comparison MaxQuantProcessingScript.R @ 23:7560a4e80a1e draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 0c7ca054e77e042c8a584c9903073da064df7d8b
author eschen42
date Thu, 30 Jun 2022 16:15:57 +0000
parents 36f183e5e4ed
children 29775869faba
comparison
equal deleted inserted replaced
22:43f1fd0ff86b 23:7560a4e80a1e
84 vector() # keep track of phosphorylation positions in peptide 84 vector() # keep track of phosphorylation positions in peptide
85 score_diff <- "" 85 score_diff <- ""
86 for (chara in phosphoprobsequence) { 86 for (chara in phosphoprobsequence) {
87 # build peptide sequence 87 # build peptide sequence
88 if (!( 88 if (!(
89 chara == " " | 89 chara == " " ||
90 chara == "(" | 90 chara == "(" ||
91 chara == ")" | 91 chara == ")" ||
92 chara == "." | 92 chara == "." ||
93 chara == "-" | 93 chara == "-" ||
94 chara == "0" | 94 chara == "0" ||
95 chara == "1" | 95 chara == "1" ||
96 chara == "2" | 96 chara == "2" ||
97 chara == "3" | 97 chara == "3" ||
98 chara == "4" | 98 chara == "4" ||
99 chara == "5" | 99 chara == "5" ||
100 chara == "6" | 100 chara == "6" ||
101 chara == "7" | 101 chara == "7" ||
102 chara == "8" | 102 chara == "8" ||
103 chara == "9") 103 chara == "9")
104 ) { 104 ) {
105 phosphopeptide <- paste(phosphopeptide, chara, sep = "") 105 phosphopeptide <- paste(phosphopeptide, chara, sep = "")
106 counter <- counter + 1 106 counter <- counter + 1
107 } 107 }
108 # generate score_diff 108 # generate score_diff
109 if (chara == "-" | 109 if (chara == "-" ||
110 chara == "." | 110 chara == "." ||
111 chara == "0" | 111 chara == "0" ||
112 chara == "1" | 112 chara == "1" ||
113 chara == "2" | 113 chara == "2" ||
114 chara == "3" | 114 chara == "3" ||
115 chara == "4" | 115 chara == "4" ||
116 chara == "5" | 116 chara == "5" ||
117 chara == "6" | 117 chara == "6" ||
118 chara == "7" | 118 chara == "7" ||
119 chara == "8" | 119 chara == "8" ||
120 chara == "9" 120 chara == "9"
121 ) { 121 ) {
122 score_diff <- paste(score_diff, chara, sep = "") 122 score_diff <- paste(score_diff, chara, sep = "")
123 } 123 }
124 # evaluate score_diff 124 # evaluate score_diff
386 # --- 386 # ---
387 full_data <- 387 full_data <-
388 read.table( 388 read.table(
389 file = input_file_name, 389 file = input_file_name,
390 sep = "\t", 390 sep = "\t",
391 header = T, 391 header = TRUE,
392 quote = "" 392 quote = ""
393 ) 393 )
394 394
395 # Filter out contaminant rows and reverse rows 395 # Filter out contaminant rows and reverse rows
396 filtered_data <- subset(full_data, !grepl("CON__", Proteins)) 396 filtered_data <- subset(full_data, !grepl("CON__", Proteins))