rare-quickprot 1.10.0__tar.gz

rare_quickprot-1.10.0/LICENSE.txt

@@ -0,0 +1,23 @@
+The MIT License
+
+Copyright (c) 2024-    School of Life and Health Sciences, Hainan University
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

rare_quickprot-1.10.0/PKG-INFO

@@ -0,0 +1,151 @@
+Metadata-Version: 2.4
+Name: rare-quickprot
+Version: 1.10.0
+Summary: homology-based method for predicting gene models across entire genomes
+Author-email: Anthony Aylward <anthony.aylward@protonmail.com>
+Project-URL: Homepage, https://github.com/anthony-aylward/quickprot
+Project-URL: Documentation, https://github.com/anthony-aylward/quickprot
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: License :: OSI Approved :: MIT License
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: biopython
+Requires-Dist: TD2
+Dynamic: license-file
+
+```sh
+conda create -n quickprot -c conda-forge -c bioconda \
+  biopython perl perl-uri miniprot td2 pip
+conda activate quickprot
+pip install rare-quickprot
+```
+
+alternatively using the `conda-environment.yml` file included in this repo:
+
+```sh
+conda env create -f conda-environment.yml
+```
+
+
+# QuickProt User Guide
+
+## Update
+
+- 2026/04/28
+  1. Major Update: The version number has been updated to 1.9.0
+  2. **BUSCO results have improved significantly！！！**
+  3. The runtime logic and results have been optimized, resulting in more comprehensive gene predictions.
+  4.  Partially overlapping genes (<0.2 overlap) are now permitted.
+  5. Compatibility with newer versions of Python has been improved.
+- 2026/04/13
+  1. extract_sequence_from_gff3.py now supports GFF3 file from NCBI. Some gene models in NCBI GFF3 contain in-frame stop codons; when translated into proteins, these are now converted to X (using the -cx option).
+- 2025/09/16
+  1. Added add_type_gff3.py script.
+  2. Optimized prediction of stop codon.
+  3. Four new options have been added, namely "-c", "-ps", "-ms", and "-an", for quality control of protein mapping, rational use to reduce pseudogenes.
+- 2025/09/08
+  1.  Added gtf_genome_to_cdna_fasta.py and gtf_genome_to_cdna_fasta.py script.
+  2. Input files now support .gz compressed files.
+  3. Now QuickProt can output more running details.
+- 2025/09/06
+  1. Provides information about the running process.
+  2. Added filter_repeatPeps_from_gff3.py script for removing repeat proteins from gff3 file.
+- 2025/05/28
+  1. Provide -ORFSoftware TD2 option, you can use TD2 as a tool for ORF prediction.
+  2. Optimization of genetic code options.
+
+##  What is QuickProt？
+
+The QuickProt algorithm is a homology-based method for predicting gene models across entire genomes, designed to rapidly construct a non-redundant set of gene models. As illustrated in Figure 1, its core principle is analogous to the blotting method. It primarily employs [miniprot](https://github.com/lh3/miniprot/) (v0.18), to align homologous protein sequences to the genome, delineates high-alignment regions to assemble pseudo-transcripts (lacking UTR regions), and predicts coding regions within these pseudo-transcripts using [TransDecoder](https://github.com/TransDecoder/TransDecoder) (v5.7.1). Subsequently, low-quality gene models are filtered out and chimeric gene models are dissected, ultimately generating a high-accuracy, non-redundant gene set.
+
+![Schema of quickprot algorithm](./docs/Schema_of_quickprot_algorithm.png#pic_center)
+
+<center>Fig1. Schema of QuickProt algorithm</center>
+
+## Installation:
+
+Before use, you need to install Perl, Python, and biopython.
+
+Python3 >= 3.8, perl >= 5 
+
+For ease of use, [miniprot](https://github.com/lh3/miniprot/) (v0.18) and  [TransDecoder](https://github.com/TransDecoder/TransDecoder) (v5.7.1)  software are integrated into QuickProt.
+
+```
+wget https://github.com/thecgs/quickprot/archive/refs/tags/quickprot-v1.8.0.tar.gz
+tar -zxvf quickprot-v1.8.0.tar.gz
+cd quickprot-v1.8.0
+./quickprot -h
+```
+
+Note:
+
+```
+# if you need to use --mask optional of qucikprot.py script, and you need to install biopython
+pip install biopython
+
+# if you need to use sort_gff3.py script, and you need to install natsort.
+pip install natsort
+
+# if you need to use -ORFSoftware TD2, and you need to install TD2
+pip install TD2
+```
+
+## Usage:
+
+To  quickly  run QuickProt software. like this, 
+
+```
+./quickprot -q protein.fasta -g genome.fasta
+```
+
+This pipeline can improve busco missing result, but you need to download [compleasm](https://github.com/huangnengCSU/compleasm) software.
+
+```
+## step1. running quickprot software
+./quickprot.py -q protein.fasta -g genome.fasta -p quickprot.raw
+
+## step2. running compleasm software
+compleasm.py run -a genome.fasta -o ./ -l your_lineage
+
+## step3. to update raw gff3 of step1 from compleasm result
+./script/update_gff3_from_minibusco.py -r quickprot.raw.longest.gff3 -m ./your_lineage/miniprot_output.gff -g genome.fasta -o improve_busco.gff3
+
+## step4. merge step1 and step3 gff3 result
+cat quickprot.raw.longest.gff3 improve_busco.gff3 > genome.longest.gff.tmp
+
+## step5. to sort by chromosomes or scaffold and gene start position and to rename gff3
+./script/sort_gff3.py genome.longest.gff.tmp | ./script/rename_gff3.py - -o genome.longest.gff3 -p QUICKPROT; rm genome.longest.gff.tmp
+
+## step6. extract protein sequence from genome and gff file
+./bin/TransDecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 genome.longest.gff3 --fasta genome.fasta --seqType prot  > genome.longest.pep.fasta
+
+## step7. extract CDS sequence from genome and gff file
+./bin/TransDecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 genome.longest.gff3 --fasta genome.fasta --seqType CDS  > genome.longest.cds.fasta
+```
+
+This step can help you remove repeat proteins (e.g. ENV, Gag, Pol, RT, RH, INT, etc.), but you need to download [diamond](https://github.com/bbuchfink/diamond).
+
+```
+./script/filter_repeatPeps_from_gff3.py -q genome.longest.pep.fasta -g genome.longest.gff3
+
+## results
+## retain.gff3 —— Gene model without repeat proteins
+## discard.gff3 —— Gene model of repeat proteins
+```
+
+## Run with Singularity
+
+Download the Singularity image [here](https://zenodo.org/records/21103261/files/quickprot.v1.9.0.sif?download=1)
+
+```
+singularity exec -B PATH -e quickprot.v1.9.0.sif quickprot.py -q protein.fasta -g genome.fasta
+```
+
+## Cite QuickProt:
+
+If you use QuickProt, please cite:
+
+> Guisen Chen, Hehe Du, Zhenjie Cao, Ying Wu, Chen Zhang, Yongcan Zhou, Jingqun Ao, Yun Sun, Zihao Yuan. 2026. “ QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics.” Molecular Ecology Resources 26, no. 2: e70097. https://doi.org/10.1111/1755-0998.70097.
+

