v2.4.0

.gitignore

@@ -1,5 +1,9 @@
 # Created by .ignore support plugin (hsz.mobi)
 ### Python template
+# Custom
+proc/*
+.DS_Store
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

README.md

@@ -1,7 +1,6 @@
-# Phigaro v2.3.0
+# Phigaro v2.4.0
 [![PyPI version](https://badge.fury.io/py/phigaro.svg)](https://badge.fury.io/py/phigaro)
-![Conda installation](https://anaconda.org/bioconda/phigaro/badges/installer/conda.svg)
-![Actions Status](https://github.com/bobeobibo/phigaro/workflows/Phigaro%20Tests/badge.svg)
+![Conda installation](https://anaconda.org/bioconda/phigaro/badges/version.svg)
 ![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 

deployment.sh

@@ -0,0 +1,28 @@
+#!/bin/bash
+conda activate main
+pip install --upgrade twine
+echo "Did you change git action and updated the package?"
+read
+git status
+read
+git pull
+read
+rm dist/*
+python setup_version.py
+python setup.py sdist bdist_wheel
+read
+git add --all
+git status
+read
+read -p commit_name="Please, make up the commit name:"
+tag=`cat tag_name`
+git commit -m $commit_name
+read
+git tag $tag
+read
+git push
+read
+git push --tags
+read
+twine upload --repository phigaro dist/*
+read

environment.yml

@@ -1,6 +1,6 @@
 name: phigaro_env
 dependencies:
-  - python=3.7
+  - python<=3.12.1
   - pip
   - bioconda::prodigal
   - bioconda::hmmer

phigaro/_version.py

@@ -1,4 +1,4 @@
 """Version information."""
 
 # The following line *must* be the last in the module, exactly as formatted:
-__version__ ="2.3.0"
+__version__ ="2.4.0"

phigaro/batch/task/base.py

@@ -14,9 +14,7 @@ class AbstractTask(object):
 
     def __init__(self):
         if self.task_name is None:
-            raise Exception(
-                "{}.task_name must by set".format(self.__class__.__name__)
-            )
+            raise Exception("{}.task_name must by set".format(self.__class__.__name__))
 
         self.directory()
         self.context = Context.instance()

phigaro/batch/task/dummy.py

@@ -4,12 +4,12 @@
 
 
 class DummyTask(AbstractTask):
-    task_name = 'dummy'
+    task_name = "dummy"
 
     def __init__(self, output, old_task_name):
         super().__init__()
         self._output = output
-        self.task_name = '{}-dummy'.format(old_task_name)
+        self.task_name = "{}-dummy".format(old_task_name)
 
     def run(self):
         pass

phigaro/batch/task/gene_mark.py

@@ -7,19 +7,20 @@
 
 
 class GeneMarkTask(AbstractTask):
-    task_name = 'gene_mark'
+    task_name = "gene_mark"
 
     def __init__(self, input):
         super().__init__()
 
         self.input = input
-        self._lst_file = input + '.lst'
-        self.gene_mark = sh.Command(self.config['genemark']['bin']).bake(
-            m=self.config['genemark']['mod_path'], A=self.output(),
+        self._lst_file = input + ".lst"
+        self.gene_mark = sh.Command(self.config["genemark"]["bin"]).bake(
+            m=self.config["genemark"]["mod_path"],
+            A=self.output(),
         )
 
     def output(self):
-        return self.file('{}.faa'.format(self.sample))
+        return self.file("{}.faa".format(self.sample))
 
     def run(self):
         self.gene_mark(self.input)

phigaro/batch/task/hmmer.py

@@ -7,7 +7,7 @@
 
 
 class HmmerTask(AbstractTask):
-    task_name = 'hmmer'
+    task_name = "hmmer"
 
     def __init__(self, prodigal_task):
         """
@@ -18,18 +18,18 @@ def __init__(self, prodigal_task):
         self.prodigal = prodigal_task
 
     def _prepare(self):
-        self.hmmer = sh.Command(self.config['hmmer']['bin'])
+        self.hmmer = sh.Command(self.config["hmmer"]["bin"])
 
     def output(self):
-        return self.file('{}.hmmer_out'.format(self.sample))
+        return self.file("{}.hmmer_out".format(self.sample))
 
     def run(self):
         self.hmmer(
-            '--cpu',
+            "--cpu",
             self.context.threads,
-            '--notextw',
-            '--tblout',
+            "--notextw",
+            "--tblout",
             self.output(),
-            self.config['hmmer']['pvog_path'],
+            self.config["hmmer"]["pvog_path"],
             self.prodigal.output(),
         )

phigaro/batch/task/parse_hmmer.py

@@ -10,11 +10,11 @@
 
 logger = logging.getLogger(__name__)
 
-INFINITY = float('inf')
+INFINITY = float("inf")
 
 
 class ParseHmmerTask(AbstractTask):
-    task_name = 'parse_hmmer'
+    task_name = "parse_hmmer"
 
     def __init__(self, hmmer_task, gene_mark_task):
         """
@@ -27,27 +27,27 @@ def __init__(self, hmmer_task, gene_mark_task):
         self.genemark_task = gene_mark_task
 
     def output(self):
-        return self.file('{}.npn'.format(self.sample))
+        return self.file("{}.npn".format(self.sample))
 
     def run(self):
         self._parse_hmmer_output()
 
