gffkit 0.3__tar.gz → 0.3.1__tar.gz

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Files changed (18) hide show
  1. {gffkit-0.3/src/gffkit.egg-info → gffkit-0.3.1}/PKG-INFO +39 -4
  2. {gffkit-0.3 → gffkit-0.3.1}/README.md +38 -3
  3. {gffkit-0.3 → gffkit-0.3.1}/pyproject.toml +1 -1
  4. {gffkit-0.3 → gffkit-0.3.1}/src/gffkit/__init__.py +1 -1
  5. {gffkit-0.3 → gffkit-0.3.1/src/gffkit.egg-info}/PKG-INFO +39 -4
  6. {gffkit-0.3 → gffkit-0.3.1}/LICENSE +0 -0
  7. {gffkit-0.3 → gffkit-0.3.1}/MANIFEST.in +0 -0
  8. {gffkit-0.3 → gffkit-0.3.1}/setup.cfg +0 -0
  9. {gffkit-0.3 → gffkit-0.3.1}/src/gffkit/__main__.py +0 -0
  10. {gffkit-0.3 → gffkit-0.3.1}/src/gffkit/add_utr.py +0 -0
  11. {gffkit-0.3 → gffkit-0.3.1}/src/gffkit/complement_annotations.py +0 -0
  12. {gffkit-0.3 → gffkit-0.3.1}/src/gffkit/detect_bridge_merged_genes.py +0 -0
  13. {gffkit-0.3 → gffkit-0.3.1}/src/gffkit/main.py +0 -0
  14. {gffkit-0.3 → gffkit-0.3.1}/src/gffkit.egg-info/SOURCES.txt +0 -0
  15. {gffkit-0.3 → gffkit-0.3.1}/src/gffkit.egg-info/dependency_links.txt +0 -0
  16. {gffkit-0.3 → gffkit-0.3.1}/src/gffkit.egg-info/entry_points.txt +0 -0
  17. {gffkit-0.3 → gffkit-0.3.1}/src/gffkit.egg-info/top_level.txt +0 -0
  18. {gffkit-0.3 → gffkit-0.3.1}/tests/test_complement_sources.py +0 -0
{gffkit-0.3/src/gffkit.egg-info → gffkit-0.3.1}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
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  Metadata-Version: 2.1
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  Name: gffkit
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- Version: 0.3
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+ Version: 0.3.1
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  Summary: Region-aware GFF annotation integration toolkit
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  Author: Qunjie Zhang
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  License: MIT
@@ -48,7 +48,8 @@ gffkit integrate \
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  --annotation-a EviAnn.gff3 \
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  --annotation-b ANNEVO.gff3 \
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  --outdir gffkit_out \
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- --prefix sample
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+ --prefix sample \
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+ -t 8
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  ```
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  Outputs:
@@ -61,7 +62,7 @@ Outputs:
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  ```bash
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  # 1. Detect suspicious merged genes in Annotation A
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- gffkit detect-bridge -i EviAnn.gff3 -o suspicious.tsv
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+ gffkit detect-bridge -i EviAnn.gff3 -o suspicious.tsv -t 8
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  # 2. Use A as the global reference, but switch to B in suspicious regions
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  gffkit complement \
@@ -69,12 +70,27 @@ gffkit complement \
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  --add ANNEVO.gff3 \
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  --swap_region_tsv suspicious.tsv \
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  --swap_region_flank 100 \
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- --output merged.gff3
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+ --output merged.gff3 \
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+ -t 8
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  # 3. Add UTR features
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  gffkit add-utr -i merged.gff3 -o final.annotation.withUTR.gff3
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  ```
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+ ### Merge three or more annotations
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+
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+ Use repeated `--add` arguments. Files are merged in the order provided.
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+
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+ ```bash
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+ gffkit complement \
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+ --ref EviAnn.gff3 \
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+ --add ANNEVO.gff3 \
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+ --add Helixer.gff3 \
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+ --add PASA.gff3 \
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+ --output merged.multi.gff3 \
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+ -t 8
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+ ```
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+
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  ## Command overview
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  ```bash
@@ -85,11 +101,30 @@ gffkit add-utr --help
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  gffkit integrate --help
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  ```
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+ ## Threads
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+
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+ Version 0.3 and later add `-t/--threads`.
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+
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+ - `detect-bridge` analyzes genes in parallel.
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+ - `complement` pre-parses multiple `--add` files in parallel, then merges them in the original command-line order.
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+ - `integrate` passes the thread count to the detect and complement steps.
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+
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+ Example:
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+
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+ ```bash
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+ gffkit integrate --annotation-a EviAnn.gff3 --annotation-b ANNEVO.gff3 -t 16
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+ ```
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+
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  ## Annotation integration strategy
89
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  - Annotation A, for example EviAnn/RNA-seq-supported GFF, is used as the global primary reference.
91
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  - Annotation B, for example ANNEVO/deep-learning GFF, is used as the local primary reference only in suspicious merged-gene regions.
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  - UTR features are reconstructed after merging using an exon-minus-CDS strategy.
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+ - When multiple tools annotate the same gene locus, the GFF source column is combined with `|`, for example `EviAnn|ANNEVO`.
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+
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+ ## Maintainer notes
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+
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+ When command-line options or behavior changes, update this `README.md` in the versioned package directory before building and uploading to PyPI.
93
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94
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  ## License
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{gffkit-0.3 → gffkit-0.3.1}/README.md RENAMED
@@ -23,7 +23,8 @@ gffkit integrate \
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  --annotation-a EviAnn.gff3 \
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  --annotation-b ANNEVO.gff3 \
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  --outdir gffkit_out \
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- --prefix sample
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+ --prefix sample \
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+ -t 8
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  ```
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  Outputs:
@@ -36,7 +37,7 @@ Outputs:
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37
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  ```bash
38
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  # 1. Detect suspicious merged genes in Annotation A
39
- gffkit detect-bridge -i EviAnn.gff3 -o suspicious.tsv
40
+ gffkit detect-bridge -i EviAnn.gff3 -o suspicious.tsv -t 8
40
41
 
