[med-svn] [Git][med-team/mcaller][master] 5 commits: Upload.

[Steffen Möller (@moeller)]

Steffen Möller pushed to branch master at Debian Med / mcaller


Commits:
ce86c9ce by Steffen Moeller at 2021-10-01T14:24:39+02:00
Upload.

- - - - -
9dd5ca68 by Steffen Moeller at 2021-10-01T14:25:13+02:00
routine-update: New upstream version

- - - - -
7e634fc7 by Steffen Moeller at 2021-10-01T14:25:15+02:00
New upstream version 1.0.3+git20210624.b415090
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81a7c2d9 by Steffen Moeller at 2021-10-01T14:25:28+02:00
Update upstream source from tag 'upstream/1.0.3+git20210624.b415090'

Update to upstream version '1.0.3+git20210624.b415090'
with Debian dir 965e1dfc189ea0ab4dc779a1edd066c6047a347a
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9d218aa1 by Steffen Moeller at 2021-10-01T14:31:01+02:00
routine-update: Ready to upload to unstable

Ok, if routine-update says so :)

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6 changed files:

- + CAAYNNNNNRTAC_model_6_m6A.pkl
- + CRAANNNNNNNTGC_model_6_m6A.pkl
- README.md
- debian/changelog
- debian/control
- debian/rules


Changes:

=====================================
CAAYNNNNNRTAC_model_6_m6A.pkl
=====================================
Binary files /dev/null and b/CAAYNNNNNRTAC_model_6_m6A.pkl differ


=====================================
CRAANNNNNNNTGC_model_6_m6A.pkl
=====================================
Binary files /dev/null and b/CRAANNNNNNNTGC_model_6_m6A.pkl differ


=====================================
README.md
=====================================
@@ -147,6 +147,10 @@ Reference fasta, PacBio calls for m6A and a subset of A positions, and eventalig
 
   This will generate the output file model_NN_6_m6A.pkl. 
   
-  ## Results with the latest model 
+  ## Results with the R9.5 model 
   ![latest results](motifs_plot.png)
   Unsurprisingly, mCaller performs best at identifying motifs similar to those it's trained on (here, E. coli). This is a clear limitation to the method, but the results are still sufficient in many cases to verify a motif of interest. 
+
+## Models provided
+- R9.4 and R9.5 models trained on E. coli data, both basecalled with albacore, as published in https://www.nature.com/articles/s41467-019-08289-9
+- R9.4 models trained on motifs “CAAYNNNNNRTAC/GTAYNNNNNRTTG” and “CRAANNNNNNNTGC/GCANNNNNNNTTYG”, respectively, basecalled with Guppy-v4.5.2, generously provided by [@wshropshire](https://github.com/wshropshire)


=====================================
debian/changelog
=====================================
@@ -1,5 +1,5 @@
-mcaller (1.0.3+git20210331.f7a616a-1) UNRELEASED; urgency=medium
+mcaller (1.0.3+git20210624.b415090-1) unstable; urgency=medium
 
   * Initial release (Closes: #969558)
 
- -- Steffen Moeller <moeller at debian.org>  Sat, 19 Jun 2021 23:59:32 +0200
+ -- Steffen Moeller <moeller at debian.org>  Fri, 01 Oct 2021 14:17:38 +0200


=====================================
debian/control
=====================================
@@ -11,7 +11,7 @@ Build-Depends: debhelper-compat (= 13),
                python3-biopython,
                python3-numpy,
                python3-sklearn
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
 Vcs-Browser: https://salsa.debian.org/med-team/mcaller
 Vcs-Git: https://salsa.debian.org/med-team/mcaller.git
 Homepage: https://github.com/al-mcintyre/mCaller


=====================================
debian/rules
=====================================
@@ -23,3 +23,4 @@ override_dh_auto_clean:
 	dh_auto_clean
 	#rm -f model_NN_6_m6A.pkl testdata/masonread1.eventalign.diffs.6 testdata/masonread1.eventalign.diffs.6.train
 	rm -rf __pycache__
+	rm -f model_NN_6_m6A.pkl



View it on GitLab: https://salsa.debian.org/med-team/mcaller/-/compare/e32f3b56f4ce99e472ef52028ec434f9a5110056...9d218aa1c2879da5e935d5cbfbec8f6f61e89ab1

-- 
View it on GitLab: https://salsa.debian.org/med-team/mcaller/-/compare/e32f3b56f4ce99e472ef52028ec434f9a5110056...9d218aa1c2879da5e935d5cbfbec8f6f61e89ab1
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