rare_quickprot-1.10.0/README.md

@@ -0,0 +1,134 @@
+```sh
+conda create -n quickprot -c conda-forge -c bioconda \
+  biopython perl perl-uri miniprot td2 pip
+conda activate quickprot
+pip install rare-quickprot
+```
+
+alternatively using the `conda-environment.yml` file included in this repo:
+
+```sh
+conda env create -f conda-environment.yml
+```
+
+
+# QuickProt User Guide
+
+## Update
+
+- 2026/04/28
+  1. Major Update: The version number has been updated to 1.9.0
+  2. **BUSCO results have improved significantly！！！**
+  3. The runtime logic and results have been optimized, resulting in more comprehensive gene predictions.
+  4.  Partially overlapping genes (<0.2 overlap) are now permitted.
+  5. Compatibility with newer versions of Python has been improved.
+- 2026/04/13
+  1. extract_sequence_from_gff3.py now supports GFF3 file from NCBI. Some gene models in NCBI GFF3 contain in-frame stop codons; when translated into proteins, these are now converted to X (using the -cx option).
+- 2025/09/16
+  1. Added add_type_gff3.py script.
+  2. Optimized prediction of stop codon.
+  3. Four new options have been added, namely "-c", "-ps", "-ms", and "-an", for quality control of protein mapping, rational use to reduce pseudogenes.
+- 2025/09/08
+  1.  Added gtf_genome_to_cdna_fasta.py and gtf_genome_to_cdna_fasta.py script.
+  2. Input files now support .gz compressed files.
+  3. Now QuickProt can output more running details.
+- 2025/09/06
+  1. Provides information about the running process.
+  2. Added filter_repeatPeps_from_gff3.py script for removing repeat proteins from gff3 file.
+- 2025/05/28
+  1. Provide -ORFSoftware TD2 option, you can use TD2 as a tool for ORF prediction.
+  2. Optimization of genetic code options.
+
+##  What is QuickProt？
+
+The QuickProt algorithm is a homology-based method for predicting gene models across entire genomes, designed to rapidly construct a non-redundant set of gene models. As illustrated in Figure 1, its core principle is analogous to the blotting method. It primarily employs [miniprot](https://github.com/lh3/miniprot/) (v0.18), to align homologous protein sequences to the genome, delineates high-alignment regions to assemble pseudo-transcripts (lacking UTR regions), and predicts coding regions within these pseudo-transcripts using [TransDecoder](https://github.com/TransDecoder/TransDecoder) (v5.7.1). Subsequently, low-quality gene models are filtered out and chimeric gene models are dissected, ultimately generating a high-accuracy, non-redundant gene set.
+
+![Schema of quickprot algorithm](./docs/Schema_of_quickprot_algorithm.png#pic_center)
+
+<center>Fig1. Schema of QuickProt algorithm</center>
+
+## Installation:
+
+Before use, you need to install Perl, Python, and biopython.
+
+Python3 >= 3.8, perl >= 5 
+
+For ease of use, [miniprot](https://github.com/lh3/miniprot/) (v0.18) and  [TransDecoder](https://github.com/TransDecoder/TransDecoder) (v5.7.1)  software are integrated into QuickProt.
+
+```
+wget https://github.com/thecgs/quickprot/archive/refs/tags/quickprot-v1.8.0.tar.gz
+tar -zxvf quickprot-v1.8.0.tar.gz
+cd quickprot-v1.8.0
+./quickprot -h
+```
+
+Note:
+
+```
+# if you need to use --mask optional of qucikprot.py script, and you need to install biopython
+pip install biopython
+
+# if you need to use sort_gff3.py script, and you need to install natsort.
+pip install natsort
+
+# if you need to use -ORFSoftware TD2, and you need to install TD2
+pip install TD2
+```
+
+## Usage:
+
+To  quickly  run QuickProt software. like this, 
+
+```
+./quickprot -q protein.fasta -g genome.fasta
+```
+
+This pipeline can improve busco missing result, but you need to download [compleasm](https://github.com/huangnengCSU/compleasm) software.
+
+```
+## step1. running quickprot software
+./quickprot.py -q protein.fasta -g genome.fasta -p quickprot.raw
+
+## step2. running compleasm software
+compleasm.py run -a genome.fasta -o ./ -l your_lineage
+
+## step3. to update raw gff3 of step1 from compleasm result
+./script/update_gff3_from_minibusco.py -r quickprot.raw.longest.gff3 -m ./your_lineage/miniprot_output.gff -g genome.fasta -o improve_busco.gff3
+
+## step4. merge step1 and step3 gff3 result
+cat quickprot.raw.longest.gff3 improve_busco.gff3 > genome.longest.gff.tmp
+
+## step5. to sort by chromosomes or scaffold and gene start position and to rename gff3
+./script/sort_gff3.py genome.longest.gff.tmp | ./script/rename_gff3.py - -o genome.longest.gff3 -p QUICKPROT; rm genome.longest.gff.tmp
+
+## step6. extract protein sequence from genome and gff file
+./bin/TransDecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 genome.longest.gff3 --fasta genome.fasta --seqType prot  > genome.longest.pep.fasta
+
+## step7. extract CDS sequence from genome and gff file
+./bin/TransDecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 genome.longest.gff3 --fasta genome.fasta --seqType CDS  > genome.longest.cds.fasta
+```
+
+This step can help you remove repeat proteins (e.g. ENV, Gag, Pol, RT, RH, INT, etc.), but you need to download [diamond](https://github.com/bbuchfink/diamond).
+
+```
+./script/filter_repeatPeps_from_gff3.py -q genome.longest.pep.fasta -g genome.longest.gff3
+
+## results
+## retain.gff3 —— Gene model without repeat proteins
+## discard.gff3 —— Gene model of repeat proteins
+```
+
+## Run with Singularity
+
+Download the Singularity image [here](https://zenodo.org/records/21103261/files/quickprot.v1.9.0.sif?download=1)
+
+```
+singularity exec -B PATH -e quickprot.v1.9.0.sif quickprot.py -q protein.fasta -g genome.fasta
+```
+
+## Cite QuickProt:
+
+If you use QuickProt, please cite:
+
+> Guisen Chen, Hehe Du, Zhenjie Cao, Ying Wu, Chen Zhang, Yongcan Zhou, Jingqun Ao, Yun Sun, Zihao Yuan. 2026. “ QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics.” Molecular Ecology Resources 26, no. 2: e70097. https://doi.org/10.1111/1755-0998.70097.
+

