ClusterInfo tool

This page provides information about the clusterInfo tool

Usage:

clusterinfo <options>

Parameter Parameter in params file Argument Default value Description
--project-dir PROJECT_DIR DIRECTORY . Project directory
--clusterbin INPUT_BIN FILE   Clustering binary data file
--inputspectra INPUT_SPECTRA FILE   Input spectra file list (txt format). The file names need to be exactly as in the INPUT_SPECTRA string in the params file to main_specnets.
--originalspectra ORIGINAL_SPECTRA FILE   Original spectra file list (txt format)
--cluster-spectra CLUSTER_SPECTRA FILE spectra/specs_ms.pklbin Cluster spectra file
--outdir OUTDIR DIRECTORY
. Output directory
--outfile OUTFILE FILE ClusterInfo.csv Output filename
--out-summary-file OUT_SUMMARY_FILE FILE cluster_summary.tsv Output filename for the summary file
--p PARAMETER_FILE FILE   Read parameters from file
--help help     Display this help and exit
--version VERSION     Output version information and exit
  GROUP_* FILE list   Group names defined in the parameters file

Output

The output may consist of two files, as below:

File ClusterInfo.csv

This file has, in each line, the following fields:

Order Field
1 Cluster
2 Fename
3 Spectrum Index
4 Scan
5 Parent Mass
6 Parent Charge
7 Retention Time
8 Precursor Intensity

File cluster_summary.tsv

This file has, in each line, the following fields:

Order Field
1 Cluster index, 1 to numClusters
2 Number of spectra in cluster
3 Cluster Spectrum::parentMass
4 Cluster Spectrum::precursorCharge
5 Cluster (Spectrum::parentMass + Spectrum::precursorCharge -1) / Spectrum::precursorCharge
6 Summed Spectrum::precursor_intensity for all spectra in the cluster
7 Group 1 contents
8 Group 2 contents
... Group n contents
Variable groups columns

The number of groups columns, as well as the groups names, is read from the the a parameters file defined via the --p option, as below:

GROUP_MY_GROUP=file1;file2;file3
GROUP_SYNC=file4;file5
GROUP_OTHER=file6

In this example, 3 groups are defined, and their names are MY_GROUP, SYNC and OTHER. Each groups defines a group of input files, and the results reflect the number of spectra that belong to which groups, according to the files they come from.

The variable groups section is displayed according to the contents of a used parameters file.

Usage example:

./clusterInfo --p parameterFile.txt  --outfile outputFileName.txt --out-summary-file mySummaryFile.txt  --cluster-spectra specs_ms.pklbin

Known issues

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