Is there any way that I can read SCF file in python like in R using sangerseqR, I have tried with Biopython, it seems it does not support this format.
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$\begingroup$ You could try converting it to ABI format as asked in this question and then import that $\endgroup$– Jan WilamowskiCommented Aug 25, 2021 at 4:56
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$\begingroup$ Alternatively, bioconvert supports conversion of SCF to FASTA and FASTQ formats. $\endgroup$– Jan WilamowskiCommented Aug 25, 2021 at 5:00
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$\begingroup$ Conversion to SCF to FASTA and FASTQ formats will not help me since I need the chromatography data not just the seq $\endgroup$– alex3465Commented Aug 25, 2021 at 11:22
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1 Answer
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It was done using sangerseqR with rpy2 in python
import rpy2.robjects as r
from rpy2.robjects.packages import importr
utils = importr('utils')
utils.install_packages('sangerseqR', repos="https://git.bioconductor.org/packages/sangerseqR")
utils.chooseBioCmirror(ind=1) # select the first mirror in the list
utils.install_packages('sangerseqR')
sangerseqR = importr('sangerseqR')
Trace = sangerseqR.readsangerseq( file="1I1_F_P1815443_047.scf") #scf sequence file is now loaded