41
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  # 2. Use A as the global reference, but switch to B in suspicious regions
42
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  gffkit complement \
@@ -44,12 +45,27 @@ gffkit complement \
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  --add ANNEVO.gff3 \
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  --swap_region_tsv suspicious.tsv \
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  --swap_region_flank 100 \
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- --output merged.gff3
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+ --output merged.gff3 \
49
+ -t 8
48
50
 
49
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  # 3. Add UTR features
50
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  gffkit add-utr -i merged.gff3 -o final.annotation.withUTR.gff3
51
53
  ```
52
54
 
55
+ ### Merge three or more annotations
56
+
57
+ Use repeated `--add` arguments. Files are merged in the order provided.
58
+
59
+ ```bash
60
+ gffkit complement \
61
+ --ref EviAnn.gff3 \
62
+ --add ANNEVO.gff3 \
63
+ --add Helixer.gff3 \
64
+ --add PASA.gff3 \
65
+ --output merged.multi.gff3 \
66
+ -t 8
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+ ```
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+
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  ## Command overview
54
70
 
55
71
  ```bash
@@ -60,11 +76,30 @@ gffkit add-utr --help
60
76
  gffkit integrate --help
61
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  ```
62
78
 
79
+ ## Threads
80
+
81
+ Version 0.3 and later add `-t/--threads`.
82
+
83
+ - `detect-bridge` analyzes genes in parallel.
84
+ - `complement` pre-parses multiple `--add` files in parallel, then merges them in the original command-line order.
85
+ - `integrate` passes the thread count to the detect and complement steps.
86
+
87
+ Example:
88
+
89
+ ```bash
90
+ gffkit integrate --annotation-a EviAnn.gff3 --annotation-b ANNEVO.gff3 -t 16
91
+ ```
92
+
63
93
  ## Annotation integration strategy
64
94
 
65
95
  - Annotation A, for example EviAnn/RNA-seq-supported GFF, is used as the global primary reference.
66
96
  - Annotation B, for example ANNEVO/deep-learning GFF, is used as the local primary reference only in suspicious merged-gene regions.
67
97
  - UTR features are reconstructed after merging using an exon-minus-CDS strategy.
98
+ - When multiple tools annotate the same gene locus, the GFF source column is combined with `|`, for example `EviAnn|ANNEVO`.
99
+
100
+ ## Maintainer notes
101
+
102
+ When command-line options or behavior changes, update this `README.md` in the versioned package directory before building and uploading to PyPI.
68
103
 
69
104
  ## License
70
105
 
{gffkit-0.3 → gffkit-0.3.1}/pyproject.toml RENAMED
@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
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  [project]
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  name = "gffkit"
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- version = "0.3"
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+ version = "0.3.1"
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  description = "Region-aware GFF annotation integration toolkit"
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  readme = "README.md"
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  requires-python = ">=3.8"
{gffkit-0.3 → gffkit-0.3.1}/src/gffkit/__init__.py RENAMED
@@ -1,3 +1,3 @@
1
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  """gffkit: region-aware GFF annotation integration utilities."""
2
2
 
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- __version__ = "0.3"
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+ __version__ = "0.3.1"
{gffkit-0.3 → gffkit-0.3.1/src/gffkit.egg-info}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: gffkit
3
- Version: 0.3
3
+ Version: 0.3.1
4
4
  Summary: Region-aware GFF annotation integration toolkit
5
5
  Author: Qunjie Zhang
6
6
  License: MIT
@@ -48,7 +48,8 @@ gffkit integrate \
48
48
  --annotation-a EviAnn.gff3 \
49
49
  --annotation-b ANNEVO.gff3 \
50
50
  --outdir gffkit_out \
51
- --prefix sample
51
+ --prefix sample \
52
+ -t 8
52
53
  ```
53
54
 
