Replidec 0.2.3.1__tar.gz → 0.3.2__tar.gz

{Replidec-0.2.3.1/Replidec.egg-info → replidec-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: Replidec
-Version: 0.2.3.1
+Version: 0.3.2
 Summary: Replication Cycle Detector for Phages
 Home-page: https://github.com/deng-lab/Replidec
 Author: Xue Peng
@@ -15,8 +15,22 @@ Classifier: Intended Audience :: Science/Research
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
-
-# Replidec: Replication Cycle Detector for Phages
+Requires-Dist: biopython>=1.77
+Requires-Dist: future>=0.18.2
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# Replidec: Replication Cycle Decipher for Phages
 
 [![PyPI](https://img.shields.io/pypi/v/Replidec.svg)](https://pypi.python.org/pypi/Replidec)
 [![Anaconda-Server Badge](https://anaconda.org/denglab/replidec/badges/version.svg)](https://anaconda.org/denglab/replidec)
@@ -29,26 +43,26 @@ Use bayes classifier combine with homology search to predict virus replication c
 
 ## Install
 
-Download database from https://zenodo.org/record/6857082/files/db.tar.gz
-
-### Method 1: using Docker (recommended)
+### Method 1: using Conda
 
 ```bash
-docker pull denglab/replidec
+conda create -n replidec
+conda activate replidec
+conda install -c conda-forge -c bioconda replidec
+or
+conda install -c denglab -c conda-forge -c bioconda replidec
 ```
 
-If you want to use `Replidec` on an HPC, singularity is recommended. You can create a singularity image using following command,
+### Method 2: using Docker
 
 ```bash
-singularity pull replidec.sif docker://denglab/replidec
+docker pull denglab/replidec
 ```
 
-### Method 2: using Conda
+If you want to use `Replidec` on an HPC, singularity is recommended. You can create a singularity image using following command,
 
 ```bash
-conda create -n replidec
-conda activate replidec
-conda install -c denglab -c conda-forge replidec
+singularity pull replidec.sif docker://denglab/replidec
 ```
 
 ### Method 3: using pip
@@ -70,9 +84,9 @@ pip3 install Replidec
 ```
 Replidec [-h] [--version] -p {multiSeqAsOne,batch,multiSeqEachAsOne}
          [-i INPUT_FILE] [-w WORKDIR] [-s SUMMARY] [-t THREADS] [-c HMMER_CRETERIA] [-H HMMER_PARAMETER] [-m MMSEQS_CRETERIA]
-         [-M MMSEQS_PARAMETER] [-b BLASTP_CRETERIA] [-B BLASTP_PARAMETER] [-d]
+         [-M MMSEQS_PARAMETER] [-b BLASTP_CRETERIA] [-B BLASTP_PARAMETER] [-d] [-D]
 ```
-## Usage: database
+## Usage: database (-d & -D)
 
 Database used in Replidec will be download automatically. 
 
@@ -80,6 +94,13 @@ Location: will be download at the where Replidec installed
 
 If you want to redownload the database, `-d` parameter can be used. The older database will be mv to "discarded_db" in the workdir(-w); This dir can be removed manually by user.
 
+We provide 2 database for user choose. Use -D to choose database. all|prokaryote
+
+1. all: This database contain all proteins from the prokaryotic, eukaryotic
+virus and prophage.
+2. prokaryote: This database contain proteins from the prokaryotic virus and
+prophage. eukaryotic virus gene was removed from this database
+
 ## Usage: Input(-i) and Propgram(-p)
 
 **Input file is different base on different program**

{Replidec-0.2.3.1 → replidec-0.3.2}/README.rst

@@ -1,4 +1,4 @@
-# Replidec: Replication Cycle Detector for Phages
+# Replidec: Replication Cycle Decipher for Phages
 
 [![PyPI](https://img.shields.io/pypi/v/Replidec.svg)](https://pypi.python.org/pypi/Replidec)
 [![Anaconda-Server Badge](https://anaconda.org/denglab/replidec/badges/version.svg)](https://anaconda.org/denglab/replidec)
@@ -11,26 +11,26 @@ Use bayes classifier combine with homology search to predict virus replication c
 
