Closed JFsanchezherrero closed 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
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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Hi,
this is fixed in the devel version.
Thanks!
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