Update seqspec check for checking files in IGVF portal

README.md

@@ -1,7 +1,6 @@
 # seqspec
 
-![github version](https://img.shields.io/badge/Version-0.3.1-informational)
-[![pypi version](https://img.shields.io/pypi/v/seqspec)](https://pypi.org/project/seqspec/0.3.1/)
+![github version](https://img.shields.io/badge/Version-0.3.0-informational)
 ![python versions](https://img.shields.io/pypi/pyversions/seqspec)
 [![license](https://img.shields.io/pypi/l/seqspec)](LICENSE)
 

docs/INSTALLATION.md

@@ -7,16 +7,8 @@ authors:
 
 # Installation
 
-The development version can be installed with
-
-```bash
-pip install git+https://github.com/pachterlab/seqspec@devel
-```
-
-The official release can be installed directly from pypi
-
 ```bash
-pip install seqspec
+pip install git+https://github.com/IGVF-DACC/seqspec.git@main
 ```
 
 Verify the installation

docs/SEQSPEC_TOOL.md

@@ -61,6 +61,12 @@ Check that the `seqspec` file is correctly formatted and consistent with the [sp
 seqspec check [-h] [-o OUT] yaml
 ```
 
+```python
+from seqspec.seqspec_check import run_check
+
+run_check(schema_fn: str, spec_fn: str, o: str)
+```
+
 - optionally, `-o OUT` can be used to write the output to a file.
 - `yaml` corresponds to the `seqspec` file.
 
@@ -133,6 +139,12 @@ $ seqspec check spec.yaml
 seqspec find [-h] [-o OUT] [-s Selector] -m MODALITY [-i IDs] yaml
 ```
 
+```python
+from seqspec.seqspec_find import run_find
+
+run_find(spec_fn: str, modality: str, id: str, idtype: str, o: str)
+```
+
 - optionally, `-o OUT` can be used to write the output to a file.
 - optionally, `-s Selector` is the type of the ID you are searching for (default: region). Can be one of
   - read
@@ -195,6 +207,12 @@ $ seqspec find -m rna -s region-type -i barcode spec.yaml
 seqspec file [-h] [-o OUT] [-i IDs] -m MODALITY [-s SELECTOR] [-f FORMAT] [-k KEY] yaml
 ```
 
+```python
+from seqspec.seqspec_file import run_file
+
+run_file(spec_fn: str, m: str, ids: List[str], idtype: str, fmt: str, k: str, o: str, fp=False)
+```
+
 - optionally, `-o OUT` can be used to write the output to a file.
 - optionally, `-s Selector` is the type of the ID you are searching for (default: read). Can be one of
   - read
@@ -266,6 +284,11 @@ Automatically fill in missing fields in the spec.
 seqspec format [-h] [-o OUT] yaml
 ```
 
+```python
+from seqspec.seqspec_format import run_format
+run_format(spec_fn: str, o: str)
+```
+
 - `-o OUT` the path to create the formatted `seqspec` file.
 - `yaml` corresponds to the `seqspec` file.
 
@@ -283,11 +306,16 @@ $ seqspec format -o spec.yaml spec.yaml
 
 Identify the position of elements in a spec for use in downstream tools. Returns the 0-indexed position of elements contained in a given region in the 5'->3' direction.
 
-```
+```bash
 seqspec index [-o OUT] [-t TOOL] [--rev] -m MODALITY -r REGION yaml
 seqspec index [-h] [-o OUT] [-t TOOL] [-s SELECTOR] [--rev] -m MODALITY [-i IDs] yaml
 ```
 
+```python
+from seqspec.seqspec_index import run_index
+run_index(spec_fn: str, modality: str, ids: List[str], idtype: str, fmt: str, rev: str, subregion_type: str, o)
+```
+
 - optionally, `-o OUT` can be used to write the output to a file.
 - optionally, `--rev` can be set to return the 3'->5' index.
 - optionally, `-t TOOL` returns the indices in the format specified by the tool. One of:
@@ -342,6 +370,11 @@ $ seqspec index -m atac -t kb -s file spec.yaml
 seqspec info [-h] [-k KEY] [-f FORMAT] [-o OUT] yaml
 ```
 
