PyamilySeq 0.3.0__py3-none-any.whl → 0.5.0__py3-none-any.whl

PyamilySeq/combine_FASTA_with_genome_IDs.py

@@ -1,49 +0,0 @@
-
-import argparse
-import gzip
-import glob
-
-def combine_files(files, split, glob_location, combined_out):
-    count = 0
-
-    for file in glob.glob(glob_location + '/' + files):
-        count += 1
-        try:
-            with gzip.open(file, 'rb') as genome:
-
-                for line in genome:
-                    if line.startswith(b'#'):
-                        continue
-                    elif line.startswith(b'>'):
-                        genome_name = bytes(file.split(split)[0].split('/')[-1], 'utf-8')
-                        line = line.split(b' ')[0]
-                        line = line.replace(b'>', b'>' + genome_name + b'|')
-                        combined_out.write(line.decode('utf-8')+'\n')
-                    else:
-                        combined_out.write(line.decode('utf-8'))
-        except gzip.BadGzipFile:
-            with open(file, 'r') as genome:
-
-                for line in genome:
-                    if line.startswith('#'):
-                        continue
-                    elif line.startswith('>'):
-                        genome_name = file.split(split)[0].split('/')[-1]
-                        line = line.replace('>', '>' + genome_name + '|')
-                        combined_out.write(line)
-                    else:
-                        combined_out.write(line)
-
-def main():
-    parser = argparse.ArgumentParser(description="Combine gzipped fasta files.")
-    parser.add_argument("files", help="File pattern to match within the specified directory.")
-    parser.add_argument("split", help="String used to split the file path and extract the genome name.")
-    parser.add_argument("glob_location", help="Directory location where the files are located.")
-    parser.add_argument("combined_out", help="Output file where the combined data will be written.")
-    args = parser.parse_args()
-
-    with open(args.combined_out, 'w') as combined_out:
-        combine_files(args.files, args.split, args.glob_location, combined_out)
-
-if __name__ == "__main__":
-    main()