rare_quickprot-1.10.0/pyproject.toml

@@ -0,0 +1,54 @@
+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "rare-quickprot"
+version = "1.10.0" # Don't forget to match with version.py
+authors = [
+    { name="Anthony Aylward", email="anthony.aylward@protonmail.com" },
+]
+description = "homology-based method for predicting gene models across entire genomes"
+readme = "README.md"
+requires-python = ">=3.11"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+    "License :: OSI Approved :: MIT License",
+]
+dependencies = [
+    "biopython",
+    "TD2"
+]
+
+[project.urls]
+"Homepage" = "https://github.com/anthony-aylward/quickprot"
+"Documentation" = "https://github.com/anthony-aylward/quickprot"
+
+[project.scripts]
+quickprot = "quickprot:main"
+
+[tool.setuptools]
+package-dir = {quickprot="src/quickprot"}
+script-files = [
+    "src/quickprot/quickprot.py",
+    "src/quickprot/add_type_gff3.py",
+    "src/quickprot/extract_sequence_from_gff3.py",
+    "src/quickprot/filter_repeatPeps_from_gff3.py",
+    "src/quickprot/get_intron_from_gff3.py",
+    "src/quickprot/get_longest_transcript_gff3.py",
+    "src/quickprot/gtf_genome_to_cdna_fasta.py",
+    "src/quickprot/rename_gff3.py",
+    "src/quickprot/sm2rmForFasta.py",
+    "src/quickprot/sort_gff3.py",
+    "src/quickprot/split_and_filter_gene_model.py",
+    "src/quickprot/stat_gff3.py",
+    "src/quickprot/update_gff3_from_minibusco.py",
+    "src/quickprot/gtf_to_alignment_gff3.pl",
+    "src/quickprot/cdna_alignment_orf_to_genome_orf.pl",
+    "src/quickprot/Fasta_reader.pm",
+    "src/quickprot/Gene_obj.pm",
+    "src/quickprot/GFF3_utils2.pm",
+    "src/quickprot/Nuc_translator.pm",
+    "src/quickprot/Longest_orf.pm"
+]