 ## Install
 
-Download database from https://zenodo.org/record/6857082/files/db.tar.gz
-
-### Method 1: using Docker (recommended)
+### Method 1: using Conda
 
 ```bash
-docker pull denglab/replidec
+conda create -n replidec
+conda activate replidec
+conda install -c conda-forge -c bioconda replidec
+or
+conda install -c denglab -c conda-forge -c bioconda replidec
 ```
 
-If you want to use `Replidec` on an HPC, singularity is recommended. You can create a singularity image using following command,
+### Method 2: using Docker
 
 ```bash
-singularity pull replidec.sif docker://denglab/replidec
+docker pull denglab/replidec
 ```
 
-### Method 2: using Conda
+If you want to use `Replidec` on an HPC, singularity is recommended. You can create a singularity image using following command,
 
 ```bash
-conda create -n replidec
-conda activate replidec
-conda install -c denglab -c conda-forge replidec
+singularity pull replidec.sif docker://denglab/replidec
 ```
 
 ### Method 3: using pip
@@ -52,9 +52,9 @@ pip3 install Replidec
 ```
 Replidec [-h] [--version] -p {multiSeqAsOne,batch,multiSeqEachAsOne}
          [-i INPUT_FILE] [-w WORKDIR] [-s SUMMARY] [-t THREADS] [-c HMMER_CRETERIA] [-H HMMER_PARAMETER] [-m MMSEQS_CRETERIA]
-         [-M MMSEQS_PARAMETER] [-b BLASTP_CRETERIA] [-B BLASTP_PARAMETER] [-d]
+         [-M MMSEQS_PARAMETER] [-b BLASTP_CRETERIA] [-B BLASTP_PARAMETER] [-d] [-D]
 ```
-## Usage: database
+## Usage: database (-d & -D)
 
 Database used in Replidec will be download automatically. 
 
@@ -62,6 +62,13 @@ Location: will be download at the where Replidec installed
 
 If you want to redownload the database, `-d` parameter can be used. The older database will be mv to "discarded_db" in the workdir(-w); This dir can be removed manually by user.
 
+We provide 2 database for user choose. Use -D to choose database. all|prokaryote
+
+1. all: This database contain all proteins from the prokaryotic, eukaryotic
+virus and prophage.
+2. prokaryote: This database contain proteins from the prokaryotic virus and
+prophage. eukaryotic virus gene was removed from this database
+
 ## Usage: Input(-i) and Propgram(-p)
 
 **Input file is different base on different program**

{Replidec-0.2.3.1 → replidec-0.3.2}/Replidec/Replidec.py

@@ -310,7 +310,8 @@ def checkdb_and_download(scriptPos, redownload=False):
 
     if not os.path.exists(os.path.join(scriptPos,"db")):
         print("db not exist! download database ...")
-        url="https://zenodo.org/record/6975142/files/db_v0.2.3.tar.gz"
+        #url="https://zenodo.org/record/6975142/files/db_v0.2.3.tar.gz"
+        url="https://zenodo.org/record/8101942/files/db_v0.3.1.tar.gz"
         file=os.path.split(url)[-1]
         cmd = "wget {0} -P {1} && cd {1} && tar -zxvf {2} && rm -rf {2}".format(url, scriptPos, file)
         obj = Popen(cmd,shell=True, stdout=PIPE)
@@ -322,6 +323,7 @@ def checkdb_and_download(scriptPos, redownload=False):
 
 
 def bayes_classifier_single(inputfile, prefix, wd,
+        db_name="prokaryte",
         hmm_creteria=1e-5, mmseqs_creteria=1e-5, blastp_creteria=1e-3,
         blastp_para="-num_threads 3",
         hmmer_para="--noali --cpu 3",
@@ -382,7 +384,15 @@ def bayes_classifier_single(inputfile, prefix, wd,
 
     # phase 2 bayes classifier
     # run mmseqs search
-    bc_mmseqsDB = os.path.join(fileDir, "db/bayes_mmseqs_index/all.protein")
+    if db_name == "all":
+        print("Using prokaryote and eukaryote protein as DB")
+        bc_mmseqsDB = os.path.join(fileDir, "db/bayes_mmseqs_index/all.protein")
+    elif db_name == "prokaryote":
+        print("Using only prokaryote protein as DB")
+        bc_mmseqsDB = os.path.join(fileDir, "db/bayes_mmseqs_index/prokaryote_only")
+    else:
+        print("Please check parameter -D")
+
     mmseqs_wd = os.path.join(wd, "BC_mmseqs")
     mmseqs_prefix = "%s.BC_mmseqs" % prefix
     mmseq_opt = runMmseqsEasysearch(inputfile, mmseqs_prefix, mmseqs_wd, bc_mmseqsDB,
@@ -390,7 +400,13 @@ def bayes_classifier_single(inputfile, prefix, wd,
     # print(mmseq_opt)
 
