multi.ps

--file_num (F1,F2,F3,etc.)                    Optional tag that will specify which files to use of the ones selected on the command line or in the filelist.  It will put them in the order that you specify here, if it is the only high priority option chosen.  The files are integer numbers, separated by a comma and no spaces.  For example, to choose only the 4th, 2nd and 5th files from a list, type: --file_num  4,2,5.  This is a high priority option when using the --filelist option, meaning it will not use any low priority options if this is used.  Repeated numbers will be shown more than once.

--line_num (L1,L2,etc.)                        Optional tag used only if using the --filelist option.  It is similar to --file_num option of choosing line numbers from those specified in the filelist.  It is integer numbers with commas separating them (no spaces). If you do no have a Line_num column in the filelist, then no files will be displayed and you should remove this option and try the program again.  This is a high priority option when using the --filelist option, meaning it will not use any low priority options if this is used.  It will put them in the order that you specify here, if it is the only high priority option chosen.  Do not repeat any line_num more than once.

--file_id (FILE_ID)                               Optional tag used only if using the --filelist option.  It will search the filenames in the filelist and print only ones that match all the search criteria.  The search pattern is similar to the * search in UNIX, but the wild character is a comma (,) instead.  For example, to choose all the timepoints that start with “time” and have a “0min” in the filename, type:  --file_id time,0min.  The results will be for files “time-0min.dat” and “time-10min.dat”.  You can have any number of commas as search separators.  This is a low priority option when using the --filelist option, meaning it is only used if no high priority search options are used. 

--identifier (IDENTIFIER)                    Optional tag used only if using the --filelist option.  It is very similar to the --file_id option except it will search the “Description” column instead of the filenames.  The search strings are also separated by commas.  For example, to search for all files that begin with an “F” and have the number “1” in them, type:  --identifier F,1.  This will result in files “F_1m” and “F_10m” being selected from the filelist.  If you do not have a description column in the filelist, then no files will be displayed and you should remove this option and try the program again.  You can have any number of commas as search separators.  This is a low priority option when using the --filelist option, meaning it is only used if no high priority search options are used. 

--timepoints (TIMEPOINTS)               Optional tag used only if using the --filelist option.  It is similar in operation to the --file_num option, except that you can use floating point numbers.  Timepoints are separated by commas, with no spaces.  For example, if you want to just choose the timepoints that have the time values of 0, 1, and 10 minutes, type:  --timepoints 0,1,10.  The resulting files selected are “time-0min.dat”, “time-1min.dat”, and time-10min.dat”.  It will put them in the order that you specify here, if it is the only high priority option chosen.  This is a high priority option when using the         --filelist option, meaning it will not use any low priority options if this is used.  Do not repeat any timepoint more than once.

--find_time (IDENTIFIER)                     Optional tag that will find the time for the xaxis within the filenames.  To use this option, type “--find_time time-“ for the examples provided and the numbers after “time-“ in the file will be interpreted.  You must have the same beginning of the filename for this to work, so in this example, every beginning of the file must start with “time-“.  The ending of the file does not have to be the same across all files.  This only used when the --filelist option is NOT used and you are reading in files from the command line directly. 

--num_files (NUMBER)                       Optional tag that specifies the number of files you want to display (must be an integer).  If more than that number is given, only the number will be displayed.  This is a low priority option and will only be used when no high priority options are specified. 

--current_file (NUMBER)                    Optional tag that specifies to HD-analysis the current file for graphing.  This is an internal option that will probably not be of much use elsewhere. 

--line_current (NUMBER)                    Optional tag that specifies to HD-analysis the current line used for graphing multiple line_num on the same graph.  This is an internal option that will probably not be of much use elsewhere. 

--rl (NUMBER)                                     Optional tag that specifies the lower range for the number of files selected.  For example, if you specify 10 files, and you type --rl 4, then the program will start selecting the files starting with the 4th one in alphabetical order.  This is a low priority option when using the --filelist option, meaning it is only used if no high priority search options are used. 

--rh (NUMBER)                                    Optional tag that specifies the upper range for the number of files selected.  It is similar to --rl in operation.  This is a low priority option when using the --filelist option, meaning it is only used if no high priority search options are used. 

--start_offset (NUMBER)                    Optional tag that changes the default offset for each spectra.  The default is 1.5, and there should be little reason to change it. 

--xaxis_scale (“log”,”linear”)                 Optional tag to set the x-axis in a linear or logarithmic value.  Default is linear when no option is specified.  If there is no Time values for each spectra or INDEX has been selected for the --xaxis_label, then the x-axis will be an index, not log or linear scale. 

--graph_format (“bar”,”point”)                Optional tag to set the values as a bar graph or by points.  Default is points when no option is specified.  The bar graphs are not stacked side-by-side, so only one or two can be displayed at the same time. 

--display_info (“yes”,”no”)                     Optional tag to have the actual values be displayed numerically above the points on the graph.  The default is “no” when no option is specified. 

--long_output (“yes”,”no”)                       Optional tag to turn off the peak cutoff function for the “Percent” column.  This may be necessary if you want to look at a peak with multiple states that the program has determined are overlapping peaks and doesn’t automatically display the peak areas for the highest masses. 

--align (“no”,”yes”)                                Optional tag to turn the automatic alignment function (to correct for shifted peaks) on or off.  Default is “yes” when no option is specified and this is the highly suggested option.  If you are sure the alignment is what you specify with the --start_offset option, then you can type “--align no”. 

--back_exchange (NUMBER)                Optional tag to apply a back exchange correction factor to the centroids before outputting them and graphing them.  Default is 0% and this is only used with the “--program cent” option.  The value should be between 0.1 and 99.9 and should represent the amount of exchange lost during the digestion and quench phase.  Thus if 33% of the deuteration is lost, type “--back_exchange 33”. 

--percent_width (NUMBER)                  Optional tag for use in determining the peak widths.  Default is 20% and this is only used with the “--program width” option.  If you want a different value between 1 and 99, use this option.  If you want the peak width at 40% of the maximum height, type “--percent_width 40”. 

--width_output (“20”,”50”,”20,50”,”user”,”all”)            Optional tag to determine what percent of maximum should be used to output.  Default is 20% if no --percent_width option is specified.  If the --percent_width option is specified, the default is the value chosen by the user.  Otherwise the user can 50%, 20% and 50% or all three values (including the user determined value). 

 

 

Examples (with Tutorial data)                                                                                                                           

Centroids

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Peak Width

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Update

Written by Matthew Hotchko and last updated last on June 19, 2006

 

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