rare_quickprot-1.10.0/rare_quickprot.egg-info/PKG-INFO

@@ -0,0 +1,151 @@
+Metadata-Version: 2.4
+Name: rare-quickprot
+Version: 1.10.0
+Summary: homology-based method for predicting gene models across entire genomes
+Author-email: Anthony Aylward <anthony.aylward@protonmail.com>
+Project-URL: Homepage, https://github.com/anthony-aylward/quickprot
+Project-URL: Documentation, https://github.com/anthony-aylward/quickprot
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Classifier: License :: OSI Approved :: MIT License
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE.txt
+Requires-Dist: biopython
+Requires-Dist: TD2
+Dynamic: license-file
+
+```sh
+conda create -n quickprot -c conda-forge -c bioconda \
+  biopython perl perl-uri miniprot td2 pip
+conda activate quickprot
+pip install rare-quickprot
+```
+
+alternatively using the `conda-environment.yml` file included in this repo:
+
+```sh
+conda env create -f conda-environment.yml
+```
+
+
+# QuickProt User Guide
+
+## Update
+
+- 2026/04/28
+  1. Major Update: The version number has been updated to 1.9.0
+  2. **BUSCO results have improved significantly！！！**
+  3. The runtime logic and results have been optimized, resulting in more comprehensive gene predictions.
+  4.  Partially overlapping genes (<0.2 overlap) are now permitted.
+  5. Compatibility with newer versions of Python has been improved.
+- 2026/04/13
+  1. extract_sequence_from_gff3.py now supports GFF3 file from NCBI. Some gene models in NCBI GFF3 contain in-frame stop codons; when translated into proteins, these are now converted to X (using the -cx option).
+- 2025/09/16
+  1. Added add_type_gff3.py script.
+  2. Optimized prediction of stop codon.
+  3. Four new options have been added, namely "-c", "-ps", "-ms", and "-an", for quality control of protein mapping, rational use to reduce pseudogenes.
+- 2025/09/08
+  1.  Added gtf_genome_to_cdna_fasta.py and gtf_genome_to_cdna_fasta.py script.
+  2. Input files now support .gz compressed files.
+  3. Now QuickProt can output more running details.
+- 2025/09/06
+  1. Provides information about the running process.
+  2. Added filter_repeatPeps_from_gff3.py script for removing repeat proteins from gff3 file.
+- 2025/05/28
+  1. Provide -ORFSoftware TD2 option, you can use TD2 as a tool for ORF prediction.
+  2. Optimization of genetic code options.
+
+##  What is QuickProt？
+
+The QuickProt algorithm is a homology-based method for predicting gene models across entire genomes, designed to rapidly construct a non-redundant set of gene models. As illustrated in Figure 1, its core principle is analogous to the blotting method. It primarily employs [miniprot](https://github.com/lh3/miniprot/) (v0.18), to align homologous protein sequences to the genome, delineates high-alignment regions to assemble pseudo-transcripts (lacking UTR regions), and predicts coding regions within these pseudo-transcripts using [TransDecoder](https://github.com/TransDecoder/TransDecoder) (v5.7.1). Subsequently, low-quality gene models are filtered out and chimeric gene models are dissected, ultimately generating a high-accuracy, non-redundant gene set.
+
+![Schema of quickprot algorithm](./docs/Schema_of_quickprot_algorithm.png#pic_center)
+
+<center>Fig1. Schema of QuickProt algorithm</center>
