Mercurial > repos > davidvanzessen > shm_csr

comparison merge_and_filter.r @ 93:8fcf31272f6e draft

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planemo upload commit a43893724cc769bed8a1f19a5b19ec1ba20cb63c
author rhpvorderman
date Mon, 06 Mar 2023 11:36:32 +0000
parents 729738462297
children 385dea3c6cb5
comparison
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92:cf8ad181628f 93:8fcf31272f6e
161 161
162 if(!all(higher_than, na.rm=T)){ #check for no unmatched 162 if(!all(higher_than, na.rm=T)){ #check for no unmatched
163 result[!higher_than,"best_match"] = paste("unmatched,", result[!higher_than,"best_match"]) 163 result[!higher_than,"best_match"] = paste("unmatched,", result[!higher_than,"best_match"])
164 } 164 }
165 165
166 if(class.filter == "101_101"){ 166 if(splt[1] == "101" & splt[2] == "101"){
167 result$best_match = "all" 167 result$best_match = splt[3]
168 } 168 }
169 169
170 write.table(x=result, file=gsub("merged.txt$", "before_filters.txt", output), sep="\t",quote=F,row.names=F,col.names=T) 170 write.table(x=result, file=gsub("merged.txt$", "before_filters.txt", output), sep="\t",quote=F,row.names=F,col.names=T)
171 171
172 print(paste("Number of empty CDR1 sequences:", sum(result$CDR1.IMGT.seq == "", na.rm=T))) 172 print(paste("Number of empty CDR1 sequences:", sum(result$CDR1.IMGT.seq == "", na.rm=T)))