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Type 'q()' to quit R. > #!/usr/bin/Rscript > > abi=readLines("/var/www/cgi-bin/hgcrap/abi.txt") > > library(sangerseqR) > > hetab1 <- read.abif(abi) > > str(hetab1, list.len = 20) Formal class 'abif' [package "sangerseqR"] with 3 slots ..@ header :Formal class 'abifHeader' [package "sangerseqR"] with 9 slots .. .. ..@ abif : chr "ABIF" .. .. ..@ version : int 101 .. .. ..@ name : raw [1:4] 74 64 69 72 .. .. ..@ number : int 1 .. .. ..@ elementtype: int 1023 .. .. ..@ elementsize: int 28 .. .. ..@ numelements: int 125 .. .. ..@ dataoffset : int 299378 .. .. ..@ datahandle : int 0 ..@ directory:Formal class 'abifDirectory' [package "sangerseqR"] with 7 slots .. .. ..@ name : chr [1:125] "AEPt" "AEPt" "APFN" "APXV" ... .. .. ..@ tagnumber : int [1:125] 1 2 2 1 1 1 1 1 1 1 ... .. .. ..@ elementtype: int [1:125] 4 4 18 19 19 19 2 5 4 4 ... .. .. ..@ elementsize: int [1:125] 2 2 1 1 1 1 1 4 2 2 ... .. .. ..@ numelements: int [1:125] 1 1 11 2 11 2 4501 1 1 1 ... .. .. ..@ datasize : int [1:125] 2 2 11 2 11 2 4501 4 2 2 ... .. .. ..@ dataoffset : int [1:125] 1048313856 1048313856 148553 838860800 288857 822083584 288868 0 65536 141426688 ... ..@ data :List of 125 .. ..$ AEPt.1 : int 15996 .. ..$ AEPt.2 : int 15996 .. ..$ APFN.2 : chr "SEQBDTV3.1" .. ..$ APXV.1 : chr "2" .. ..$ APrN.1 : chr "SEQBDTV3.1" .. ..$ APrV.1 : chr "1" .. ..$ APrX.1 : chr "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?><AnalysisProtocolContainer doAnalysis=\"true\" name=\"SEQBDTV3.1\""| __truncated__ .. ..$ ARTN.1 : int 0 .. ..$ ASPF.1 : int 1 .. ..$ ASPt.1 : int 2158 .. ..$ ASPt.2 : int 2158 .. ..$ AUDT.1 : int [1:1400] 111 35 57 58 56 88 89 43 56 85 ... .. ..$ B1Pt.1 : int 2135 .. ..$ B1Pt.2 : int 2135 .. ..$ BCTS.1 : chr "2017-04-10 11:45:30 +05:30" .. ..$ CTID.1 : chr "SEQ29_3_2017" .. ..$ CTNM.1 : chr "SEQ29_3_2017" .. ..$ CTOw.1 : chr "ABI" .. ..$ CTTL.1 : chr "Comment:" .. ..$ CpEP.1 : chr "" .. .. [list output truncated] > > homosangerseq <- sangerseq(hetab1) > > str(homosangerseq) Formal class 'sangerseq' [package "sangerseqR"] with 7 slots ..@ primarySeqID : chr "From ab1 file" ..@ primarySeq :Formal class 'DNAString' [package "Biostrings"] with 5 slots .. .. ..@ shared :Formal class 'SharedRaw' [package "XVector"] with 2 slots .. .. .. .. ..@ xp :<externalptr> .. .. .. .. ..@ .link_to_cached_object:<environment: 0x66d0408> .. .. ..@ offset : int 0 .. .. ..@ length : int 402 .. .. ..@ elementMetadata: NULL .. .. ..@ metadata : list() ..@ secondarySeqID: chr "From ab1 file" ..@ secondarySeq :Formal class 'DNAString' [package "Biostrings"] with 5 slots .. .. ..@ shared :Formal class 'SharedRaw' [package "XVector"] with 2 slots .. .. .. .. ..@ xp :<externalptr> .. .. .. .. ..@ .link_to_cached_object:<environment: 0x66d0408> .. .. ..@ offset : int 0 .. .. ..@ length : int 402 .. .. ..@ elementMetadata: NULL .. .. ..@ metadata : list() ..@ traceMatrix : int [1:15335, 1:4] 40 41 42 44 47 49 51 53 53 55 ... ..@ peakPosMatrix : num [1:402, 1:4] 5 26 33 47 64 86 99 112 137 153 ... ..@ peakAmpMatrix : int [1:402, 1:4] 75 156 176 244 68 293 157 128 576 535 ... > > Seq1=primarySeq(homosangerseq) > > reverseComplement(Seq1) 402-letter "DNAString" instance seq: AAAAAAAAAAAAAAGGGTTCCCCCCCAAATTTTTTT...CCCGCGCGTACCAACTCACCAAACAACCGTACTAAC > > primarySeq(homosangerseq, string = TRUE) [1] "GTTAGTACGGTTGTTTGGTGAGTTGGTACGCGCGGGAACGTGTGGGTGCGCGTTTTGCGGGTTTTTGTCGGGTTGATTTTTAGTTTGTGTCGCGGGCGTGTATGAGCGGAAGGCGTTCGGCGGTTTTGTTTGGTCGCGAGTGTGCGCGCGCGGGGTTTCGGGTCGGCGTGTACGTCGGTGTGAGTGCGAGTGCGAGTGAGTGTGGCGTCGCGGGGGTTTTTTCGTTTCGCGTCGTTCGCGTAATTCGTATATTTATTTTGTTTGGATGTTGTCGAATGACGCCCCCTCCGGTTCCCCACTTTTTACAACCCCAGTTTAAATTTCGCTCGGCCCCCTCGAAACCCGGCCAAATAAACCATTACCTAAAAAAAAATTTGGGGGGGAACCCTTTTTTTTTTTTTT" > > chromatogram(homosangerseq, width = 50, height = 2, trim5 = 50, trim3 = 100, showcalls = "both",filename = "/var/www/cgi-bin/hgcrap/chromatogram_homo.pdf") Chromatogram saved to /var/www/cgi-bin/hgcrap/chromatogram_homo.pdf in the current working directory> > hetcalls <- makeBaseCalls(homosangerseq, ratio = 0.33) > > chromatogram(hetcalls, width = 50, height = 2,showcalls = "both",filename = "/var/www/cgi-bin/hgcrap/chromatogram_hetero.pdf") Chromatogram saved to /var/www/cgi-bin/hgcrap/chromatogram_hetero.pdf in the current working directory> > #chromatogram(hetcalls, width = 50, height = 2,showcalls = "both",filename = "chromatogram_hetero.pdf") > dev.off() null device 1 > dev.off()
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/var/www/cgi-bin/demo/hgcrap/abi_dir//file.ab1