biofiles 0.1.1__tar.gz → 0.1.2__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {biofiles-0.1.1 → biofiles-0.1.2}/PKG-INFO +1 -1
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/dialects/gencode.py +2 -2
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/dialects/genomic_base.py +2 -2
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/dialects/refseq.py +2 -2
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles.egg-info/PKG-INFO +1 -1
- {biofiles-0.1.1 → biofiles-0.1.2}/pyproject.toml +1 -1
- {biofiles-0.1.1 → biofiles-0.1.2}/LICENSE +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/README.md +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/__init__.py +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/bam.py +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/common.py +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/dialects/__init__.py +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/dialects/detector.py +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/dialects/stringtie.py +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/fai.py +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/fasta.py +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/gff.py +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/gtf.py +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/repeatmasker.py +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/types/__init__.py +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/types/alignment.py +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/types/feature.py +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/types/repeat.py +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/types/sequence.py +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/utility/__init__.py +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/utility/cli.py +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles/utility/feature.py +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles.egg-info/SOURCES.txt +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles.egg-info/dependency_links.txt +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/biofiles.egg-info/top_level.txt +0 -0
- {biofiles-0.1.1 → biofiles-0.1.2}/setup.cfg +0 -0
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
Metadata-Version: 2.4
|
|
2
2
|
Name: biofiles
|
|
3
|
-
Version: 0.1.
|
|
3
|
+
Version: 0.1.2
|
|
4
4
|
Summary: Pure-Python, zero-dependency collection of bioinformatics-related file readers and writers
|
|
5
5
|
Author-email: Tigran Saluev <tigran@saluev.com>
|
|
6
6
|
Maintainer-email: Tigran Saluev <tigran@saluev.com>
|
|
@@ -144,7 +144,7 @@ stop_codon_exon, _ = relation(source=("transcript_id", "exon_number"), one_to_on
|
|
|
144
144
|
|
|
145
145
|
class Gene(BaseGene, type="gene"):
|
|
146
146
|
id: str = id_field(source="gene_id")
|
|
147
|
-
|
|
147
|
+
biotype: GeneType = field(source="gene_type")
|
|
148
148
|
name: str = field(source="gene_name")
|
|
149
149
|
transcripts: list["Transcript"] = gene_transcripts
|
|
150
150
|
tags: list[str] = field(source="tag", default_factory=list)
|
|
@@ -152,7 +152,7 @@ class Gene(BaseGene, type="gene"):
|
|
|
152
152
|
|
|
153
153
|
class Transcript(BaseTranscript, type="transcript"):
|
|
154
154
|
id: str = id_field(source="transcript_id")
|
|
155
|
-
|
|
155
|
+
biotype: TranscriptType = field(source="transcript_type")
|
|
156
156
|
name: str = field(source="transcript_name")
|
|
157
157
|
gene: Gene = transcript_gene
|
|
158
158
|
exons: list["Exon"] = transcript_exons
|
|
@@ -90,7 +90,7 @@ stop_codon_exon, _ = relation(source=("transcript_id", "exon_number"), one_to_on
|
|
|
90
90
|
|
|
91
91
|
class Gene(BaseGene, type="gene"):
|
|
92
92
|
id: str = id_field(source="gene_id")
|
|
93
|
-
|
|
93
|
+
biotype: GeneType = field(source="gene_biotype")
|
|
94
94
|
name: str = field(source="gene")
|
|
95
95
|
synonyms: list[str] = field(source="gene_synonym", default_factory=list)
|
|
96
96
|
transcripts: list["Transcript"] = gene_transcripts
|
|
@@ -98,7 +98,7 @@ class Gene(BaseGene, type="gene"):
|
|
|
98
98
|
|
|
99
99
|
class Transcript(BaseTranscript, type="transcript"):
|
|
100
100
|
id: str = id_field(source="transcript_id")
|
|
101
|
-
|
|
101
|
+
biotype: TranscriptType = field(source="transcript_biotype")
|
|
102
102
|
product: str | None = field(source="product", default=None)
|
|
103
103
|
gene: Gene = transcript_gene
|
|
104
104
|
exons: list["Exon"] = transcript_exons
|
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
Metadata-Version: 2.4
|
|
2
2
|
Name: biofiles
|
|
3
|
-
Version: 0.1.
|
|
3
|
+
Version: 0.1.2
|
|
4
4
|
Summary: Pure-Python, zero-dependency collection of bioinformatics-related file readers and writers
|
|
5
5
|
Author-email: Tigran Saluev <tigran@saluev.com>
|
|
6
6
|
Maintainer-email: Tigran Saluev <tigran@saluev.com>
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|
|
File without changes
|