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Danis102 / seqpac

seqpac - A Framework for small RNA analysis in R using Sequence-Based Counts
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PAC_mapper does not accept ref #17

Closed signeskog closed 3 years ago

signeskog commented 3 years ago

Running PAC_mapper throws

Error in file.exists(ref) : invalid 'file' argument

when using Biostrings to read in ref.

ref <- Biostrings::readDNAStringSet("C:/Users/sigsk47/Documents/PhD/R/Genomes/Drosophila_melanogaster/tRNA/tRNA.fa")

Running with file location instead, as

ref<-"C:/Users/sigsk47/Documents/PhD/R/Genomes/Drosophila_melanogaster/tRNA/tRNA.fa")

starts the reanno flow, but soon throws error message;

`map_tRNA <- PAC_mapper2(PAC_dn, ref=ref, mapper="reanno", threads=1, mismatches = 0, report_string = TRUE)

Reading reference from file ...

R internal mapping using the Rbowtie package was specified. This package uses bowtie version bowtie.exeversion1.2.2. If you need a newer version, please install Bowtie manually outside R and then use option type='external'.

|--- Mismatch 0 started at 09:19:04 |--- Bowtie mapping: |---> reference...

Error: '\U' used without hex digits in character string starting "'C:\U" `

Strangely, this does not happen in the normal reanno-flow. Adding double dash "\" instead of "/" does not fix this error.

Danis102 commented 3 years ago

Function has been updated and this issue is no longer valid.