add templates

regulatory-genomics · Sep 30, 2024 · 7487d84 · 7487d84
1 parent e7f7177
commit 7487d84
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diff --git a/python/Cargo.toml b/python/Cargo.toml
@@ -12,6 +12,7 @@ crate-type = ["cdylib"]
 anyhow = "1.0"
 bwa-mem2 = { git = "https://github.com/regulatory-genomics/bwa-mem2-rust.git", rev = "07eda9b9c2815ae52b3fa30b01de0e19fae31fe0" }
 bstr = "1.0"
+cached-path = "0.6"
 either = "1.13"
 itertools = "0.13"
 noodles = { version = "0.80", features = ["core", "fastq", "bam", "sam", "bgzf"] }

diff --git a/python/src/pyseqspec.rs b/python/src/pyseqspec.rs
@@ -4,6 +4,7 @@ use pyo3::prelude::*;
 use seqspec::{Assay, File, Modality, Read, Region, Strand, UrlType};
 use anyhow::Result;
 use termtree::Tree;
+use cached_path::Cache;
 
 /** A SeqSpec object.
     
@@ -17,7 +18,7 @@ use termtree::Tree;
     Parameters
     ----------
     path
-        Path to the AnnData file.
+        The local path or url to the seqspec file.
 
     See Also
     --------
@@ -32,7 +33,9 @@ impl SeqSpec {
     #[new]
     #[pyo3(signature = (path))] 
     pub fn new(path: &str) -> Result<Self> {
-        let assay = Assay::from_path(path)?;
+        let cache = Cache::new()?;
+        let file = cache.cached_path(path)?;
+        let assay = Assay::from_path(file)?;
         Ok(SeqSpec(assay))
     }
 

