[med-svn] [Git][med-team/ariba][upstream] New upstream version 2.14.5+ds

Sascha Steinbiss gitlab at salsa.debian.org
Fri May 22 13:38:19 BST 2020 


Sascha Steinbiss pushed to branch upstream at Debian Med / ariba


Commits:
3e10523f by Sascha Steinbiss at 2020-05-21T19:18:17+02:00
New upstream version 2.14.5+ds
- - - - -


6 changed files:

- .travis.yml
- CHANGELOG.md
- README.md
- ariba/megares_zip_parser.py
- ariba/tasks/summary.py
- setup.py


Changes:

=====================================
.travis.yml
=====================================
@@ -11,6 +11,7 @@ python:
 - '3.6'
 sudo: false
 install:
+- pip install pysam
 - source ./install_dependencies.sh
 before_script:
 - pip install codecov


=====================================
CHANGELOG.md
=====================================
@@ -1,38 +1,67 @@
 # Change Log
 
-[v2.14.4](https://github.com/sanger-pathogens/ariba/tree/v2.14.4) (2019-09-24)
-[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.3...v2.14.4)
+## [v2.14.5](https://github.com/sanger-pathogens/ariba/tree/v2.14.5) (2020-05-14)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.4...v2.14.5)
 
-**Fixed bugs:**
+**Closed issues:**
 
+- Megares Downloading Error [\#294](https://github.com/sanger-pathogens/ariba/issues/294)
+- Summarising MLST reports? [\#292](https://github.com/sanger-pathogens/ariba/issues/292)
+- CARD 3.0.6 introduces white space in seq id causing fasta/metadata mismatch [\#284](https://github.com/sanger-pathogens/ariba/issues/284)
 - ARGannot download fails [\#281](https://github.com/sanger-pathogens/ariba/issues/281)
 
-[v2.14.3](https://github.com/sanger-pathogens/ariba/tree/v2.14.3) (2019-08-23)
+**Merged pull requests:**
+
+- bump version number [\#297](https://github.com/sanger-pathogens/ariba/pull/297) ([puethe](https://github.com/puethe))
+- Handle megares 2.0.0 [\#295](https://github.com/sanger-pathogens/ariba/pull/295) ([martinghunt](https://github.com/martinghunt))
+- Correct swapped col and row filters [\#288](https://github.com/sanger-pathogens/ariba/pull/288) ([aunderwo](https://github.com/aunderwo))
+- Remove support information [\#286](https://github.com/sanger-pathogens/ariba/pull/286) ([kpepper](https://github.com/kpepper))
+
+## [v2.14.4](https://github.com/sanger-pathogens/ariba/tree/v2.14.4) (2019-09-24)
+[Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.3...v2.14.4)
+
+**Merged pull requests:**
+
+- Fixed GitHub issue \#281 - ARG-ANNOT Fails to Download [\#282](https://github.com/sanger-pathogens/ariba/pull/282) ([kpepper](https://github.com/kpepper))
+
+## [v2.14.3](https://github.com/sanger-pathogens/ariba/tree/v2.14.3) (2019-08-30)
 [Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.2...v2.14.3)
 
-**Fixed bugs:**
+**Closed issues:**
 
 - Version 3.0.3 of CARD breaks prepareref [\#278](https://github.com/sanger-pathogens/ariba/issues/278)
-- RT 667288: Change docker file Ariba git clone to a copy
+- matplotlib listed twice as a dep in setup.py [\#275](https://github.com/sanger-pathogens/ariba/issues/275)
+- v2.14.1	attributeError: 'Namespace' object has no attribute 'cdhit\_max\_memory' [\#273](https://github.com/sanger-pathogens/ariba/issues/273)
+- Use ariba run for several isolates in batch [\#262](https://github.com/sanger-pathogens/ariba/issues/262)
+- Stopping! Signal received: 13 [\#238](https://github.com/sanger-pathogens/ariba/issues/238)
+
+**Merged pull requests:**
+
+- Added default locale to docker file [\#280](https://github.com/sanger-pathogens/ariba/pull/280) ([kpepper](https://github.com/kpepper))
+- Fix for issue \#278 Version 3.0.3 of CARD breaks prepareref [\#279](https://github.com/sanger-pathogens/ariba/pull/279) ([kpepper](https://github.com/kpepper))
+- Remove extra matplotlib entry in install\_requires [\#277](https://github.com/sanger-pathogens/ariba/pull/277) ([andersgs](https://github.com/andersgs))
+- Removed the specific Ariba release number from the docker file [\#276](https://github.com/sanger-pathogens/ariba/pull/276) ([kpepper](https://github.com/kpepper))
 
