Trailing Slash for samples

[JFsanchezherrero]

Dear mirtop developers,
I have noticed a bug in the last version of mirtop (0.3.17) when dealing with back slashes.

I run mirtop gff conversion from sRNAbench data.

mirtop gff --sps hsa --hairpin ../sRNAtoolboxDB/libs/hairpin.fa --gtf ../hsa.gff3 --format srnabench -vd -o test1 isomiR_sRNAbenchtoolbox/sample_1/

I noticed that if I leave the backslash for the folder from sRNAbench data ( isomiR_sRNAbenchtoolbox/sample_1/), mirtop gff generates only a mirtop.gff file with no COLDATA information.

## mirGFF3. VERSION 0.9
## source-ontology: miRBasev22 doi:10.25504/fairsharing.hmgte8
## COLDATA:

But if I removed the backslash, (isomiR_sRNAbenchtoolbox/sample_1) mirtop gff would generate a mirtop.gff and a sample_1.gff file containing information in the COLDATA section

## mirGFF3. VERSION 0.9
## source-ontology: miRBasev22 doi:10.25504/fairsharing.hmgte8
## COLDATA: sample_1

I know it is not a big issue, but I took a while to discover why mirtop stats was failing after mirtop gff step.

Adding a back slash is a very common practice and some users might experience the same problem. Adding a simple if folder.endswith("/") clause should sort it out.

Thank you very much in advance,

Great code and program!
Greetings from IGTP

[lpantano]

Hi! Thanks so much for debugging this. I will test this with the devel branch and see whether we still have it, it is a very annoying bug! Thanks so much for your help! Cheers Lorena Pantano, P.h.D Research Scientist Biostatistics Department Harvard T.H. Chan School of Public Health https://mirtop.github.io https://lpantano.github.io I'll be out of office from Dec-17th to Jan9th

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On Tue, Jan 22, 2019 at 5:11 AM Jose Francisco Sanchez-Herrero < ***@***.***> wrote: Dear mirtop developers, I have noticed a bug in the last version of mirtop (0.3.17) when dealing with back slashes. I run mirtop gff conversion from sRNAbench data. mirtop gff --sps hsa --hairpin ../sRNAtoolboxDB/libs/hairpin.fa --gtf ../hsa.gff3 --format srnabench -vd -o test1 isomiR_sRNAbenchtoolbox/sample_1/ I noticed that if I leave the backslash for the folder from sRNAbench data ( isomiR_sRNAbenchtoolbox/sample_1/), mirtop gff generates only a mirtop.gff file with no COLDATA information. *## mirGFF3. VERSION 0.9* *## source-ontology: miRBasev22 doi:10.25504/fairsharing.hmgte8* *## COLDATA:* But if I removed the backslash, (isomiR_sRNAbenchtoolbox/sample_1) mirtop gff would generate a mirtop.gff and a sample_1.gff file containing information in the COLDATA section *## mirGFF3. VERSION 0.9* *## source-ontology: miRBasev22 doi:10.25504/fairsharing.hmgte8* *## COLDATA: sample_1* I know it is not a big issue, but I took a while to discover why mirtop stats was failing after mirtop gff step. Adding a back slash is a very common practice and some users might experience the same problem. Adding a simple if folder.endswith("/") clause should sort it out. Thank you very much in advance, Great code and program! Greetings from IGTP — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#52>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABi_HDIKDzZ6VF0iC7iBaQqL2vPOXEBvks5vFuPTgaJpZM4aMVfU> .

[lpantano]

Hi,

this is fixed in the devel version.

Thanks!