     # load score file
-    score_file = os.path.join(fileDir, "db/score.tsv")
+    if db_name == "all":
+        score_file = os.path.join(fileDir, "db/all_mmseq2_linclust_cluster.stat.scoreOpt.tsv")
+    elif db_name == "prokaryote":
+        score_file = os.path.join(fileDir, "db/prokaryote_only_mmseq2_linclust_cluster.stat.scoreOpt.tsv")
+    else:
+        print("Please check parameter -D")
+
     member2scoreD = load_scoreD(score_file)
 
     # read mmseqs easy search file

{Replidec-0.2.3.1 → replidec-0.3.2}/Replidec/Replidec_cmdline.py

@@ -51,6 +51,9 @@ parser.add_argument("-B", "--bp",default="-num_threads 3", dest="blastp_paramete
 
 parser.add_argument("-d", "--db",action='store_true',default=False,dest="db_redownload", help="remove db and redownload")
 
+parser.add_argument("-D", "--databaseN",default="prokaryote",choices=["all","prokaryote"],dest="db_name", 
+                    help="specific which database will use. all contain protein from prokaryote and eukaryote; prokaryote contain protein only from prokaryote")
+
 args = parser.parse_args()
 
 
@@ -62,15 +65,18 @@ def main():
 
     print("Using %s"%args.program)
     if args.program == "multiSeqAsOne":
-        bayes_classifier_genomes(args.input_file, args.workdir, summaryfile=args.summary, threads=args.threads,
+        bayes_classifier_genomes(args.input_file, args.workdir,db_name=args.db_name, 
+                                summaryfile=args.summary, threads=args.threads,
                                 hmm_creteria=args.hmmer_creteria, mmseqs_creteria=args.mmseqs_creteria, blastp_creteria=args.blastp_creteria,
                                 hmmer_para=args.hmmer_parameter, mmseqs_para=args.mmseqs_parameter, blastp_para=args.blastp_parameter)
     elif args.program == "multiSeqEachAsOne":
-        bayes_classifier_contig(args.input_file, args.workdir, summaryfile=args.summary, threads=args.threads,
+        bayes_classifier_contig(args.input_file, args.workdir,db_name=args.db_name, 
+                               summaryfile=args.summary, threads=args.threads,
                                hmm_creteria=args.hmmer_creteria, mmseqs_creteria=args.mmseqs_creteria, blastp_creteria=args.blastp_creteria,
                                hmmer_para=args.hmmer_parameter, mmseqs_para=args.mmseqs_parameter, blastp_para=args.blastp_parameter)
     elif args.program == "batch":
-        bayes_classifier_batch(args.input_file, args.workdir, summaryfile=args.summary, threads=args.threads,
+        bayes_classifier_batch(args.input_file, args.workdir,db_name=args.db_name, 
+                               summaryfile=args.summary, threads=args.threads,
                               hmm_creteria=args.hmmer_creteria, mmseqs_creteria=args.mmseqs_creteria, blastp_creteria=args.blastp_creteria,
                               hmmer_para=args.hmmer_parameter, mmseqs_para=args.mmseqs_parameter, blastp_para=args.blastp_parameter)
     #elif args.program == "test_multiSeqAsOne":

{Replidec-0.2.3.1 → replidec-0.3.2}/Replidec/Replidec_multi.py

@@ -9,7 +9,7 @@ from subprocess import Popen
 
 
 
-def bayes_classifier_batch(inputfile, wd, summaryfile="BC_predict.summary",threads=10,
+def bayes_classifier_batch(inputfile, wd, db_name="prokaryte", summaryfile="BC_predict.summary",threads=10,
          hmm_creteria=1e-5, mmseqs_creteria=1e-5, blastp_creteria=1e-5,
          blastp_para="-num_threads 3",
          hmmer_para="--noali --cpu 3",
@@ -41,7 +41,8 @@ def bayes_classifier_batch(inputfile, wd, summaryfile="BC_predict.summary",threa
     executor = ThreadPoolExecutor(max_workers=threads)
     all_task = []
     kwargsD={"hmm_creteria":hmm_creteria, "mmseqs_creteria":mmseqs_creteria, "blastp_creteria":blastp_creteria,
-             "blastp_para":blastp_para,"hmmer_para":hmmer_para,"mmseqs_para":mmseqs_para}
+             "blastp_para":blastp_para,"hmmer_para":hmmer_para,"mmseqs_para":mmseqs_para,
+             "db_name":db_name}
 