PyamilySeq-0.3.0.dist-info/METADATA

@@ -1,103 +0,0 @@
-Metadata-Version: 2.1
-Name: PyamilySeq
-Version: 0.3.0
-Summary: PyamilySeq - A a tool to look for sequence-based gene families identified by clustering methods such as CD-HIT, DIAMOND, BLAST or MMseqs2.
-Home-page: https://github.com/NickJD/PyamilySeq
-Author: Nicholas Dimonaco
-Author-email: nicholas@dimonaco.co.uk
-Project-URL: Bug Tracker, https://github.com/NickJD/PyamilySeq/issues
-Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
-Classifier: Operating System :: OS Independent
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
-License-File: LICENSE
-
-# PyamilySeq - !BETA!
-PyamilySeq (Family Seek) is a Python tool for clustering gene sequences into families based on sequence similarity identified by tools such as CD-HIT, DIAMOND or MMseqs2.
-This work is an extension of the gene family / pangenome tool developed for the StORF-Reporter publication in NAR (https://doi.org/10.1093/nar/gkad814).
-
-## Features
-
-- **Clustering**: Supports input from CD-HIT formatted files as well as TSV and CSV Edge List formats.
-- **Reclustering**: Allows for the addition of new sequences post-initial clustering.
-- **Output**: Generates a gene 'Roary' presence-absence CSV formatted file for downstream analysis.
-
-## Installation
-
-PyamilySeq requires Python 3.6 or higher. Install dependencies using pip:
-
-```bash
-pip install PyamilySeq
-```
-
-## Usage - Menu
-```
-usage: PyamilySeq_Species.py [-h] -c CLUSTERS -f {CD-HIT,CSV,TSV} [-w WRITE_FAMILIES] [-con CON_CORE] [-fasta FASTA] [-rc RECLUSTERED] [-st SEQUENCE_TAG]
-                             [-groups CORE_GROUPS] [-gpa GENE_PRESENCE_ABSENCE_OUT] [-verbose {True,False}] [-v]
-
-PyamilySeq v0.3.0: PyamilySeq Run Parameters.
-
-Required Arguments:
-  -c CLUSTERS           Clustering output file from CD-HIT, TSV or CSV Edge List
-  -f {CD-HIT,CSV,TSV}   Which format to use (CD-HIT or Comma/Tab Separated Edge-List (such as MMseqs2 tsv output))
-
-Output Parameters:
-  -w WRITE_FAMILIES     Default - No output: Output sequences of identified families (provide levels at which to output "-w 99,95" - Must provide FASTA file
-                        with -fasta
-  -con CON_CORE         Default - No output: Output aligned and concatinated sequences of identified families - used for MSA (provide levels at which to
-                        output "-w 99,95" - Must provide FASTA file with -fasta
-  -fasta FASTA          FASTA file to use in conjunction with "-w" or "-con"
-
-Optional Arguments:
-  -rc RECLUSTERED       Clustering output file from secondary round of clustering
-  -st SEQUENCE_TAG      Default - "StORF": Unique identifier to be used to distinguish the second of two rounds of clustered sequences
-  -groups CORE_GROUPS   Default - ('99,95,15'): Gene family groups to use
-  -gpa GENE_PRESENCE_ABSENCE_OUT
-                        Default - False: If selected, a Roary formatted gene_presence_absence.csv will be created - Required for Coinfinder and other
-                        downstream tools
-
-Misc:
-  -verbose {True,False}
-                        Default - False: Print out runtime messages
-  -v                    Default - False: Print out version number and exit
-
-
-```
-
-### Clustering Analysis
-
-To perform clustering analysis:
-
-```bash
-python pyamilyseq.py -c clusters_file -f format
-```
-
-Replace `clusters_file` with the path to your clustering output file and `format` with one of: `CD-HIT`, `CSV`, or `TSV`.
-
-### Reclustering
-
-To add new sequences and recluster:
-
-```bash
-PyamilySeq -c clusters_file -f format --reclustered reclustered_file
-```
-
-Replace `reclustered_file` with the path to the file containing additional sequences.
-
-## Output
-
-PyamilySeq generates various outputs, including:
-
-- **Gene Presence-Absence File**: This CSV file details the presence and absence of genes across genomes.
-- **FASTA Files for Each Gene Family**:  
-
-## Gene Family Groups
-
-After analysis, PyamilySeq categorizes gene families into several groups:
-
-- **First Core**: Gene families present in all analysed genomes initially.
-- **Extended Core**: Gene families extended with additional sequences.
-- **Combined Core**: Gene families combined with both initial and additional sequences.
-- **Second Core**: Gene families identified only in the additional sequences.
-- **Only Second Core**: Gene families exclusively found in the additional sequences.

PyamilySeq-0.3.0.dist-info/RECORD

@@ -1,11 +0,0 @@
-PyamilySeq/CD-Hit_StORF-Reporter_Cross-Genera_Builder.py,sha256=UzQ5iOKCNfurxmj1pnkowF11YfWBO5vnBCKxQK6goB8,26538
-PyamilySeq/Constants.py,sha256=PdgSIux2jfv6QlAOxRIFgbsH95Xq6DMQcvZodGsk7tw,399
-PyamilySeq/PyamilySeq_Species.py,sha256=zLGfyTtxk4znoUevyjfb978pT3XNjWu44-8Seqnl7ec,38961
-PyamilySeq/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-PyamilySeq/combine_FASTA_with_genome_IDs.py,sha256=aMUVSk6jKnKX0g04RMM360QueZS83lRLqLLysBtQbLo,2009
-PyamilySeq-0.3.0.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-PyamilySeq-0.3.0.dist-info/METADATA,sha256=iJOcBDtkFBUZTFGQMBwdUuaZnKAO1I9Pc-YFgvvhySQ,4382
-PyamilySeq-0.3.0.dist-info/WHEEL,sha256=-oYQCr74JF3a37z2nRlQays_SX2MqOANoqVjBBAP2yE,91
-PyamilySeq-0.3.0.dist-info/entry_points.txt,sha256=zGtA2Ycf0LG3PR7zuuT0wjaAKLFxtyGgBc0O_W7E250,66
-PyamilySeq-0.3.0.dist-info/top_level.txt,sha256=J6JhugUQTq4rq96yibAlQu3o4KCM9WuYfqr3w1r119M,11
-PyamilySeq-0.3.0.dist-info/RECORD,,

PyamilySeq-0.3.0.dist-info/entry_points.txt

@@ -1,2 +0,0 @@
-[console_scripts]
-PyamilySeq = PyamilySeq.PyamilySeq_Species:main