54
55
  Outputs:
@@ -61,7 +62,7 @@ Outputs:
61
62
 
62
63
  ```bash
63
64
  # 1. Detect suspicious merged genes in Annotation A
64
- gffkit detect-bridge -i EviAnn.gff3 -o suspicious.tsv
65
+ gffkit detect-bridge -i EviAnn.gff3 -o suspicious.tsv -t 8
65
66
 
66
67
  # 2. Use A as the global reference, but switch to B in suspicious regions
67
68
  gffkit complement \
@@ -69,12 +70,27 @@ gffkit complement \
69
70
  --add ANNEVO.gff3 \
70
71
  --swap_region_tsv suspicious.tsv \
71
72
  --swap_region_flank 100 \
72
- --output merged.gff3
73
+ --output merged.gff3 \
74
+ -t 8
73
75
 
74
76
  # 3. Add UTR features
75
77
  gffkit add-utr -i merged.gff3 -o final.annotation.withUTR.gff3
76
78
  ```
77
79
 
80
+ ### Merge three or more annotations
81
+
82
+ Use repeated `--add` arguments. Files are merged in the order provided.
83
+
84
+ ```bash
85
+ gffkit complement \
86
+ --ref EviAnn.gff3 \
87
+ --add ANNEVO.gff3 \
88
+ --add Helixer.gff3 \
89
+ --add PASA.gff3 \
90
+ --output merged.multi.gff3 \
91
+ -t 8
92
+ ```
93
+
78
94
  ## Command overview
79
95
 
80
96
  ```bash
@@ -85,11 +101,30 @@ gffkit add-utr --help
85
101
  gffkit integrate --help
86
102
  ```
87
103
 
104
+ ## Threads
105
+
106
+ Version 0.3 and later add `-t/--threads`.
107
+
108
+ - `detect-bridge` analyzes genes in parallel.
109
+ - `complement` pre-parses multiple `--add` files in parallel, then merges them in the original command-line order.
110
+ - `integrate` passes the thread count to the detect and complement steps.
111
+
112
+ Example:
113
+
114
+ ```bash
115
+ gffkit integrate --annotation-a EviAnn.gff3 --annotation-b ANNEVO.gff3 -t 16
116
+ ```
117
+
88
118
  ## Annotation integration strategy
89
119
 
90
120
  - Annotation A, for example EviAnn/RNA-seq-supported GFF, is used as the global primary reference.
91
121
  - Annotation B, for example ANNEVO/deep-learning GFF, is used as the local primary reference only in suspicious merged-gene regions.
92
122
  - UTR features are reconstructed after merging using an exon-minus-CDS strategy.
123
+ - When multiple tools annotate the same gene locus, the GFF source column is combined with `|`, for example `EviAnn|ANNEVO`.
124
+
125
+ ## Maintainer notes
126
+
127
+ When command-line options or behavior changes, update this `README.md` in the versioned package directory before building and uploading to PyPI.
93
128
 
94
129
  ## License
95
130
 
{gffkit-0.3 → gffkit-0.3.1}/LICENSE RENAMED
File without changes
{gffkit-0.3 → gffkit-0.3.1}/MANIFEST.in RENAMED
File without changes
{gffkit-0.3 → gffkit-0.3.1}/setup.cfg RENAMED
File without changes
{gffkit-0.3 → gffkit-0.3.1}/src/gffkit/__main__.py RENAMED
File without changes
{gffkit-0.3 → gffkit-0.3.1}/src/gffkit/add_utr.py RENAMED
File without changes
{gffkit-0.3 → gffkit-0.3.1}/src/gffkit/main.py RENAMED
File without changes