... | ... | @@ -12,66 +12,10 @@ Run `peakStrainer.py <file.raw>` |
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To run Peak Strainer with custom settings go to the *utils* folder and
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run `msps.py -h` to display a list of available flags and options.
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sample options`usage: msps.py [-h] [-w CONFIG_OUTPUT_PATH] [-c MY_CONFIG] [--csv] [--verbose]
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[--filterRetentionTime FILTERRETENTIONTIME FILTERRETENTIONTIME | --filterText FILTERTEXT FILTERTEXT | --filterSamples FILTERSAMPLES]
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[--prefilter PREFILTER PREFILTER PREFILTER | --preliminaryReductionFilter PRELIMINARYREDUCTIONFILTER PRELIMINARYREDUCTIONFILTER]
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[--binsDecimal BINSDECIMAL | --binsResolution BINSRESOLUTION | --binsTheoResolution BINSTHEORESOLUTION]
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[--inFirstBin | --inWindowBin INWINDOWBIN | --inNarrowBin]
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filename [output_path]
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Combine and filter spectra signals to remove random signals Args that start
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with '--' (eg. --csv) can also be set in a config file (./.ini or specified
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via -c). Config file syntax allows: key=value, flag=true, stuff=[a,b,c] (for
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details, see syntax at https://goo.gl/R74nmi). If an arg is specified in more
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than one place, then commandline values override config file values which
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override defaults.
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positional arguments:
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filename The thermo-raw file
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output_path Path for the output.mzxml file
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optional arguments:
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-h, --help show this help message and exit
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-w CONFIG_OUTPUT_PATH, --write-out-config-file CONFIG_OUTPUT_PATH
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takes the current command line args and writes them
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out to a config file at the given path, then exits
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-c MY_CONFIG, --my-config MY_CONFIG
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config file path
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--csv generate csv report files (default: do not generate)
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--verbose, -v (set the logging level 1-5 (up to -vvvvv)
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--filterRetentionTime FILTERRETENTIONTIME FILTERRETENTIONTIME, -fr FILTERRETENTIONTIME FILTERRETENTIONTIME
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filterScanBy_retentionTime: -fr 0.0 10000.0
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;lowSeconds=0.5, highSeconds=float("inf")
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--filterText FILTERTEXT FILTERTEXT, -ft FILTERTEXT FILTERTEXT
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filterScanBy_filterline text: -ft ms False ;subtext =
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ms , keep=False
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--filterSamples FILTERSAMPLES, -fs FILTERSAMPLES
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filterScanBy_samples eg. 1 out of every 10: -fs 10
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;step_size = 10
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--prefilter PREFILTER PREFILTER PREFILTER, -p PREFILTER PREFILTER PREFILTER
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Default prefilter : -p 2 2 0.5 ;decimal_places=2,
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minCount=2, minRepetitionRate=0.5
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--preliminaryReductionFilter PRELIMINARYREDUCTIONFILTER PRELIMINARYREDUCTIONFILTER, -pr PRELIMINARYREDUCTIONFILTER PRELIMINARYREDUCTIONFILTER
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Reduction settings: -p 0.10 10 reduce to 0.10 of
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original, minPeaks = 10
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--binsDecimal BINSDECIMAL, -b BINSDECIMAL
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generateBins by decimalPlaces: -b 4 decimal_places = 4
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--binsResolution BINSRESOLUTION, -br BINSRESOLUTION
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generateBins by resolution: -br 4 resolutions
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decimal_places = 4
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--binsTheoResolution BINSTHEORESOLUTION, -bt BINSTHEORESOLUTION
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generateBins by theoretical Resolution -bt 4
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resolutions decimal_places = 4
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--inFirstBin, -i sortMassIn_FirstBin
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--inWindowBin INWINDOWBIN, -iw INWINDOWBIN
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sortMassIn_first bin in Window width 200: -iw 200
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;window = 200
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--inNarrowBin, -in sortMassIn_NarrowestBin
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`
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I would recommend that you look at the code in ```peakStrainer.py```
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Because of the complexity of the options from the command line,
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we recommend that you change the code in ```peakStrain
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er.py```
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in the main method and update it there,
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the code should be readable and you can change it to your setting.
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