时间戳

首页 > 解决方案 > finding each pattern ina set of sequences

r - finding each pattern ina set of sequences

问题描述

I am trying to find a pattern in a set of sequences. What i am trying to do is that first take the 1st sequence of the pattern and match it with all subjects one by one and give an output (p1 vs s1,p1 vs s2, p1 vs s3, p1 vs s4), then take the 2nd pattern and match with all subjects (p2 vs s1, p2 vs s2, p2 vs s3,p2 vs s4) and so on i.e. in an iterative way. The input (pattern and subjects) are DNAstringSet instance (Biostrings).

I have used the function

mat=nucleotideSubstitutionMatrix(match=2,mismatch = -3,baseOnly = TRUE)
localAlign=pairwiseAlignment(pattern,subject,type="local",
                             substitutionMatrix=mat,
                             gapOpening=-5, gapExtension=-2)

But this way it actually matches p1 vs s1, p2 vs s2, p3 vs s3 nd p4 vs s4

Example:

input:pattern

A DNAStringSet instance of length 734
      width seq                                                                         names               
  [1]  1000 GGTAAGAGTTTCTTAACAGATCTCAACATTTGCTATATAC...AGATTATTTGTCCTTTGAGATAAAATTACCAC P1 
  [2]  1000 TGTAAGTAATACTTAATGGTAATTTTTGTTTTCTCTTTCA...AGAAGCAAGGAGACCCGTTAGAGGAAGCATCC P2
  [3]  1000 GGTGAGTGTATGATTGATAACTAATCTCTTAGATTAACCA...CATGATATGAAATGGTTCCTAAAGATCCAGAC P3
  [4]  1000 GGTGAGCAAAATCAAGCAATGCATTGTTTGTTTTGGAGGG...CTATTTATGTACTACCTTTTTTTTTTAGAAAA P4

input: subject

A DNAStringSet instance of length 1000
       width seq                                                                        names               
   [1]  1000 GTAGGTACCTGGGAATTCACAAATTAAGACTTTTGAATA...TTCTTATTCAACCGTAGTAACATTAGATGAATA S1
   [2]  1000 GTGAGCGCTGCTGCCCAAGCCGCCTGGCTATGCTCGATT...AGATGGCCTTTTCTCTCAGCCCACTGTGACCTA S2
   [3]  1000 GTAAGTACAGGCTGAAAGTTACATGCTCTCCAAGGGTGA...ACATAGTAATGAATAGACTTTCAGACACAGCAT S3
   [4]  1000 GTAAGTTGCTTGTTTCTTAAATGTTAGGATCTATTACTT...AACAATATAGGTAAGTCTAGCCCTCAAGGCGCT S4

标签： rloopspattern-matching

解决方案

如果我正确理解了你的问题，那么你可以试试这个。

library(dplyr)

df <- pattern_df %>%
  left_join(subject_df, "seq") %>%
  group_by(width.x, seq, names.x) %>%
  summarise(subject_names = paste(names.y, collapse=",")) %>%
  `colnames<-`(c("width", "seq", "names", "subject_names"))

输出是：

> df
  width seq                                                                         names subject_names     
1  1000 GGTAAGAGTTTCTTAACAGATCTCAACATTTGCTATATAC...AGATTATTTGTCCTTTGAGATAAAATTACCAC P1    NA           
2  1000 GGTGAGCAAAATCAAGCAATGCATTGTTTGTTTTGGAGGG...CTATTTATGTACTACCTTTTTTTTTTAGAAAA P4    S5,S6        
3  1000 GGTGAGTGTATGATTGATAACTAATCTCTTAGATTAACCA...CATGATATGAAATGGTTCCTAAAGATCCAGAC P3    NA           
4  1000 TGTAAGTAATACTTAATGGTAATTTTTGTTTTCTCTTTCA...AGAAGCAAGGAGACCCGTTAGAGGAAGCATCC P2    NA

