ubuntu2004
.TH statistics_calculation 1 "29 November 2021" .SH NAME the ion statistics calculator \- Several modes to calculate some statistics for the output from task3. .SH SYNOPSIS \fBthe ion statistics calculator\fP \fI-filename\fP [ -i ] [ -a ] [ -w ] [ -s ] [ -m ] .SH DESCRIPTION \fBthe ion statistics calculator\fP can calculate the number of peptides within a user-defined range using a sliding window. It can find proteins with all unique m/z. It can also find a user-defined amino acid in the sequence with different patterns. .SS Options .TP \fBinputfile Name of the input file for statistics calculation. It is necessary for following operations. .TP \fBcreate_file Name of the output file for statistics calculation. It is necessary for following operations. .TP \fB-i --minimum mass to charge ratio range The minimum range of mass-to-charge of the found peptide fragments. 1000 is the default. .TP \fB-a --maximum mass to charge ratio range The maximum range of mass-to-charge of the found peptide fragments. 1500 is the default. .TP \fB-w --window size The size of the sliding window. 0.5 is the default. .TP \fB-s --step size The size of the step the sliding window slides, must be smaller than the size of the sliding window. 0.2 is the default. .TP \fB-m --match pattern The match pattern of the input amino acid with the sequence. "start with","contain" and "all" are options. Default is contain. .TP \fB-p --amino acid matches sequence The input amino acid for matching. Options are K, N, R, T, S, I, M, Q, H, P, L, E, D, A, G, V, Y, S, C, W, F, no. No is the default option, the function will not run. .SH FILES .TP \fC/home/Group07/group7_task4.py\fR .SH EXAMPLES .TP python3 task4.py dummy.pepmasses sequence1.txt -i 1100 -a 1400 -w 2 -s 1 -m start with -p K .TP .PP Read 'dummy.pepmasses' file, find and output peptides start with amino acid 'K' as well as with mass to charge ratio between 1100 and 1400. The window size is 2, it slides 1 each step to find peptides in the window. Output proteins consist of at least one peptide with unique mass to charge ratio. All output data will store in a file called "sequence1.txt". .TP python3 task4.py task_3_output.mass sequence.txt .TP .PP Read 'task_3_output.mass' file, find and output peptides with mass to charge ratio between 1000 and 1500. The window size is 0.5, it slides 0.2 each step to find peptides in the window. Output proteins consist of at least one peptide with unique mass to charge ratio.All output data will store in a file called "sequence.txt". .SH AUTHOR Liyue Chang