Collapse a list of DNAstringsets into a single DNAStingset in order to apply writeXStringSet() and turn it into fasta file in R -
Use of R for Bioinformatics here: I have a list of DNAstringsSets (seen below) and want to use the write string (Stringset) function which is a FASTA file as any command.Anyone knows how to make a single DNAStringset A DNAstringset takes the object as an argument to save the list of DNAstringsets in the object and can be used as an argument?
$ NM_008866 say a DNAStringSet length 13 width seq name [1] 693 ATGTGCGGCAACAACATGTCCGCTCCGA ... GATAAGCTCCTACCTCCAATTGATTGA NM_008866 [2] 72 ATGGATGGGCAGAAGCCTTTGCAGGTAT ... AATACATCTGTCCACATGCCCCTGTGA NM_008866 [3] 114 ATGGGCAGAAGCCTTTGCAGGTATCAAA ... GAATATGGCTATGCCTTCTTGGTTTGA Nm_008866 [4] 213 ATGGCATTCCTTCTAACAGGATTATTTT ... Agtgktgggttgtgakstttg Nm_008866 [5] 63 ATGTCAAGCACTTCATTGATAAGCTCCT ... Ttgttgktkataggcsattga Nm_008866 ... ... ... ... 9 9 21 ATGGCCCTTCTATTGGGAGACCAGGCTT ... Kgggkggsggtktktgtkatg Nm_008866 [10] 144 ATGTTATGCTTAAAACCAAATACTGTTC ... CAGTCTCCTGTACAAATATT AAAATAA NM_008866 [11] 78 ATGTTGCAAAAATTATGGTTATTTCTGA ... CCAACCAACCAAGAAGCACCTTTATAA NM_008866 [12] 75 ATGGTTATTTCTGAACGGTTGCTTTTCT ... AGAAGCACCTTTATAAACAGGTGCTAA NM_008866 [13] 90 ATGTCTGGATTTAAAACAATTTCAAACA ... AATTTACTTCAGTTATTCTATCTGTAA $ NM_001159750 a DNAStringSet length 9 width seq right [1] 903 ATGGAGGACGAGGTGGTTCGCATTGCCA example ... ATGTGGAAATCGGTGGAAGTTCTGTTGA NM_001159750 [2] 105 ATGGACCATCAACTGATAAAGACCCTGA ... AGAGAAGAAAGTTCCAGCAGCAATGTAA NM_001159750 [3] 75 ATGAGACAAATGCTCGAGATACATATGT ... CCAAGCACTTCTGATTCTGTGCGATTAA NM_001159750 [4] 75 ATGATTATGTTGCAATTGGAGCTGATGA ... ATTGAGGAAGCTATATATCAAGAAATAA NM_001159750 [5] 129 ATGAATGTGGAAATCGGTGGAAGTTCTG ... GCCAGGCAACTCGTTTCCTTGCAAGTGA NM_001159750 [6] 63 ATGTGGAAATCGGTGGAAGTTCTGTTGA ... AGAATTGGCAAAGTATCTGGACCATTAA NM_001159750 [7] 102 ATGTGTCCCACTTGTTTTGCTAGTAATA ... TATAGTAAAGGCCACTTTTATAAATTAA NM_001159750 [8] 102 ATGGAAAACAATATGTCCATGTTAAAAG ... CGGGAGGCAGAGGCAGGCGGATTTCTGA NM_001159750 [9] 75 ATGGATAATTTCTGTCACTTTAAAAATA ... TAGTTTAAAAGT length AATAAGGTTAAAATAG NM_00ll59750 9 width seq names $ NM_011541 Example of a DNAStringSet [1] 906 ATGGAGGACGAGGTGGTTCGCATTGCCA ... ATGTGGAAATCGGTGGAAGTTCTGTTGA NM_011541 [2] 108 ATGGACCATCAACT Gtagakstga ... Gagaagtagttkgkgkttgta Nm_0ll54l [3] 75 ATGAGACAAATGCTCGAGATACATATGT ... Ksagkkttktgttktgtgkgtta Nm_0ll54l [4] 75 ATGATTATGTTGCAATTGGAGCTGATGA .. Kattgggagkttttkagata Nm_0ll54l [5] 129 ATGAATGTGGAAATCGGTGGAAGTTCTG ... Gkggsaktkgtttkkttgkagtga Nm_0ll54l [6] 63 ATGTGGAAATCGGTGGAAGTTCTGTTGA ... Agattggkyaagttktggktta Nm_0ll54l [7] 102 Atgtgtkkkttgttttgstagtata ... Ttgtaaggkkttttttttttta Nm_0ll54l [8] 102 ATGGAAAACAATATGTCCATGTTAAAAG ... Kgggggkgggkyaggkggtttktga Nm_0ll54l [9] 75 ATGGATAATTTCTGTCACTTTAAAAATA .. Ktgtttaagtataaggttaatag Nm_0ll54l
Very little copy example. The interesting thing is that it will not work if every element of the list has a name (i.e. it returns the same list). Make sure name (dna_list) & lt; - NULL . I'm unsure about the specific reason for this, maybe someone else can know and would like to comment is required (Biostrings) x0 & lt; -. DNAStringSet (c ("CTCCCAGTAT", "TTCCCGA", "TACCTAGAG")) x 1 & lt; - DNAStringSet (c ("AGGTCGT", "GTCAGTGGTCCCC", "CATTTTAGG")) x2 & lt; - DNAStringSet (c ("TGCTAGCTA", "AGTCTTGC", "AGCTTTCGAG")) dna_list & lt; - List (x0, x1, x2) & gt; Dna_list [[1]] A DNAStringSet example of length 3 width seq [1] 10 CTCCCAGTAT [2] 7 TTCCCGA [3] 9 TACCTAGAG [2]] A DNAStringSet example of length 3 width seq [1] 7 AGGTCGT [2] 13 GTCAGTGGTCCCC [3] 9 CATTTTAGG [[3]] A DNAStringSet example of length 3 width seq [1] 9 TGCTAGCTA [2] 8 AGTCTTGC [3] 10 AGCTTTCGAG do.call (c, dna_list) & gt; Do.call (c, dna_list) length 9 width seq [1] 10 CTCCCAGTAT [2] 7 TTCCCGA [3] 9 TACCTAGAG [4] 7 AGGTCGT [5] 13 GTCAGTGGTCCCC [6] 9 CATTTTAGG [7] A DNAStringSet example of 9 TGTAGCTA [8] 8 AGTTTGCC [9] 10 AGCTTTCGAG
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