+
+## Installation:
+
+Before use, you need to install Perl, Python, and biopython.
+
+Python3 >= 3.8, perl >= 5 
+
+For ease of use, [miniprot](https://github.com/lh3/miniprot/) (v0.18) and  [TransDecoder](https://github.com/TransDecoder/TransDecoder) (v5.7.1)  software are integrated into QuickProt.
+
+```
+wget https://github.com/thecgs/quickprot/archive/refs/tags/quickprot-v1.8.0.tar.gz
+tar -zxvf quickprot-v1.8.0.tar.gz
+cd quickprot-v1.8.0
+./quickprot -h
+```
+
+Note:
+
+```
+# if you need to use --mask optional of qucikprot.py script, and you need to install biopython
+pip install biopython
+
+# if you need to use sort_gff3.py script, and you need to install natsort.
+pip install natsort
+
+# if you need to use -ORFSoftware TD2, and you need to install TD2
+pip install TD2
+```
+
+## Usage:
+
+To  quickly  run QuickProt software. like this, 
+
+```
+./quickprot -q protein.fasta -g genome.fasta
+```
+
+This pipeline can improve busco missing result, but you need to download [compleasm](https://github.com/huangnengCSU/compleasm) software.
+
+```
+## step1. running quickprot software
+./quickprot.py -q protein.fasta -g genome.fasta -p quickprot.raw
+
+## step2. running compleasm software
+compleasm.py run -a genome.fasta -o ./ -l your_lineage
+
+## step3. to update raw gff3 of step1 from compleasm result
+./script/update_gff3_from_minibusco.py -r quickprot.raw.longest.gff3 -m ./your_lineage/miniprot_output.gff -g genome.fasta -o improve_busco.gff3
+
+## step4. merge step1 and step3 gff3 result
+cat quickprot.raw.longest.gff3 improve_busco.gff3 > genome.longest.gff.tmp
+
+## step5. to sort by chromosomes or scaffold and gene start position and to rename gff3
+./script/sort_gff3.py genome.longest.gff.tmp | ./script/rename_gff3.py - -o genome.longest.gff3 -p QUICKPROT; rm genome.longest.gff.tmp
+
+## step6. extract protein sequence from genome and gff file
+./bin/TransDecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 genome.longest.gff3 --fasta genome.fasta --seqType prot  > genome.longest.pep.fasta
+
+## step7. extract CDS sequence from genome and gff file
+./bin/TransDecoder-5.7.1/util/gff3_file_to_proteins.pl --gff3 genome.longest.gff3 --fasta genome.fasta --seqType CDS  > genome.longest.cds.fasta
+```
+
+This step can help you remove repeat proteins (e.g. ENV, Gag, Pol, RT, RH, INT, etc.), but you need to download [diamond](https://github.com/bbuchfink/diamond).
+
+```
+./script/filter_repeatPeps_from_gff3.py -q genome.longest.pep.fasta -g genome.longest.gff3
+
+## results
+## retain.gff3 —— Gene model without repeat proteins
+## discard.gff3 —— Gene model of repeat proteins
+```
+
+## Run with Singularity
+
+Download the Singularity image [here](https://zenodo.org/records/21103261/files/quickprot.v1.9.0.sif?download=1)
+
+```
+singularity exec -B PATH -e quickprot.v1.9.0.sif quickprot.py -q protein.fasta -g genome.fasta
+```
+
+## Cite QuickProt:
+
+If you use QuickProt, please cite:
+
+> Guisen Chen, Hehe Du, Zhenjie Cao, Ying Wu, Chen Zhang, Yongcan Zhou, Jingqun Ao, Yun Sun, Zihao Yuan. 2026. “ QuickProt: A Fast and Accurate Homology-Based Protein Annotation Tool for Non-Model Organisms to Advance Comparative Genomics.” Molecular Ecology Resources 26, no. 2: e70097. https://doi.org/10.1111/1755-0998.70097.
+

