Matteo MatteoLacki

## imputations.R
library("impute")

# simulating a matrix
peptideCnt = 1000
runsCnt = 6

expressions = matrix(
  data=rnorm(peptideCnt*runsCnt, mean=1000, sd=400),
  nrow=peptideCnt,
  ncol=runsCnt

## results.sage.for.ms2rescore.tsv
peptide	proteins	num_proteins	filename	scannr	precursor_id	frame_id	rank	label	expmass	calcmass	charge	peptide_len	missed_cleavages	isotope_error	precursor_ppm	precursor_signed_ppm	fragment_ppm	fragment_signed_ppm	hyperscore	delta_next	delta_best	ion_mobility	rt	aligned_rt	predicted_rt	delta_rt_model	matched_peaks	longest_b	longest_y	longest_y_pct	matched_intensity_pct	scored_candidates	poisson	sage_discriminant_score	posterior_error	spectrum_q	peptide_q	protein_q	ms1_intensity	ms2_intensity	longest_b_exp_mz	longest_y_exp_mz	longest_b_calc_mz	longest_y_calc_mz	matched_b_exp_mz	matched_y_exp_mz	matched_b_calc_mz	matched_y_calc_mz	MS1_ClusterID
HLHFTLVK	sp|P00489|PYGM_RABIT;sp|P06737|PYGL_HUMAN;sp|P11216|PYGB_HUMAN;sp|P11217|PYGM_HUMAN	4	mz_recalibrated@xgboost.mgf	"_.1796.1796.2 File:""G8027.d"", NativeID:""merged=8630 frame=8631 scanStart=794 scanEnd=821"", IonMobility:""0.7284"""	0	0	1	1	994.57874	993.576	3	8	0	1.00335	0.60733896	-0.60733896	0.365797	0.17182219	27.22087946471433	4.391146980615357	0.0	0.0	989

## sorted_merge_competition.py
import numpy as np


# holy settings
K = 100


# static sequences
sequences = [
    list(

## fedora36_afterinstallparty
# vim /etc/dnf/dnf.conf
# # speed optimizations
# fastestmirror=True
# max_parallel_downloads=10
# keepcache=True

sudo dnf install vim alacritty i3 byobu arandr flameshot arandr
sudo dnf copr enable kallepm/tuxedo-keyboard
sudo dnf install tuxedo-keyboard
sudo dnf install kallepm/tuxedo-control-center

## total_time_insured.py
"""
A single thread function to get the total amount of time spent being insured.
"""


def get_time_being_insured(intervals) -> float:
    """Get the time being insured"""

    events = []
    for start, end in intervals:

## syncFiles.py
"""All this is meant to work only on Windows."""
import os
from pathlib import Path
import subprocess
import sys
import time
import hashlib
import argparse
import logging

## punnett_rectangles.R
install.packages(c('data.table','IsoSpecR','ggplot2','ggthemes'))

library(data.table)
library(IsoSpecR)
library(ggplot2)
library(ggthemes)

isoDist = function(mol, P=.99, ...) as.data.table(IsoSpecify(molecule=mol, P, showCounts=1,...))
marginal = function(mol, cutoff, space=0) isoDist(mol, cutoff, algo=3)[order(prob, decreasing=TRUE)][,rprob:=prob/prob[1]][,R:=cumsum(rprob) + (0:(nrow(.SD)-1))*space][,L:=R-rprob ]

## Renauld.R
# hello Ute, long time no see.
library(LFQBench2)
library(data.table)
library(readxl)
library(stringr)
library(rstatix)
library(readr)
# reading in the report
R = read_wide_report('2019-107_115 Renauld remeasure_user designed 20200306-122426_quantification_report_UD_sent.xlsx',
                     skip=1, sheet="TOP3 quantification")

## ohelahela.R
# Comparing different executions of the same isoquant projects
# install.packages("igraph")
library(LFQBench2)
library(stringr)
library(igraph)
library(purrr)

is.error <- function(x) inherits(x, "try-error")
dp = "/mnt/ms/symphony/HELA_BENCHMARK/2020_02_18/REPEAT_WITH_SETTINGS_OF_TeslaS/"
comps = list.files(dp)

## sh.txt
C1526H2425N439O435S15
C508H799N129O167S4
C732H1196N204O243S4
C1093H1729N301O327S19
C560H905N175O145S4
C286H477N99O65S2
C2333H3644N608O630S26
C1907H2967N507O481S14
C145H272N64O28S3
C2114H3535N663O561S15
	library("impute")

	# simulating a matrix
	peptideCnt = 1000
	runsCnt = 6

	expressions = matrix(
	data=rnorm(peptideCnt*runsCnt, mean=1000, sd=400),
	nrow=peptideCnt,
	ncol=runsCnt
	import numpy as np


	# holy settings
	K = 100


	# static sequences
	sequences = [
	list(
	# vim /etc/dnf/dnf.conf
	# # speed optimizations
	# fastestmirror=True
	# max_parallel_downloads=10
	# keepcache=True

	sudo dnf install vim alacritty i3 byobu arandr flameshot arandr
	sudo dnf copr enable kallepm/tuxedo-keyboard
	sudo dnf install tuxedo-keyboard
	sudo dnf install kallepm/tuxedo-control-center
	"""
	A single thread function to get the total amount of time spent being insured.
	"""


	def get_time_being_insured(intervals) -> float:
	"""Get the time being insured"""

	events = []
	for start, end in intervals:
	"""All this is meant to work only on Windows."""
	import os
	from pathlib import Path
	import subprocess
	import sys
	import time
	import hashlib
	import argparse
	import logging
	install.packages(c('data.table','IsoSpecR','ggplot2','ggthemes'))

	library(data.table)
	library(IsoSpecR)
	library(ggplot2)
	library(ggthemes)

	isoDist = function(mol, P=.99, ...) as.data.table(IsoSpecify(molecule=mol, P, showCounts=1,...))
	marginal = function(mol, cutoff, space=0) isoDist(mol, cutoff, algo=3)[order(prob, decreasing=TRUE)][,rprob:=prob/prob[1]][,R:=cumsum(rprob) + (0:(nrow(.SD)-1))*space][,L:=R-rprob ]
	# hello Ute, long time no see.
	library(LFQBench2)
	library(data.table)
	library(readxl)
	library(stringr)
	library(rstatix)
	library(readr)
	# reading in the report
	R = read_wide_report('2019-107_115 Renauld remeasure_user designed 20200306-122426_quantification_report_UD_sent.xlsx',
	skip=1, sheet="TOP3 quantification")
	# Comparing different executions of the same isoquant projects
	# install.packages("igraph")
	library(LFQBench2)
	library(stringr)
	library(igraph)
	library(purrr)

	is.error <- function(x) inherits(x, "try-error")
	dp = "/mnt/ms/symphony/HELA_BENCHMARK/2020_02_18/REPEAT_WITH_SETTINGS_OF_TeslaS/"
	comps = list.files(dp)
	C1526H2425N439O435S15
	C508H799N129O167S4
	C732H1196N204O243S4
	C1093H1729N301O327S19
	C560H905N175O145S4
	C286H477N99O65S2
	C2333H3644N608O630S26
	C1907H2967N507O481S14
	C145H272N64O28S3
	C2114H3535N663O561S15