示例数据：（ 请注意，我在末尾添加了两行subject_df）

pattern_df <- structure(list(width = c(1000L, 1000L, 1000L, 1000L), seq = c("GGTAAGAGTTTCTTAACAGATCTCAACATTTGCTATATAC...AGATTATTTGTCCTTTGAGATAAAATTACCAC", 
"TGTAAGTAATACTTAATGGTAATTTTTGTTTTCTCTTTCA...AGAAGCAAGGAGACCCGTTAGAGGAAGCATCC", 
"GGTGAGTGTATGATTGATAACTAATCTCTTAGATTAACCA...CATGATATGAAATGGTTCCTAAAGATCCAGAC", 
"GGTGAGCAAAATCAAGCAATGCATTGTTTGTTTTGGAGGG...CTATTTATGTACTACCTTTTTTTTTTAGAAAA"
), names = c("P1", "P2", "P3", "P4")), .Names = c("width", "seq", 
"names"), class = "data.frame", row.names = c(NA, -4L))
#  width                                                                         seq names
#1  1000 GGTAAGAGTTTCTTAACAGATCTCAACATTTGCTATATAC...AGATTATTTGTCCTTTGAGATAAAATTACCAC    P1
#2  1000 TGTAAGTAATACTTAATGGTAATTTTTGTTTTCTCTTTCA...AGAAGCAAGGAGACCCGTTAGAGGAAGCATCC    P2
#3  1000 GGTGAGTGTATGATTGATAACTAATCTCTTAGATTAACCA...CATGATATGAAATGGTTCCTAAAGATCCAGAC    P3
#4  1000 GGTGAGCAAAATCAAGCAATGCATTGTTTGTTTTGGAGGG...CTATTTATGTACTACCTTTTTTTTTTAGAAAA    P4


subject_df <- structure(list(width = c(1000L, 1000L, 1000L, 1000L, 1000L, 1000L
), seq = c("GTAGGTACCTGGGAATTCACAAATTAAGACTTTTGAATA...TTCTTATTCAACCGTAGTAACATTAGATGAATA", 
"GTGAGCGCTGCTGCCCAAGCCGCCTGGCTATGCTCGATT...AGATGGCCTTTTCTCTCAGCCCACTGTGACCTA", 
"GTAAGTACAGGCTGAAAGTTACATGCTCTCCAAGGGTGA...ACATAGTAATGAATAGACTTTCAGACACAGCAT", 
"GTAAGTTGCTTGTTTCTTAAATGTTAGGATCTATTACTT...AACAATATAGGTAAGTCTAGCCCTCAAGGCGCT", 
"GGTGAGCAAAATCAAGCAATGCATTGTTTGTTTTGGAGGG...CTATTTATGTACTACCTTTTTTTTTTAGAAAA", 
"GGTGAGCAAAATCAAGCAATGCATTGTTTGTTTTGGAGGG...CTATTTATGTACTACCTTTTTTTTTTAGAAAA"
), names = c("S1", "S2", "S3", "S4", "S5", "S6")), .Names = c("width", 
"seq", "names"), class = "data.frame", row.names = c(NA, -6L))
#  width                                                                         seq names
#1  1000 GTAGGTACCTGGGAATTCACAAATTAAGACTTTTGAATA...TTCTTATTCAACCGTAGTAACATTAGATGAATA    S1
#2  1000 GTGAGCGCTGCTGCCCAAGCCGCCTGGCTATGCTCGATT...AGATGGCCTTTTCTCTCAGCCCACTGTGACCTA    S2
#3  1000 GTAAGTACAGGCTGAAAGTTACATGCTCTCCAAGGGTGA...ACATAGTAATGAATAGACTTTCAGACACAGCAT    S3
#4  1000 GTAAGTTGCTTGTTTCTTAAATGTTAGGATCTATTACTT...AACAATATAGGTAAGTCTAGCCCTCAAGGCGCT    S4
#5  1000 GGTGAGCAAAATCAAGCAATGCATTGTTTGTTTTGGAGGG...CTATTTATGTACTACCTTTTTTTTTTAGAAAA    S5
#6  1000 GGTGAGCAAAATCAAGCAATGCATTGTTTGTTTTGGAGGG...CTATTTATGTACTACCTTTTTTTTTTAGAAAA    S6

推荐阅读