     ## n is try to control the sceond job will be submit after the first, cause some env or dir will be confilct when run all jobs at same time
     n=0
@@ -62,7 +63,7 @@ def bayes_classifier_batch(inputfile, wd, summaryfile="BC_predict.summary",threa
             #opt.flush()
     opt.close()
 
-def bayes_classifier_contig(inputfile, wd, summaryfile="BC_predict.summary",threads=10,
+def bayes_classifier_contig(inputfile, wd, db_name="prokaryte",summaryfile="BC_predict.summary",threads=10,
           hmm_creteria=1e-5, mmseqs_creteria=1e-5, blastp_creteria=1e-5,
           blastp_para="-num_threads 3",
           hmmer_para="--noali --cpu 3",
@@ -95,14 +96,18 @@ def bayes_classifier_contig(inputfile, wd, summaryfile="BC_predict.summary",thre
     executor = ThreadPoolExecutor(max_workers=threads)
     all_task = []
     kwargsD={"hmm_creteria":hmm_creteria, "mmseqs_creteria":mmseqs_creteria, "blastp_creteria":blastp_creteria,
-              "blastp_para":blastp_para,"hmmer_para":hmmer_para,"mmseqs_para":mmseqs_para}
+              "blastp_para":blastp_para,"hmmer_para":hmmer_para,"mmseqs_para":mmseqs_para,
+              "db_name":db_name}
+
     faaDict = {}
     for seq in SeqIO.parse(inputfile,"fasta"):
-        tmpfile="./%s.tmp"%seq.id
+        tmpdir = "%s/tmp"%wd
+        mkdirs(tmpdir)
+        seq.id=seq.id.replace("|","_")
+        tmpfile="%s/%s.tmp"%(tmpdir,seq.id)
         SeqIO.write(seq,tmpfile,"fasta")
         faaFile = runProdigal(tmpfile, seq.id, "%s/BC_prodigal"%wd, program="meta", otherPara="-g 11")
         faaDict[seq.id] = faaFile
-        #res = ["sample_name"] + ['NA']*6 + [0]
     #print(faaDict)
 
     n = 0
@@ -118,15 +123,15 @@ def bayes_classifier_contig(inputfile, wd, summaryfile="BC_predict.summary",thre
     for future in as_completed(all_task):
         res = future.result()
         faaFile = faaDict[res[0]]
-        tmpfile="./%s.tmp"%res[0]
+        tmpfile_com="%s/%s.tmp"%(tmpdir,res[0])
         res.append(faaFile)
         opt.write("\t".join([str(i) for i in res])+"\n")
         #opt.flush()
-        os.remove(tmpfile)
+        os.remove(tmpfile_com)
     opt.close()
 
 
-def bayes_classifier_genomes(inputfile, wd, summaryfile="BC_predict.summary",threads=10,
+def bayes_classifier_genomes(inputfile, wd, db_name="prokaryte",summaryfile="BC_predict.summary",threads=10,
            hmm_creteria=1e-5, mmseqs_creteria=1e-5, blastp_creteria=1e-5,
            blastp_para="-num_threads 3",
            hmmer_para="--noali --cpu 3",
@@ -160,7 +165,8 @@ def bayes_classifier_genomes(inputfile, wd, summaryfile="BC_predict.summary",thr
     executor = ThreadPoolExecutor(max_workers=threads)
     all_task = []
     kwargsD={"hmm_creteria":hmm_creteria, "mmseqs_creteria":mmseqs_creteria, "blastp_creteria":blastp_creteria,
-              "blastp_para":blastp_para,"hmmer_para":hmmer_para,"mmseqs_para":mmseqs_para}
+              "blastp_para":blastp_para,"hmmer_para":hmmer_para,"mmseqs_para":mmseqs_para,
+              "db_name":db_name}
     faaDict = {}
 
     with open(inputfile) as f:

{Replidec-0.2.3.1 → replidec-0.3.2}/Replidec/__init__.py

@@ -15,7 +15,7 @@ The package consists of the following Python modules:
 