     @staticmethod
     def parse_line(line):
-        tokens = re.split(r'\s+', line)
-        scaffold = '>' + line.split('>')[1]
+        tokens = re.split(r"\s+", line)
+        scaffold = ">" + line.split(">")[1]
         name = tokens[0]
         evalue = float(tokens[4])
         return scaffold, name, evalue
 
     def _parse_hmmer_output(self):
-        max_evalue = self.config['hmmer']['e_value_threshold']
+        max_evalue = self.config["hmmer"]["e_value_threshold"]
 
         with open(self.hmmer_task.output()) as f:
             lines_it = (
                 self.parse_line(line.strip())
                 for line in f
-                if not line.startswith('#') and line.strip()
+                if not line.startswith("#") and line.strip()
             )
 
             hmm_res = {}
@@ -63,12 +63,10 @@ def _parse_hmmer_output(self):
                     hmm_res[scaffold][gene_name] = evalue
 
         with open(self.genemark_task.output()) as f:
-            with open(self.output(), 'w') as of:
-                writer = csv.writer(of, delimiter='\t')
+            with open(self.output(), "w") as of:
+                writer = csv.writer(of, delimiter="\t")
                 lines_it = (
-                    line.strip().split('\t')
-                    for line in f
-                    if line.startswith('>')
+                    line.strip().split("\t") for line in f if line.startswith(">")
                 )
 
                 for scaffold, group in groupby(lines_it, key=lambda t: t[1]):
@@ -81,7 +79,5 @@ def _parse_hmmer_output(self):
                         for gene_name, _ in group
                     )
 
-                    is_phage_it = (
-                        'P' if is_phage else 'N' for is_phage in is_phage_it
-                    )
-                    writer.writerow((scaffold, ''.join(is_phage_it)))
+                    is_phage_it = ("P" if is_phage else "N" for is_phage in is_phage_it)
+                    writer.writerow((scaffold, "".join(is_phage_it)))

phigaro/batch/task/path.py

@@ -5,15 +5,15 @@
 
 def sample_name(sample_path):
     sample_path = basename(sample_path)
-    tokens = sample_path.split('.')
+    tokens = sample_path.split(".")
     if len(tokens) == 1:
         return sample_path
     else:
-        return '.'.join(tokens[:-1])
+        return ".".join(tokens[:-1])
 
 
 def path(*items):
-    items = ('proc',) + items
+    items = ("proc",) + items
     return join(*items)
 
 

phigaro/batch/task/preprocess.py

@@ -6,7 +6,7 @@
 
 
 class PreprocessTask(AbstractTask):
-    task_name = 'input_file'
+    task_name = "input_file"
 
     def __init__(self, input):
         super().__init__()
@@ -15,8 +15,8 @@ def __init__(self, input):
 
     def check_fastafile(self):
         def get_users_answer(question):
-            yes = ['yes', 'y']
-            no = ['no', 'n']
+            yes = ["yes", "y"]
+            no = ["no", "n"]
             try:
                 input_ = raw_input
             except NameError:
@@ -40,20 +40,20 @@ def get_users_answer(question):
         SeqIO.write(records_to_save, self.output(), "fasta")
         del records_to_save
 
-        if not self.config['phigaro']['delete_shorts']:
+        if not self.config["phigaro"]["delete_shorts"]:
             if len(sequences_to_delete) > 0:
                 print(
-                    'Error! Your fasta file contains at least one sequence length < 20000.  The short sequences are: '
+                    "Error! Your fasta file contains at least one sequence length < 20000.  The short sequences are: "
                 )
-                print('\n'.join(sequences_to_delete))
+                print("\n".join(sequences_to_delete))
                 if not get_users_answer(
-                    'Do you want to start Phigaro without these sequences?'
+                    "Do you want to start Phigaro without these sequences?"
                 ):
                     self.clean()
                     exit(1)
 
     def output(self):
-        return self.file('{}.fasta'.format(self.sample))
+        return self.file("{}.fasta".format(self.sample))
 
     def run(self):
         self.check_fastafile()

phigaro/batch/task/prodigal.py

@@ -5,18 +5,18 @@
 
 
 class ProdigalTask(AbstractTask):
-    task_name = 'prodigal'
+    task_name = "prodigal"
 
     def __init__(self, preprocess_task):
         super().__init__()
 
         self.preprocess_task = preprocess_task
-        self.prodigal = sh.Command(self.config['prodigal']['bin']).bake(
+        self.prodigal = sh.Command(self.config["prodigal"]["bin"]).bake(
             i=self.preprocess_task.output(), a=self.output()
         )
 
     def output(self):
-        return self.file('{}.faa'.format(self.sample))
+        return self.file("{}.faa".format(self.sample))
 
     def run(self):
         self.prodigal()