From 53d7fd5034c3f877933646d058bfb904403f2396 Mon Sep 17 00:00:00 2001 From: ynowatzk Date: Wed, 2 Nov 2022 11:04:17 +0100 Subject: [PATCH] Update README --- example/README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/example/README.md b/example/README.md index 15020a8..0ce0788 100644 --- a/example/README.md +++ b/example/README.md @@ -1,10 +1,10 @@ # Mistle Example Usage -A toy example is provided to test the program. A library of simulated mass spectra (predicted by Prosit) of 1000 yeast peptides is used for reference. 3 experimental spectra matching the species are retrieved from 9MM FASP dataset (Study ) +A toy example is provided to test the program. A library of 1000 simulated mass spectra (predicted by Prosit (Gessulat et al., 2019)) of yeast peptides (*Saccharomyces cerevisiae*) is used for reference. 3 experimental spectra matching the species are selected from the 9MM FASP dataset (Tanca et al., 2013). -## Commands +## Running the test -Open terminal or change into this example directory. To construct the fragment index from the example spectral library, run +Open terminal or change into this directory (path/to/mistle/example). To construct the fragment index from the example spectral library, run mistle-build -i yeast_1000.msp -o index/ -n 4 -t 1 @@ -14,8 +14,8 @@ Next, perform example searches mistle-search -s yeast_exp.mgf -i index/ -o example_results.csv -p 10 -b 0.2 -t 1 --hits_per_spectrum 1 -This should produce a *example_results.csv* file in the index directory. Compare the output to the *example_results_control.csv*, which is already present in the index/ directory. If they align, *mistle* is configured correctly and is read to use. (Note that floating-point inaccuracy may occur when using different hardware or advanced vector extensions. Results may deviate from the control in the last digit(s)). +This should produce an *example_results.csv* file in the index/ directory. Compare the output to the *example_results_control.csv*, which is already present in the index/ directory. If they align, *mistle* is configured correctly and is read to use. (Note that floating-point inaccuracy may occur when using different hardware or advanced vector extensions. Results and scores may deviate from the control in the last digit(s)). -Below, the first match of the list is displayed as mirror plot (experimental spectrum top; matched simulated spectrum bottom) generated using the python *spectrum_utils* package. +Below, the first match of the list is displayed by a mirror plot (experimental spectrum top; matched simulated spectrum bottom) generated using the python *spectrum_utils* package. Logo