Question

我有这个DNA字符串集，但是我想创建一个包含此信息的新file.fa。保存这些的有效方法是什么？我尝试使用write.fasta但它崩溃了。

genes_seq <- 
  A DNAStringSet instance of length 254667
       width seq                                                                    names               
   [1]  2298 ATGGTGTCGTCTCCTTTCTATGTGAACAAGTTCA...AAAAAAATCAAAAACAAATCAAAAATCAAAAAA 22
   [2]  2600 CTGACATAGATAAGTTTAGAGTTACCTCCCCTGT...GATACATACACATATATATCCATGTAAGATAGA 22
   [3]  1351 ACACATTTATATATATTTATAAATATCAATAAAT...CGCATGTGTGTGTATGAGAGAGAGAGAGAGAGC 22
   [4]  3668 TTGTTGATCAGCAGTAATGGTAAGGAAGTTAGTA...CACGAAATCATTGGGTTATTTTTTATACCAGTA 22
   [5]   762 ATGACCATCTTTGGGGCAGAATCCACTTTTCATC...TCATTGGTCAGTTTTATTAAAGGCAGCATTTAA 22
   ...   ... ...
[2544]   558 CTAGATCCTTCTCCTGCTGTTATCAAAAGTAGAC...ACTGATGTAATACTGCAATTAAACATGATAGCA 22
[2545]  1319 TTGAAAATGAATTATAGAAATGTCTTTTTCACGA...ACTTGCACTAAAACATTTAGCAATTTGGTTAGC 22
[2546]  1365 GTATTTTGTTTCAAATGTACAAGCTTGGACAACA...GACTGCATGCATTTACATTTATGTAAATACAAA 22
[2547]  1970 CAGAATACCAGAAACAGCGAAGAATTTTTCACAT...GAAATATATATGTGTGTGTATATATAAATAAAT 22
[2548]   260 TTTATTTTTATTCAAAAGACATGGACATTAAAGG...TCTACAGCTTTGCATTATGCTGTGACGGGGTAA OCBIM_22024624mg
>

Answer 1

解决方案来自https://bioinformatics.stackexchange.com/questions/3538/combine-fastq-by-writefastq-is-not-working-properly

# Non reproducible example
library(ShortRead)
library(Biostrings)

head(fasta)
 # A DNAStringSet instance of length 6
# width seq                                                                                                                                                                                   names                                                                                                                                                                                                    
# [1]  1786 GGGGAGCCCGCAGAATTCGGAAAAAATCGTACGCTAAGGTTTTCCGGGCATCCGTAAGGGCCGAAACTTCCCGTCTTCCAGTCTGCG...GGTGCATCGGCCGGCACCTTGCGCAGGTTGTCGGCGTTCATCTCACGCAGGGTCTGCACGGCTGCCAGCACGCCTTGCGCGGCCGGC NODE_108_length_1...
# [2]   590 GGTCAGCCAGGATTTCACTTTCCAGCCGGTCGAGCATCTGCACCAGCACCGGCGGGAACACCACACTGCCACCGTCTTCGCCGCCGG...TGACGGTCATACCGGTAAAGATAGTGCGCGTCACGGGCGATACGGTTATCCGGCCACATGCTGAGGGTGCTGTCCGGGTGCAGCTCC NODE_145_length_5...
# [3]  2618 CTCTCCCGCACCTACAGCAGTTACCGGACAAAAACGCCCGCGCCGGTGGGGAGCCTCGGCCCCGGCTGGAAAATGCCTGCGGATATC...GGACAGCACCCTCAGCATGTGGCCGGATAACCGTATCGCCCGTGACGCGCACTATCTTTACCGGTATGACCGTCACGGCAGGCTGAC NODE_96_length_26...
# [4]   446 CTGCTGTGCTGTTTTGGTCCATCGGTGCCGCATACATGCCCGATACAGCCGCGGCACCCAGCCAGCCCACAGGGTTCCACCATGCCA...AAATCCCCGTAAAGGCAGATGCGTGCCATGCCCGGTGACGCCAGAGGGAGTGTGTGCGTCGCTGCCATTTGTCGGTGTACCTCTCTC NODE_192_length_4...
# [5]   235 CCCCTGCAGCGGGTCATAATAGCGGTGGCGGTTGTAATACAGGCCGGACTCCTCATCATACTGCTGCCCCGGCAGGCGGATAAGCTG...CACGCTGTTGCCCCTTCCGTGCTGATAAGCGCCAGCGGCAGGCCGCGATGGTCGCAGTGGTACAGGTGGATTTTTCGCGCCGGCGTG NODE_556_length_2...
# [6]   650 CCCTGCCAGGTGTACTGCAGTTGTGGCTCCAGCATCAGGTTGTCAGTGATACTGAAGGGCAGACCGGTTTCCAGTGAGCCCAGCCAG...ACGATAAGCATTTTCACTGCGCAGGTACCAGTCTTCATCGCTGTCACGGTTCAGGGTGTAGTTAAAGGCGCCGGCCTGAAGCGGGCG NODE_137_length_6...

fasta_dir <- file.path(getwd(), "refs")
outfile <- file.path(dirname(fasta_dir), "seq_fasta.fasta")
writeFasta(fasta, outfile, mode = "a")

从字符串集创建和保存fasta文件

1 个答案: