PyamilySeq 0.4.0__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-0.4.0.dist-info/METADATA

@@ -1,92 +0,0 @@
-Metadata-Version: 2.1
-Name: PyamilySeq
-Version: 0.4.0
-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, BLAST, 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
-- **End-to-End**: PyamilySeq can take a directory of GFF+FASTA files, run CD-HIT for clustering and process the results.
-- **Clustering**: Supports input from CD-HIT formatted files as well as CSV and TSV edge lists (-outfmt 6 from BLAST/DIAMOND).
-- **Reclustering**: Allows for the addition of new sequences post-initial clustering.
-- **Output**: Generates a gene 'Roary/Panaroo' formatted presence-absence CSV formatted file for downstream analysis.
-  - Align representative sequences using MAFFT.
-  - Output concatenated aligned sequences for downstream analysis.
-  - Optionally output sequences of identified families.
-
-
-### Installation
-PyamilySeq requires Python 3.6 or higher. Install using pip:
-
-```bash
-pip install PyamilySeq
-```
-
-## Usage - Menu
-```
-usage: PyamilySeq.py [-h] -id INPUT_DIR -od OUTPUT_DIR -it {separate,combined} -ns NAME_SPLIT -pid PIDENT -ld LEN_DIFF -co CLUSTERING_OUT -ct {CD-HIT,BLAST,DIAMOND,MMseqs2} [-w WRITE_FAMILIES] [-con CON_CORE] [-fasta FASTA] [-rc RECLUSTERED] [-st SEQUENCE_TAG] [-groups CORE_GROUPS]
-                     [-gpa GENE_PRESENCE_ABSENCE_OUT]
-                     ...
-
-PyamilySeq v0.4.0: PyamilySeq Run Parameters.
-
-positional arguments:
-  pyamilyseq_args       Additional arguments for PyamilySeq.
-
-options:
-  -h, --help            show this help message and exit
-
-Required Arguments:
-  -id INPUT_DIR         Directory containing GFF/FASTA files.
-  -od OUTPUT_DIR        Directory for all output files.
-  -it {separate,combined}
-                        Type of input files: 'separate' for separate FASTA and GFF files, 'combined' for GFF files with embedded FASTA sequences.
-  -ns NAME_SPLIT        Character used to split the filename and extract the genome name.
-  -pid PIDENT           Pident threshold for CD-HIT clustering.
-  -ld LEN_DIFF          Length difference (-s) threshold for CD-HIT clustering.
-  -co CLUSTERING_OUT    Output file for initial clustering.
-  -ct {CD-HIT,BLAST,DIAMOND,MMseqs2}
-                        Clustering format for PyamilySeq.
-
-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
-```
-
-### Example Run End-to-End - 'genomes' is a test-directory containing GFF files with ##FASTA at the bottom
-
-```bash
-PyamilySeq -id .../genomes -it combined -ns _combined.gff3 -pid 0.90 -ld 0.60 -co testing_cd-hit -ct CD-HIT -od .../testing
-```
-
-```Calculating Groups
-Calculating Groups
-Gene Groups:
-first_core_99: 3103
-first_core_95: 0
-first_core_15: 3217
-first_core_0: 4808
-Total Number of Gene Groups (Including Singletons): 11128
-```
-
-

PyamilySeq-0.4.0.dist-info/RECORD

@@ -1,12 +0,0 @@
-PyamilySeq/CD-Hit_StORF-Reporter_Cross-Genera_Builder.py,sha256=UzQ5iOKCNfurxmj1pnkowF11YfWBO5vnBCKxQK6goB8,26538
-PyamilySeq/Constants.py,sha256=971sO5fjptv27yRtg595ex8VuNURb2Nh4mFSdGx6HJ4,399
-PyamilySeq/PyamilySeq.py,sha256=Zy84pSBXY9EnMmk30SrfbQr9-SWYJ4rPHb9xbV3L9lU,8971
-PyamilySeq/PyamilySeq_Species.py,sha256=kTXeCgplHfCglii_g099zdt2iy0lc5wDX3k4HuSaIgo,39167
-PyamilySeq/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-PyamilySeq/combine_FASTA_with_genome_IDs.py,sha256=aMUVSk6jKnKX0g04RMM360QueZS83lRLqLLysBtQbLo,2009
-PyamilySeq-0.4.0.dist-info/LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-PyamilySeq-0.4.0.dist-info/METADATA,sha256=d0goQEGZZz_q6_sZUwoPr-h7FR-Ad7WmupIJuK8MTFc,4462
-PyamilySeq-0.4.0.dist-info/WHEEL,sha256=rWxmBtp7hEUqVLOnTaDOPpR-cZpCDkzhhcBce-Zyd5k,91
-PyamilySeq-0.4.0.dist-info/entry_points.txt,sha256=aEpNchWXaSR7_hGQqXYGtvXz14FgIcfFdXESpEhsvXg,58
-PyamilySeq-0.4.0.dist-info/top_level.txt,sha256=J6JhugUQTq4rq96yibAlQu3o4KCM9WuYfqr3w1r119M,11
-PyamilySeq-0.4.0.dist-info/RECORD,,