 __author__ = """Xue Peng"""
 __email__ = 'xue.peng@helmholtz-muenchen.de'
-__version__ = '0.2.3'
+__version__ = '0.3.2'
 from Replidec import *
 #from .Replidec_cmdline import *
 #from .Replidec_multi import *

{Replidec-0.2.3.1 → replidec-0.3.2/Replidec.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: Replidec
-Version: 0.2.3.1
+Version: 0.3.2
 Summary: Replication Cycle Detector for Phages
 Home-page: https://github.com/deng-lab/Replidec
 Author: Xue Peng
@@ -15,8 +15,22 @@ Classifier: Intended Audience :: Science/Research
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
 License-File: LICENSE
-
-# Replidec: Replication Cycle Detector for Phages
+Requires-Dist: biopython>=1.77
+Requires-Dist: future>=0.18.2
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# Replidec: Replication Cycle Decipher for Phages
 
 [![PyPI](https://img.shields.io/pypi/v/Replidec.svg)](https://pypi.python.org/pypi/Replidec)
 [![Anaconda-Server Badge](https://anaconda.org/denglab/replidec/badges/version.svg)](https://anaconda.org/denglab/replidec)
@@ -29,26 +43,26 @@ Use bayes classifier combine with homology search to predict virus replication c
 
 ## Install
 
-Download database from https://zenodo.org/record/6857082/files/db.tar.gz
-
-### Method 1: using Docker (recommended)
+### Method 1: using Conda
 
 ```bash
-docker pull denglab/replidec
+conda create -n replidec
+conda activate replidec
+conda install -c conda-forge -c bioconda replidec
+or
+conda install -c denglab -c conda-forge -c bioconda replidec
 ```
 
-If you want to use `Replidec` on an HPC, singularity is recommended. You can create a singularity image using following command,
+### Method 2: using Docker
 
 ```bash
-singularity pull replidec.sif docker://denglab/replidec
+docker pull denglab/replidec
 ```
 
-### Method 2: using Conda
+If you want to use `Replidec` on an HPC, singularity is recommended. You can create a singularity image using following command,
 
 ```bash
-conda create -n replidec
-conda activate replidec
-conda install -c denglab -c conda-forge replidec
+singularity pull replidec.sif docker://denglab/replidec
 ```
 
 ### Method 3: using pip
@@ -70,9 +84,9 @@ pip3 install Replidec
 ```
 Replidec [-h] [--version] -p {multiSeqAsOne,batch,multiSeqEachAsOne}
          [-i INPUT_FILE] [-w WORKDIR] [-s SUMMARY] [-t THREADS] [-c HMMER_CRETERIA] [-H HMMER_PARAMETER] [-m MMSEQS_CRETERIA]
-         [-M MMSEQS_PARAMETER] [-b BLASTP_CRETERIA] [-B BLASTP_PARAMETER] [-d]
+         [-M MMSEQS_PARAMETER] [-b BLASTP_CRETERIA] [-B BLASTP_PARAMETER] [-d] [-D]
 ```
-## Usage: database
+## Usage: database (-d & -D)
 
 Database used in Replidec will be download automatically. 
 
@@ -80,6 +94,13 @@ Location: will be download at the where Replidec installed
 
 If you want to redownload the database, `-d` parameter can be used. The older database will be mv to "discarded_db" in the workdir(-w); This dir can be removed manually by user.
 
+We provide 2 database for user choose. Use -D to choose database. all|prokaryote
+
+1. all: This database contain all proteins from the prokaryotic, eukaryotic
+virus and prophage.
+2. prokaryote: This database contain proteins from the prokaryotic virus and
+prophage. eukaryotic virus gene was removed from this database
+
 ## Usage: Input(-i) and Propgram(-p)
 
 **Input file is different base on different program**

{Replidec-0.2.3.1 → replidec-0.3.2}/setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.3
+current_version = 0.3.2
 commit = True
 tag = True
 

{Replidec-0.2.3.1 → replidec-0.3.2}/setup.py

@@ -11,7 +11,7 @@ requirements = ["biopython>=1.77",
 
 setup(
     name='Replidec',
-    version='0.2.3.1',
+    version='0.3.2',
     author="Xue Peng",
     author_email='xue.peng@helmholtz-muenchen.de',
     keywords='Replidec',