added ability to check onlist files (under updated schema) and modifi…

…ed the seqpsec load to add properties to onlist regions if the version is older than 0.3.0. Updated 10xv1/2/3 templates to the most recent version and added their onlists

examples/specs/template/10xv1-template.yaml

@@ -0,0 +1,137 @@
+!Assay
+seqspec_version: 0.3.0
+assay_id: 10xv2
+name: 10xv2
+doi: https://doi.org/10.1126/science.aam8999
+date: 15 March 2018
+description: 10x Genomics v2 single-cell rnaseq
+modalities:
+- rna
+lib_struct: https://teichlab.github.io/scg_lib_structs/methods_html/10xChromium3.html
+sequence_protocol: Not-specified
+sequence_kit: Not-specified
+library_protocol: 10xv2 RNA
+library_kit: Not-specified
+sequence_spec:
+- !Read
+  read_id: R1.fastq.gz
+  name: Read 1
+  modality: rna
+  primer_id: custom_primer1
+  min_len: 98
+  max_len: 98
+  strand: pos
+  files:
+  - !File
+    filename: R1.fastq.gz
+    filetype: fastq
+    filesize: 0
+    url: "./fastq/R1.fastq.gz"
+    urltype: local
+    md5: 0
+- !Read
+  read_id: I1.fastq.gz
+  name: Read 2
+  modality: rna
+  primer_id: custom_primer2
+  min_len: 14
+  max_len: 14
+  strand: pos
+  files:
+  - !File
+    filename: I1.fastq.gz
+    filetype: fastq
+    filesize: 0
+    url: "./fastq/I1.fastq.gz"
+    urltype: local
+    md5: 0
+- !Read
+  read_id: R2.fastq.gz
+  name: Read 2
+  modality: rna
+  primer_id: custom_primer2
+  min_len: 10
+  max_len: 10
+  strand: neg
+  files:
+  - !File
+    filename: R2.fastq.gz
+    filetype: fastq
+    filesize: 0
+    url: "./fastq/R2.fastq.gz"
+    urltype: local
+    md5: 0
+library_spec:
+- !Region
+  parent_id: null
+  region_id: rna
+  region_type: rna
+  name: rna
+  sequence_type: joined
+  sequence: AAAAAAAAAAAAAAAANNNNNNNNNNNNNNNNNNNNNNNNNNXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXAAAAAAAAAAAAAAAA
+  min_len: 59
+  max_len: 208
+  onlist: null
+  regions:
+  - !Region
+    parent_id: rna
+    region_id: custom_primer1
+    region_type: custom_primer
+    name: custom_primer1
+    sequence_type: fixed
+    sequence: ''
+    min_len: 0
+    max_len: 0
+    onlist: null
+    regions: null
+  - !Region
+    parent_id: rna
+    region_id: cdna
+    region_type: cdna
+    name: cdna
+    sequence_type: random
+    sequence: XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
+    min_len: 1
+    max_len: 150
+    onlist: null
+    regions: null
+  - !Region
+    parent_id: rna
+    region_id: umi
+    region_type: umi
+    name: umi
+    sequence_type: random
+    sequence: XXXXXXXXXX
+    min_len: 10
+    max_len: 10
+    onlist: null
+    regions: null
+  - !Region
+    parent_id: rna
+    region_id: custom_primer2
+    region_type: custom_primer
+    name: custom_primer2
+    sequence_type: fixed
+    sequence: ''
+    min_len: 0
+    max_len: 0
+    onlist: null
+    regions: null
+  - !Region
+    parent_id: rna
+    region_id: barcode
+    region_type: barcode
+    name: barcode
+    sequence_type: onlist
+    sequence: NNNNNNNNNNNNNNNN
+    min_len: 16
+    max_len: 16
+    onlist: !Onlist
+      location: remote
+      filename: 737K-april-2014.txt.gz
+      filetype: txt
+      filesize: 11059200
+      url: https://github.com/pachterlab/qcbc/raw/main/tests/10xRNAv1/737K-april-2014.txt.gz
+      urltype: http
+      md5: 9911f5f3fbab451d79b6b38068a001f0
+    regions: null

seqspec/Region.py

@@ -368,10 +368,10 @@ def __init__(
     def __repr__(self) -> str:
         d = {
             "filename": self.filename,
-            # "filetype": self.filetype,
-            # "filesize": self.filesize,
-            # "url": self.url,
-            # "urltype": self.urltype,
+            "filetype": self.filetype,
+            "filesize": self.filesize,
+            "url": self.url,
+            "urltype": self.urltype,
             "md5": self.md5,
             "location": self.location,
         }
@@ -380,10 +380,10 @@ def __repr__(self) -> str:
     def to_dict(self):
         d = {
             "filename": self.filename,
-            # "filetype": self.filetype,
-            # "filesize": self.filesize,
-            # "url": self.url,
-            # "urltype": self.urltype,
+            "filetype": self.filetype,
+            "filesize": self.filesize,
+            "url": self.url,
+            "urltype": self.urltype,
             "md5": self.md5,
             "location": self.location,
         }

seqspec/seqspec_check.py

@@ -99,9 +99,14 @@ def run_check(schema, spec, spec_fn):
                     idx += 1
         elif ol.location == "remote":
             # ping the link with a simple http request to check if the file exists at that URI
-            if not file_exists(ol.filename):
-                errors.append(f"[error {idx}] {ol.filename} does not exist")
-                idx += 1
+            if spec.seqspec_version == "0.3.0":
+                if not file_exists(ol.url):
+                    errors.append(f"[error {idx}] {ol.filename} does not exist")
+                    idx += 1
+            else:
+                if not file_exists(ol.filename):
+                    errors.append(f"[error {idx}] {ol.filename} does not exist")
+                    idx += 1
 
     # get all of the regions with type fastq in the spec and check that those files exist relative to the path of the spec
     fqrgns = []

seqspec/utils.py

@@ -22,10 +22,27 @@ def load_spec_stream(spec_stream: io.IOBase):
         r.set_parent_id(None)
 
     # for backwards compatibilty, for specs < v0.3.0 set the files to empty
-    for r in data.sequence_spec:
-        if version.parse(data.seqspec_version) < version.parse("0.3.0"):
+    # TODO for backwards compatibility of the specs < v0.3.0, set the onlist regions with missing properties
+    if version.parse(data.seqspec_version) < version.parse("0.3.0"):
+        for r in data.sequence_spec:
             r.set_files([])
 
+        for r in data.library_spec:
+            for lf in r.get_leaves():
+                if lf.onlist is not None:
+                    filename = lf.onlist.filename
+                    location = lf.onlist.location
+                    md5 = lf.onlist.md5
+                    lf.onlist = Onlist(
+                        filename,
+                        filetype="",
+                        filesize=0,
+                        url="",
+                        urltype="",
+                        md5=md5,
+                        location=location,
+                    )
+
     return data