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larssnip / micropan

R package for microbial pangenomics
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tutorial error #5

Closed am821 closed 4 years ago

am821 commented 4 years ago

Hi, following the tutorial I encountered this error and am wondering how to fix it? Thanks for(i in 1:nrow(gnm.tbl)){

larssnip commented 4 years ago

Hi,

I am not capable of reproducing this error, but it could be due to an error in the readFasta-function of the microseq package. This has been corrected, and has been uploaded to CRAN, but it takes some days before it is available. I enclose the latest version of both packages here, but they will soon be available on CRAN as well. Please let me know if this helps.

LS

From: am821 notifications@github.com Sent: torsdag 4. juni 2020 01:45 To: larssnip/micropan micropan@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [larssnip/micropan] tutorial error (#5)

Hi, following the tutorial I encountered this error and am wondering how to fix it? Thanks for(i in 1:nrow(gnm.tbl)){

· gnm.tbl$GID.tag[i],

*

· file.path("faa", str_c(gnm.tbl$GenBank_ID[i], ".faa")))

*

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am821 commented 4 years ago

Thank you for the swift reply! sorry where are the latest versions of both packages enclosed? Thank you!

larssnip commented 4 years ago

Well, I tried to attach them but since they are tar archives they may have been discarded by the spam filter.

You can install from GitHub. First, make certain you have the devtools package installed (from CRAN). Then

devtools::install_github("larssnip/microseq")

…should do the trick. Then repeat it for micropan.

LS

From: am821 notifications@github.com Sent: torsdag 4. juni 2020 12:55 To: larssnip/micropan micropan@noreply.github.com Cc: Lars-Gustav Snipen lars.snipen@nmbu.no; Comment comment@noreply.github.com Subject: Re: [larssnip/micropan] tutorial error (#5)

Thank you for the swift reply! sorry where are the latest versions of both packages enclosed? Thank you!

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am821 commented 4 years ago

Still not working and I think the issue might actually be earlier in the code

for(i in 1:nrow(gnm.tbl)){ genome <- readFasta(file.path("rawdata", str_c(gnm.tbl$GenBank_ID[i], "_genomic.fna"))) # for use below findGenes(file.path("rawdata", str_c(gnm.tbl$GenBank_ID[i], "_genomic.fna"))) %>% filter(Score > 40) %>% gff2fasta(genome) %>% mutate(Sequence = translate(Sequence)) %>% writeFasta(file.path("tmp", str_c(gnm.tbl$GenBank_ID[i], ".faa"))) } ive attached the outputs from this command as images thanks again! Screenshot from 2020-06-04 13-06-16 Screenshot from 2020-06-04 13-06-42

am821 commented 4 years ago

Nevermind it is working now thank you for the help!

larssnip commented 4 years ago

OK, nice. I could see from the Viewer of the genome that the > at the start of the FASTA Header-lines is present, which was the error in microseq I mentioned. With the newest version of microseq this should not be there…(silly error introduced in the previous version)

LS

From: am821 notifications@github.com Sent: torsdag 4. juni 2020 14:26 To: larssnip/micropan micropan@noreply.github.com Cc: Lars-Gustav Snipen lars.snipen@nmbu.no; Comment comment@noreply.github.com Subject: Re: [larssnip/micropan] tutorial error (#5)

Nevermind it is working now thank you for the help!

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