diff --git a/seqspec_templates/10x_rna_atac.yaml b/seqspec_templates/10x_rna_atac.yaml
@@ -0,0 +1,231 @@
+!Assay
+seqspec_version: 0.3.0
+assay_id: 10xMultiome
+name: 10x-ATAC-RNA
+doi: https://www.globenewswire.com/en/news-release/2020/09/15/2093690/0/en/10x-Genomics-First-to-Market-With-Product-to-Simultaneously-Capture-Epigenome-and-Transcriptome.html
+date: 15 September 2020
+description: Single Cell Multiome ATAC + Gene Expression
+modalities:
+- rna
+- atac
+lib_struct: https://teichlab.github.io/scg_lib_structs/methods_html/10xChromium_multiome.html
+library_protocol: Any
+library_kit: Illumina Truseq Dual Index
+sequence_protocol: Illumina NovaSeq 6000
+sequence_kit: NovaSeq 6000 v1.5
+sequence_spec: []
+library_spec:
+- !Region
+  parent_id: null
+  region_id: rna
+  region_type: rna
+  name: 10x-ATAC-RNA-MULTI-seq RNA
+  sequence_type: joined
+  sequence: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNNNNXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG
+  min_len: 153
+  max_len: 250
+  onlist: null
+  regions:
+  - !Region
+    parent_id: rna
+    region_id: rna-illumina_p5
+    region_type: illumina_p5
+    name: Illumina P5
+    sequence_type: fixed
+    sequence: AATGATACGGCGACCACCGAGATCTACAC
+    min_len: 29
+    max_len: 29
+    onlist: null
+    regions: null
+  - !Region
+    parent_id: rna
+    region_id: rna-truseq_read1
+    region_type: truseq_read1
+    name: RNA Truseq Read 1
+    sequence_type: fixed
+    sequence: TCTTTCCCTACACGACGCTCTTCCGATCT
+    min_len: 29
+    max_len: 29
+    onlist: null
+    regions: null
+  - !Region
+    parent_id: rna
+    region_id: rna-cell_barcode
+    region_type: barcode
+    name: Cell Barcode
+    sequence_type: onlist
+    sequence: NNNNNNNNNNNNNNNN
+    min_len: 16
+    max_len: 16
+    onlist: !Onlist
+      file_id: gex_737K-arc-v1.txt.gz
+      filename: gex_737K-arc-v1.txt.gz
+      filetype: txt
+      filesize: 0
+      url: https://teichlab.github.io/scg_lib_structs/data/10X-Genomics/gex_737K-arc-v1.txt.gz
+      urltype: https
+      md5: 0
+      location: local
+    regions: null
+  - !Region
+    region_id: rna-umi
+    region_type: umi
+    name: GEX UMI
+    sequence_type: random
+    sequence: XXXXXXXXXXXX
+    min_len: 12
+    max_len: 12
+    onlist: null
+    regions: null
+    parent_id: rna
+  - !Region
+    parent_id: rna
+    region_id: rna-cDNA
+    region_type: cdna
+    name: RNA-cDNA
+    sequence_type: random
+    sequence: XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
+    min_len: 1
+    max_len: 98
+    onlist: null
+    regions: null
+  - !Region
+    parent_id: rna
+    region_id: rna-truseq_read2
+    region_type: truseq_read2
+    name: Truseq Read 2
+    sequence_type: fixed
+    sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
+    min_len: 34
+    max_len: 34
+    onlist: null
+    regions: null
+  - !Region
+    parent_id: rna
+    region_id: rna-index7
+    region_type: index7
+    name: Truseq Read 2
+    sequence_type: onlist
+    sequence: NNNNNNNN
+    min_len: 8
+    max_len: 8
+    onlist: null
+    regions: null
+  - !Region
+    parent_id: rna
+    region_id: rna-illumina_p7
+    region_type: illumina_p7
+    name: Illumina P7
+    sequence_type: fixed
+    sequence: ATCTCGTATGCCGTCTTCTGCTTG
+    min_len: 24
+    max_len: 24
+    onlist: null
+    regions: null
+- !Region
+  parent_id: null
+  region_id: atac
+  region_type: atac
+  name: ATAC
+  sequence_type: joined
+  sequence: AATGATACGGCGACCACCGAGATCTACACNNNNNNNNNNNNNNNNCGCGTCTGTCGTCGGCAGCGTCAGATGTGTATAAGAGACAGXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCTGTCTCTTATACACATCTCCGAGCCCACGAGACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG
+  min_len: 153
+  max_len: 250
+  onlist: null
+  regions:
+  - !Region
+    parent_id: atac
+    region_id: atac-illumina_p5
+    region_type: illumina_p5
+    name: Illumina P5
+    sequence_type: fixed
+    sequence: AATGATACGGCGACCACCGAGATCTACAC
+    min_len: 29
+    max_len: 29
+    onlist: null
+    regions: null
+  - !Region
+    parent_id: atac
+    region_id: atac-cell_barcode
+    region_type: barcode
+    name: R2 Cell Barcode
+    sequence_type: onlist
+    sequence: NNNNNNNNNNNNNNNN
+    min_len: 16
+    max_len: 16
+    onlist: !Onlist
+      file_id: atac_737K-arc-v1.txt.gz
+      filename: atac_737K-arc-v1.txt.gz
+      filetype: txt
+      filesize: 0
+      url: https://teichlab.github.io/scg_lib_structs/data/10X-Genomics/atac_737K-arc-v1.txt.gz
+      urltype: https
+      md5: 0
+      location: remote
+    regions: null
+  - !Region
+    parent_id: atac
+    region_id: atac-linker
+    region_type: linker
+    name: atac linker
+    sequence_type: fixed
+    sequence: CGCGTCTG
+    min_len: 8
+    max_len: 8
+    onlist: null
+    regions: null
+  - !Region
+    parent_id: atac
+    region_id: atac-nextera_read1
+    region_type: nextera_read1
+    name: nextera_read1
+    sequence_type: fixed
+    sequence: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG
+    min_len: 33
+    max_len: 33
+    onlist: null
+    regions: null
+  - !Region
+    parent_id: atac
+    region_id: gDNA
+    region_type: gdna
+    name: gDNA
+    sequence_type: random
+    sequence: XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
+    min_len: 1
+    max_len: 98
+    onlist: null
+    regions: null
+  - !Region
+    parent_id: atac
+    region_id: atac-nextera_read2
+    region_type: nextera_read2
+    name: nextera_read2
+    sequence_type: fixed
+    sequence: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC
+    min_len: 34
+    max_len: 34
+    onlist: null
+    regions: null
+  - !Region
+    parent_id: atac
+    region_id: atac-index7
+    region_type: index7
+    name: ATAC index7
+    sequence_type: onlist
+    sequence: NNNNNNNN
+    min_len: 8
+    max_len: 8
+    onlist: null
+    regions: null
+  - !Region
+    parent_id: atac
+    region_id: atac-illumina_p7
+    region_type: illumina_p7
+    name: Illumina P7
+    sequence_type: fixed
+    sequence: ATCTCGTATGCCGTCTTCTGCTTG
+    min_len: 24
+    max_len: 24
+    onlist: null
+    regions: null