rare_quickprot-1.10.0/rare_quickprot.egg-info/SOURCES.txt

@@ -0,0 +1,31 @@
+LICENSE.txt
+README.md
+pyproject.toml
+rare_quickprot.egg-info/PKG-INFO
+rare_quickprot.egg-info/SOURCES.txt
+rare_quickprot.egg-info/dependency_links.txt
+rare_quickprot.egg-info/entry_points.txt
+rare_quickprot.egg-info/requires.txt
+rare_quickprot.egg-info/top_level.txt
+src/quickprot/Fasta_reader.pm
+src/quickprot/GFF3_utils2.pm
+src/quickprot/Gene_obj.pm
+src/quickprot/Longest_orf.pm
+src/quickprot/Nuc_translator.pm
+src/quickprot/__init__.py
+src/quickprot/add_type_gff3.py
+src/quickprot/cdna_alignment_orf_to_genome_orf.pl
+src/quickprot/extract_sequence_from_gff3.py
+src/quickprot/filter_repeatPeps_from_gff3.py
+src/quickprot/get_intron_from_gff3.py
+src/quickprot/get_longest_transcript_gff3.py
+src/quickprot/gtf_genome_to_cdna_fasta.py
+src/quickprot/gtf_to_alignment_gff3.pl
+src/quickprot/quickprot.py
+src/quickprot/rename_gff3.py
+src/quickprot/sm2rmForFasta.py
+src/quickprot/sort_gff3.py
+src/quickprot/split_and_filter_gene_model.py
+src/quickprot/stat_gff3.py
+src/quickprot/update_gff3_from_minibusco.py
+src/quickprot/version.py

rare_quickprot-1.10.0/rare_quickprot.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

rare_quickprot-1.10.0/rare_quickprot.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+quickprot = quickprot:main

rare_quickprot-1.10.0/rare_quickprot.egg-info/requires.txt

@@ -0,0 +1,2 @@
+biopython
+TD2

rare_quickprot-1.10.0/rare_quickprot.egg-info/top_level.txt

@@ -0,0 +1 @@
+quickprot

rare_quickprot-1.10.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+