-[v2.14.2](https://github.com/sanger-pathogens/ariba/tree/v2.14.2) (2019-06-18)
+## [v2.14.2](https://github.com/sanger-pathogens/ariba/tree/v2.14.2) (2019-06-21)
 [Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.1...v2.14.2)
 
 **Fixed bugs:**
 
-- Added Spades assembler into Docker file - RT ticket 660940
-- Incremented release number
-- Added LICENSE file into release distribution - RT ticket 660890
+- Issue with ariba and slurm \(signal 18, signal 20\) [\#263](https://github.com/sanger-pathogens/ariba/issues/263)
 
-[v2.14.1](https://github.com/sanger-pathogens/ariba/tree/v2.14.1) (2019-06-13)
+**Merged pull requests:**
+
+- RT 660940 - add spades to docker file [\#274](https://github.com/sanger-pathogens/ariba/pull/274) ([kpepper](https://github.com/kpepper))
+- Added AUTHORS and LICENSE to the manifest [\#272](https://github.com/sanger-pathogens/ariba/pull/272) ([kpepper](https://github.com/kpepper))
+
+## [v2.14.1](https://github.com/sanger-pathogens/ariba/tree/v2.14.1) (2019-06-13)
 [Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.14.0...v2.14.1)
 
-**Fixed bugs:**
+**Merged pull requests:**
 
-- Ariba fails to install from PyPI due to missing .h files in distribution. Related to MANIFEST.in change in [\#269](https://github.com/sanger-pathogens/ariba/pull/269)
-- Fix for Issue [\#263](https://github.com/sanger-pathogens/ariba/issues/263)
+- Backed out MANIFEST.in change. Bumped release number to v2.14.1. [\#271](https://github.com/sanger-pathogens/ariba/pull/271) ([kpepper](https://github.com/kpepper))
 
-[v2.14.0](https://github.com/sanger-pathogens/ariba/tree/v2.14.0) (2019-06-06)
+## [v2.14.0](https://github.com/sanger-pathogens/ariba/tree/v2.14.0) (2019-06-06)
 [Full Changelog](https://github.com/sanger-pathogens/ariba/compare/v2.13.5...v2.14.0)
 
 **Closed issues:**
@@ -688,4 +717,4 @@
 
 
 
-\* *This Change Log was automatically generated by [github_changelog_generator](https://github.com/skywinder/Github-Changelog-Generator)*
\ No newline at end of file
+\* *This Change Log was automatically generated by [github_changelog_generator](https://github.com/skywinder/Github-Changelog-Generator)*


=====================================
README.md
=====================================
@@ -4,6 +4,9 @@ Antimicrobial Resistance Identification By Assembly
 
 For how to use ARIBA, please see the [ARIBA wiki page][ARIBA wiki].
 
+PLEASE NOTE: we currently do not have the resources to provide support for Ariba - see the [Feedback/Issues](#feedbackissues) section.
+
+[![Unmaintained](http://unmaintained.tech/badge.svg)](http://unmaintained.tech/)  
 [![Build Status](https://travis-ci.org/sanger-pathogens/ariba.svg?branch=master)](https://travis-ci.org/sanger-pathogens/ariba)   
 [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/sanger-pathogens/ariba/blob/master/LICENSE)   
 [![status](https://img.shields.io/badge/MGEN-10.1099%2Fmgen.0.000131-brightgreen.svg)](http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000131)   
@@ -55,9 +58,12 @@ Summarise data from several runs:
 
 Please read the [ARIBA wiki page][ARIBA wiki] for full usage instructions.
 
+## Tutorials
+[The Jupyter notebook tutorial](https://github.com/sanger-pathogens/pathogen-informatics-training)
+
 ## Installation
 
-If you encounter an issue when installing ARIBA please contact your local system administrator. If you encounter a bug please log it [here](https://github.com/sanger-pathogens/ariba/issues) or email us at ariba-help at sanger.ac.uk.
+If you encounter an issue when installing ARIBA please contact your local system administrator. If you encounter a bug you can log it [here](https://github.com/sanger-pathogens/ariba/issues).
 
 ### Required dependencies
   * [Python3][python] version >= 3.6.0
@@ -107,7 +113,7 @@ To use ARIBA use a command like this (substituting in your directories), where y
 When calling Ariba via Docker (as above) you'll also need to add **/data/** in front of all the passed in file or directory names (e.g. /data/my_output_folder).
 
 
-### Debian (testing)
+### Debian (Ariba version may not be the latest)
 ARIBA is available in the latest version of Debian, and over time will progressively filter through to Ubuntu and other distributions which use Debian. To install it as root:
 
     sudo apt-get install ariba
@@ -211,7 +217,7 @@ Please read the [ARIBA wiki page][ARIBA wiki] for full usage instructions.
 ARIBA is free software, licensed under [GPLv3](https://github.com/sanger-pathogens/ariba/blob/master/LICENSE).
 