+```python
+from seqspec.seqspec_info import run_info
+run_info(spec_fn: str, f: str, k=None, o=None)
+```
+
 - optionally, `-o OUT` path to write the info.
 - optionally, `-k KEY` the object to display (default: meta). Can be one of
   - modalities
@@ -413,6 +446,11 @@ $ seqspec info -f json -k sequence_spec spec.yaml
 seqspec init [-h] -n NAME -m MODALITIES -r READS [-o OUT] newick
 ```
 
+```python
+from seqspec.seqspec_info import run_info
+run_info(spec_fn: str, f: str, k: str = None, o: str = None)
+```
+
 - optionally, `-o OUT` path to create `seqspec` file.
 - `-m MODALITIES` is a comma-separated list of modalities (e.g. rna,atac)
 - `-n NAME` is the name associated with the `seqspec` file.
@@ -432,14 +470,19 @@ $ seqspec init -n myassay -m rna -o spec.yaml -r rna,R1.fastq.gz,r1_primer,26,po
 $ seqspec init -n myassay -m rna,atac -o spec.yaml -r rna,rna_R1.fastq.gz,rna_r1_primer,26,pos:rna,rna_R2.fastq.gz,rna_r2_primer,100,neg:atac,atac_R1.fastq.gz,atac_r1_primer,100,pos:atac,atac_R2.fastq.gz,atac_r1_primer,16,neg:atac,atac_R3.fastq.gz,atac_r2_primer,100,neg "(((rna_r1_primer:0,barcode:16,umi:12,cdna:150,rna_r2_primer:0)rna),(barcode:16,atac_r1_primer:1,gdna:150,atac_r2_primer)atac)"
 ```
 
-## `seqsoec methods`: Convert seqspec file into methods section
+## `seqspec methods`: Convert seqspec file into methods section
 
 Generate a methods section from a seqspec file.
 
 ```bash
 seqspec methods [-h] -m MODALITY [-o OUT] yaml
 ```
 
+```python
+from seqspec.seqspec_methods import run_methods
+run_methods(spec_fn: str, m: str, o: str)
+```
+
 - optionally, `-o OUT` path to write the methods section.
 - `-m MODALITY` is the modality to write the methods for.
 - `yaml` corresponds to the `seqspec` file.
@@ -479,6 +522,13 @@ The library was sequenced on a Illumina NovaSeq 6000 (EFO:0008637) using the Nov
 seqspec modify [-h] [--read-id READID] [--read-name READNAME] [--primer-id PRIMERID] [--strand STRAND] [--files FILES] [--region-id REGIONID] [--region-type REGIONTYPE] [--region-name REGIONNAME] [--sequence-type SEQUENCETYPE] [--sequence SEQUENCE] [--min-len MINLEN] [--max-len MAXLEN] [-o OUT] [-i IDs] [-s SELECTOR] -m MODALITY yaml
 ```
 
+```python
+from seqspec.seqspec_modify import run_modify_read, run_modify_region
+
+run_modify_read(spec, modality, target_read, read_id, read_name, primer_id, min_len, max_len, strand, files)
+run_modify_region(spec, modality, target_region, region_id, region_type, name, sequence_type, sequence, min_len, max_len)
+```
+
 Read modifications
 
 - optionally, `--read-id READID` specifies the new `read_id`.
@@ -529,6 +579,12 @@ $ seqspec modify -m atac -o mod_spec.yaml -i atac_R1 --files "R1_1.fastq.gz,fast
 seqspec onlist [-h] [-o OUT] [-s SELECTOR] [-f FORMAT] [-i IDs] -m MODALITY yaml
 ```
 
+```python
+from seqspec.seqspec_onlist import run_onlist
+
+run_onlist(spec_fn, modality, ids, idtype, fmt, o)
+```
+
 - optionally, `-o OUT` to set the path of the onlist file.
 - `-m MODALITY` is the modality in which you are searching for the region.
 - `-i ID` is the `id` of the object to search for the onlist.
@@ -563,6 +619,11 @@ Print sequence and/or library structure as ascii, png, or html.
 seqspec print [-h] [-o OUT] [-f FORMAT] yaml
 ```
 
+```python
+from seqspec.seqspec_print import run_seqspec_print
+run_seqspec_print(spec_fn, fmt, o)
+```
+
 - optionally, `-o OUT` to set the path of printed file.
 - optionally, `-f FORMAT` is the format of the printed file. Can be one of:
   - `library-ascii`: prints an ascii tree of the library_spec
@@ -651,6 +712,11 @@ $ seqspec print -o spec.png -f seqspec-png spec.yaml
 seqspec split [-h] -o OUT yaml
 ```
 
+```python
+from seqspec.seqspec_split import run_split
+run_split(spec_fn, o)
+```
+
 - optionally, `-o OUT` name prepended to split specs.
 - `yaml` corresponds to the `seqspec` file.
 
