mimseq - npm Package Compare versions

Comparing version 1.3.9 to 1.3.10

tests/test_cli.py

+import hashlib
+import os
+import subprocess
+import yaml
+
+def read_yaml(filepath = 'tests/md5sums.yml'):
+    with open(filepath, 'r') as infile:
+        yaml_dict = yaml.load(infile.read(), Loader=yaml.Loader)
+    return yaml_dict
+
+def get_md5(filepath, encoding = 'utf-8'):
+    with open(filepath, 'r') as file:
+        md5sum = hashlib.md5(file.read().encode(encoding)).hexdigest()
+    return md5sum
+
+def check_snapshot_md5sums(files):
+    all_equal = True
+    for snapshot in files:
+        observed_md5 = get_md5(snapshot['path'])
+        expected_md5 = snapshot['md5sum']
+        if observed_md5 != expected_md5:
+            all_equal = False
+            print("md5sum changed for", snapshot['path'], '\n\texpected:', expected_md5, "observed:", observed_md5)
+    return all_equal
+
+def run_cli(command):
+    out = subprocess.run(
+        command,
+        shell=True,
+        text=True,
+        capture_output=True,
+    )
+    if out.returncode:
+        print(out.stdout)
+        print(out.stderr)
+    return out
+
+def test_cli():
+    mimseq_out = run_cli(
+        "mimseq --species Hsap --cluster-id 0.97 --threads 2 --min-cov 0.0005 --max-mismatches 0.075 --control-condition HEK293T -n hg38_test --out-dir test_cli --max-multi 4 --remap --remap-mismatches 0.05 tests/data/sampleData_subset_HEKvsK562.txt"
+    )
+    is_success = mimseq_out.returncode == 0
+    snapshot_files = read_yaml('tests/md5sums.yml')['test_cli']
+    assert is_success and check_snapshot_md5sums(snapshot_files)
+
+# def test_cli_local_modomics():
+#     mimseq_out = run_cli(
+#         "mimseq --species Hsap --cluster-id 0.97 --threads 2 --min-cov 0.0005 --max-mismatches 0.075 --control-condition HEK293T -n hg38_test --out-dir test_cli_local_modomics --max-multi 4 --remap --remap-mismatches 0.05 --local-modomics tests/data/sampleData_subset_HEKvsK562.txt"
+#     )
+#     is_success = mimseq_out.returncode == 0
+#     snapshot_files = read_yaml('tests/md5sums.yml')['test_cli_local_modomics']
+#     assert is_success and check_snapshot_md5sums(snapshot_files)

mimseq.egg-info/PKG-INFO

 Metadata-Version: 2.1
 Name: mimseq
-Version: 1.3.9
+Version: 1.3.10
 Summary: Custom high-throughput tRNA sequencing alignment and quantification pipeline based on modification induced misincorporation cDNA synthesis.
@@ -5,0 +5,0 @@ Home-page: https://github.com/nedialkova-lab/mim-tRNAseq

mimseq.egg-info/SOURCES.txt

@@ -172,2 +172,3 @@ LICENSE.txt
 mimseq/data/schiPomb-eColitK/schiPomb_972H-tRNAs.fa
-mimseq/data/schiPomb-eColitK/schiPomb_eschColi-tRNAs.out
+mimseq/data/schiPomb-eColitK/schiPomb_eschColi-tRNAs.out
+tests/test_cli.py

mimseq/tRNAtools.py

@@ -129,4 +129,2 @@ #!/usr/bin/env python3
 				anticodon = data['anticodon']
-				if anticodon == None:
-					print(data)
 				new_anticodon = getUnmodSeq(anticodon, modifications)
@@ -278,3 +276,3 @@ if "N" in new_anticodon:
 		for data in modifications_table.values():
-			modifications[data["abbrev"].strip()] = {'name':data["name"].strip(), 'abbr':data["short_name"].strip(), 'ref':data["reference_moiety"][0].strip()}
+			modifications[data["new_abbrev"].strip()] = {'name':data["name"].strip(), 'abbr':data["short_name"].strip(), 'ref':data["reference_moiety"][0].strip()}
 		
@@ -281,0 +279,0 @@ elif not fetch:

mimseq/version.py

@@ -1,1 +0,1 @@
-__version__ = "v1.3.9"
+__version__ = "v1.3.10"

PKG-INFO

 Metadata-Version: 2.1
 Name: mimseq
-Version: 1.3.9
+Version: 1.3.10
 Summary: Custom high-throughput tRNA sequencing alignment and quantification pipeline based on modification induced misincorporation cDNA synthesis.
@@ -5,0 +5,0 @@ Home-page: https://github.com/nedialkova-lab/mim-tRNAseq

README.md

@@ -43,5 +43,11 @@ <p align="center">
 	conda activate mimseq
-	mamba install -c bioconda mimseq
+	mamba install -c conda-forge -c bioconda mimseq
 ```
 
+Sometimes using `mamba` we have noticed that very old versions of `mimseq` are installed. Please check using `mimseq --version` that you have the latest [version](https://github.com/nedialkova-lab/mim-tRNAseq/blob/master/mimseq/version.py) installed. If not, try running the following in your `mimseq` environment: 
+```
+mamba install mimseq=VERSION
+#replace VERSION with version number, e.g., mimseq=1.3.9
+```
+
 usearch needs to be acquired and installed. Please do the following:
@@ -48,0 +54,0 @@ ```bash

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Improved metrics

Total package byte prevSize

17725842

0.01%

Number of package files

175

0.57%

Lines of code

3655

1.22%