 ## Feedback/Issues
-Please report any issues to the [issues page](https://github.com/sanger-pathogens/ariba/issues) or email ariba-help at sanger.ac.uk
+We currently do not have the resources to provide support for Ariba. However, the community might be able to help you out if you report any issues about usage of the software to the [issues page](https://github.com/sanger-pathogens/ariba/issues).
 
 ## Citation
 If you use this software please cite:


=====================================
ariba/megares_zip_parser.py
=====================================
@@ -24,8 +24,22 @@ class MegaresZipParser:
         except:
             raise Error('Error making directory ' + outdir)
 
+        # Old <2.0.0 megares has eg these files:
+        #  megares_annotations_v1.01.csv
+        #  megares_database_v1.01.fasta
+        #  megares_to_external_header_mappings_v1.01.tsv
+        # megares 2.0.0 has these files:
+        #  megares_drugs_annotations_v2.00.csv
+        #  megares_drugs_database_v2.00.fasta
+        #  megares_modified_annotations_v2.00.csv
+        #  megares_modified_database_v2.00.fasta
+        #  megares_to_external_header_mappings_v2.00.csv
+        # The sequences in *_modified_* files seem to be a superset of
+        # *_drugs_*, so use the *_modified_* ones. This will happen
+        # as long as we loop over sorted filenames, because the _modified_
+        # csv and fasta are listed last
         zfile = zipfile.ZipFile(zip_file)
-        for member in zfile.namelist():
+        for member in sorted(zfile.namelist()):
             if '_annotations_' in member:
                 original_files['annotations'] = member
             elif '_database_' in member and member.endswith('.fasta'):
@@ -51,7 +65,7 @@ class MegaresZipParser:
 
         with open(infile) as f:
             reader = csv.DictReader(f, delimiter=delimiter)
-            if set(expected_columns) != set(reader.fieldnames):
+            if not set(expected_columns).issubset(set(reader.fieldnames)):
                 raise Error('Unexpected header in annotations file. Expected columns: ' + ','.join(expected_columns) + ' but got: ' + ','.join(reader.fieldnames))
 
             for row in reader:
@@ -67,7 +81,21 @@ class MegaresZipParser:
 
     @classmethod
     def _load_header_mappings_file(cls, infile):
-        return MegaresZipParser._csv_to_dict(infile, '\t', {'Source_Database', 'MEGARes_Header', 'Source_Headers(space_separated)'}, 'MEGARes_Header')
+        # Megares <2.0.0 uses a tsv file, whereas 2.0.0 uses csv.
+        # Also, the column names changed slightly for 2.0.0, so we'll change
+        # them to be the same as <2.0.0 after loading the file
+        if infile.endswith(".tsv"):
+            return MegaresZipParser._csv_to_dict(infile, '\t', {'Source_Database', 'MEGARes_Header', 'Source_Headers(space_separated)'}, 'MEGARes_Header')
+        else:
+            assert infile.endswith(".csv")
+            data = MegaresZipParser._csv_to_dict(infile, ',', {'Database', 'MEGARes_v2_header', 'Source_header'}, 'MEGARes_v2_header')
+            fixed_data = {}
+            for key, d in data.items():
+                fixed_data[key] = {
+                    "Source_Database": d["Database"],
+                    "Source_Headers(space_separated)": d["Source_header"]
+                }
+            return fixed_data
 
 
     @classmethod


=====================================
ariba/tasks/summary.py
=====================================
@@ -64,8 +64,8 @@ def run(options):
         options.outprefix,
         fofn=options.fofn,
         filenames=options.infiles,
-        filter_rows=options.col_filter == 'y',
-        filter_columns=options.row_filter == 'y',
+        filter_rows=options.row_filter == 'y',
+        filter_columns=options.col_filter == 'y',
         min_id=options.min_id,
         cluster_cols=options.cluster_cols,
         make_phandango_tree=(not options.no_tree),


=====================================
setup.py
=====================================
@@ -55,7 +55,7 @@ vcfcall_mod = Extension(
 setup(
     ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod],
     name='ariba',
-    version='2.14.4',
+    version='2.14.5',
     description='ARIBA: Antibiotic Resistance Identification By Assembly',
     packages = find_packages(),
     package_data={'ariba': ['test_run_data/*', 'tb_data/*']},



View it on GitLab: https://salsa.debian.org/med-team/ariba/-/commit/3e10523fdc9389d71e7a7c272d4fb5b1f94c14e2

-- 
View it on GitLab: https://salsa.debian.org/med-team/ariba/-/commit/3e10523fdc9389d71e7a7c272d4fb5b1f94c14e2
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