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miRTop / mirtop

command lines tool to annotate miRNAs with a standard mirna/isomir naming
https://mirtop.readthedocs.org
MIT License
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Trailing Slash for samples #52

Closed JFsanchezherrero closed 5 years ago

JFsanchezherrero commented 5 years ago

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: sample1

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 commented 5 years ago

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

On Tue, Jan 22, 2019 at 5:11 AM Jose Francisco Sanchez-Herrero < notifications@github.com> 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

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lpantano commented 5 years ago

Hi,

this is fixed in the devel version.

Thanks!