[BioC] NuPoP cannot recognize my fasta file

[Jiping Wang]

Can you send me the DNA sequence file? so I can check into it.

On 8/1/14, 4:35 PM, "Catherine [guest]" <guest at bioconductor.org> wrote:

>Hi,
>Thank you in advance for any help.
>Here is my code and results
>> writeXStringSet(DNAcutout1.seq, "DNAcutout2.fa", append=FALSE,
>>compress=FALSE, compression_level=NA, format="fasta")
>and when I read it, it looks fine
>> readDNAStringSet(file="DNAcutout1.fa", format="fasta")
>  A DNAStringSet instance of length 3615
>       width seq                                        names
>  
>   [1]   831 TTTCGGCTGTTTAAGAGTCT...CGTCCACTCGTGTGATAGG chr2L:27661:28491
>   [2]   760 CCGCGCCAAGAACAACCGTT...AGTAATCATTACAAACTTT chr2L:28501:29260
>   [3]   610 TTAATACATAATATGTATGC...AAGCTTTCGAGAAAAGAAT chr2L:66591:67200
>   [4]   851 CCTCAAGCCCCCAAAATCCG...GGTCGAGCCTTGACGTTGA chr2L:90861:91711
>   [5]   570 AACGTTCGAAAAAGTAACAT...CTAAACTATTCCAAGCATT
>chr2L:160751:161320
>   ...   ... ...
>
>but when I use the NuPoP, it has errors, and I have no idea what went
>wrong.
>> library(NuPoP)
>> predNuPoP("DNAcutout1.fa", species=5, model=4)
>[1] "The input file is not in FASTA format, or contains characters other
>than A/a, C/c, G/g, T/t, N/n, stop!"
>> 
>
>
> -- output of sessionInfo():
>
>> sessionInfo()
>R version 3.1.0 (2014-04-10)
>Platform: x86_64-apple-darwin13.1.0 (64-bit)
>
>locale:
>[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
>attached base packages:
>[1] parallel  stats     graphics  grDevices utils     datasets
>[7] methods   base
>
>other attached packages:
>[1] NuPoP_1.14.1  
>[2] BSgenome.Dmelanogaster.UCSC.dm3_1.3.99
>[3] BSgenome_1.32.0
>[4] Biostrings_2.32.1
>[5] XVector_0.4.0 
>[6] GenomicRanges_1.16.3
>[7] GenomeInfoDb_1.0.2
>[8] IRanges_1.22.10
>[9] BiocGenerics_0.10.0
>[10] BiocInstaller_1.14.2
>[11] RSQLite_0.11.4
>[12] DBI_0.2-7    
>
>loaded via a namespace (and not attached):
>[1] bitops_1.0-6     Rsamtools_1.16.1 stats4_3.1.0
>[4] tools_3.1.0      zlibbioc_1.10.0
>
>--
>Sent via the guest posting facility at bioconductor.org.