@@ -673,6 +739,11 @@ split.tag.yaml
 seqspec version [-h] [-o OUT] yaml
 ```
 
+```python
+from seqspec.seqspec_version import run_version
+run_version(spec_fn, o)
+```
+
 - optionally, `-o OUT` path to file to write output.
 - `yaml` corresponds to the `seqspec` file.
 
@@ -693,6 +764,11 @@ This is a hidden subcommand that upgrades an old version of the spec to the curr
 seqspec upgrade [-h] [-o OUT] yaml
 ```
 
+```python
+from seqspec.seqspec_upgrade import run_upgrade
+run_upgrade(spec_fn, o)
+```
+
 ### Examples
 
 ```bash

docs/SPECIFICATION.md

@@ -153,6 +153,7 @@ Each `Region` has the following properties which are useful to annotate the elem
   - `rna`: The modality corresponding to assaying RNA.
   - `s5`: A sequencing primer or adaptor typically used in the Nextera kit in conjunction with ME1.
   - `s7`: A sequencing primer or adaptor typically used in the Nextera kit in conjunction with ME2.
+  - `sgrna_target`: A sequence corresponding to the guide RNA spacer region that determines the genomic target of CRISPR-based perturbations.
   - `tag`: A short sequence of DNA or RNA used to label or identify a sample, protein, or other grouping.
   - `truseq_read1`: The first read primer in a paired-end sequencing run using the Illumina TruSeq Library preparation kit.
   - `truseq_read2`: The second read primer in a paired-end sequencing run using the Illumina TruSeq Library preparation kit.

docs/assays/10xcrispr.spec.yaml

@@ -203,7 +203,7 @@ library_spec:
     parent_id: crispr
   - !Region
     region_id: sgrna_target
-    region_type: crispr
+    region_type: sgrna_target
     name: sgrna_target
     sequence_type: onlist
     sequence: NNNNNNNNNNNNNNNNNXXX

docs/assays/sccrispra.spec.yaml

@@ -223,7 +223,7 @@ library_spec:
     - !Region
       parent_id: crispr_R2_001.fastq.gz
       region_id: gRNA
-      region_type: gRNA
+      region_type: sgrna_target
       name: Guide RNAs
       sequence_type: onlist
       sequence: NNNNNNNNNNNNNNNNNNNN

requirements.txt

@@ -3,4 +3,5 @@ jsonschema
 newick
 requests
 biopython
-packaging
+packaging
+matplotlib>=3.4.0

seqspec/File.py

@@ -24,26 +24,18 @@ def __init__(
         self.md5 = md5
 
     def __repr__(self) -> str:
-        d = {
-            "file_id": self.file_id,
-            "filename": self.filename,
-            "filetype": self.filetype,
-            "filesize": self.filesize,
-            "url": self.url,
-            "urltype": self.urltype,
-            "md5": self.md5,
-        }
+        d = self.to_dict()
         return f"{d}"
 
     def to_dict(self):
         d = {
-            "file_id": self.file_id,
-            "filename": self.filename,
-            "filetype": self.filetype,
-            "filesize": self.filesize,
-            "url": self.url,
-            "urltype": self.urltype,
-            "md5": self.md5,
+            "file_id": getattr(self, "file_id", None),
+            "filename": getattr(self, "filename", None),
+            "filetype": getattr(self, "filetype", None),
+            "filesize": getattr(self, "filesize", None),
+            "url": getattr(self, "url", None),
+            "urltype": getattr(self, "urltype", None),
+            "md5": getattr(self, "md5", None),
         }
         return d
 

seqspec/Read.py

@@ -32,24 +32,13 @@ def set_files(self, files: Optional[List["File"]] = []):
         self.files = files
 
     def __repr__(self) -> str:
-        d = {
-            "read_id": self.read_id,
-            "name": self.name,
-            "modality": self.modality,
-            "primer_id": self.primer_id,
-            "min_len": self.min_len,
-            "max_len": self.max_len,
-            "strand": self.strand,
-            "files": self.files,
-        }
+        d = self.to_dict()
         return f"{d}"
 
     def to_dict(self):
         # TODO is this necessary for backwards compatibility?
-        if self.files:
-            files = [i.to_dict() for i in self.files]
-        else:
-            files = []
+        files = getattr(self, "files", [])
+        files = [i.to_dict() for i in files]
         d = {
             "read_id": self.read_id,
             "name": self.name,

seqspec/Region.py

@@ -417,7 +417,7 @@ def __init__(
         url: str,
         urltype: str,
         md5: str,
-        location: Optional[str],
+        # location: Optional[str],
     ) -> None:
         super().__init__()
         self.file_id = file_id

seqspec/__init__.py

@@ -1 +1,8 @@
-__version__ = "0.3.1"
+__version__ = "0.3.0"
+
+
+def get_version():
+    """
+    Returns the version of the package.
+    """
+    return __version__