Integron_Finder

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[BUG] Error in find_attc_max function

4

Hello there, Thank you for developing IntegronFinder. I am updating to version 2.0.3 to check if some issues related to negative coordinates and other bugs we have been experimenting with...

Ales-ibt

[BUG] Wrong coordinates in results

12

**Describe the bug** Hi, First thanks for the nice work on this tool. I have been using this tool in a pipeline of mine and it has been working awesomely....

fmalmeida

**Is your feature request related to a problem? Please describe.** It would be great if the option --prot-file could be used without the option --annot-parser. Given that IntegronFinder can already...

lcoffion

Integron_Finder bogs down server's I/O when ran on metagenomes with ~million contigs

3

## Version of Integron_Finder: version 2 ### OS Linux ## Problem1: I/O overloaded for metagenomes with hundreds of thousands of contigs. Usually, only a small subset of the contigs have...

JuntaoZhong

[FEAT] Remove/Relax Matplotlib version requirement

5

Hello, We are developing a genome annotation and visualization program `beav` that relies on `Integron Finder`. We are using Bioconda to distribute our program. Our visualization script requires `Matplotlib >=...

acarafat

[BUG] IF crashes with --gbk option in a specific caase

3

**Describe the bug** When using the --gbk option, IF crashes if a feature (e.g. cassette, attC site) spans over both borders of a replicon. **To Reproduce** Steps to reproduce the...

eloilit

**Is your feature request related to a problem? Please describe.** Often I already have annotations for a genome, including gene calls/ORFs with locus_tags. Running Integron_Finder on the fasta file results...

alexweisberg

**Describe the bug** A clear and concise description of what the bug is. whith the last gembase (version 0523) is used (--gembase) and there is a pseudogene (gene indicated as...

bneron

This PR fixes the coordinate overflow issue for P_intI promoter and attI site predictions on linear contigs, as reported in issue #120. ## Problem - Kpne_VR_40131: P_intI1 predicted at 188068-188102,...

djken2009

[BUG] Coordinates error

2

Hi, I have observed an error referring to the coordinates, although different from the previously addressed on issue #114 . When looking for integrons on a set of samples, I...

rpalcab