getrpf 0.4.0__py3-none-any.whl

getRPF/__init__.py

@@ -0,0 +1,7 @@
+"""getRPF - Get Ribosome Protected Fragment features.
+
+A toolkit for analyzing Ribosome Protected Fragments (RPFs) from Ribo-seq experiments.
+"""
+
+__version__ = "0.4.0"
+__author__ = "Jack Tierney"

getRPF/architectures/arabidopsis_thaliana_timeseries.yaml

@@ -0,0 +1,27 @@
+seqspec_version: "0.3.0"
+assay_id: "arabidopsis_thaliana_timeseries_2024"
+name: "Arabidopsis Thaliana Time-Series Protocol"
+description: "Ribo-seq protocol with 5nt 3' UMI, custom adapter, and optional 5' random trimming"
+library_kit: "Custom Protocol (Chen et al., 2018; Smith et al., 2017)"
+modalities: ["rna"]
+sequence_spec:
+  - region_id: rpf_start
+    region_type: cdna
+    sequence_type: joined
+    min_len: 20
+    max_len: 35
+  - region_id: umi_3prime
+    region_type: umi
+    sequence_type: random
+    min_len: 5
+    max_len: 5
+  - region_id: adapter
+    region_type: adapter
+    sequence: AGCTAAGATCGGAAGAGCACACGTCTGAA
+    min_len: 29
+    max_len: 29
+quality_markers:
+  # Protocol mentions "one or two random nucleotides may be added to the 5′ end"
+  # This implies a variable 5' trim might be needed.
+  adapter_match_threshold: 0.8
+  variable_5prime_trim_expected: true

getRPF/architectures/comprehensive_adapter_check.yaml

@@ -0,0 +1,50 @@
+seqspec_version: "0.3.0"
+assay_id: "comprehensive_adapter_check"
+name: "Comprehensive Adapter Scan"
+description: "Automated check against 30+ known Ribo-seq adapters"
+library_kit: "Automated Comprehensive Adapter Scan"
+modalities: ["rna"]
+sequence_spec:
+  - region_id: rpf
+    region_type: cdna
+    sequence_type: joined
+    min_len: 20
+    max_len: 40
+  - region_id: adapter_list
+    region_type: adapter
+    sequence_type: list
+    # Longest to shortest sort order is maintained by logic, but listed here for completeness
+    sequences:
+      - TGGAATTCTCGGGTGCCAAGG
+      - AGATCGGAAGAGCACACGTCT
+      - GTGTCAGTCACTTCCAGCGG
+      - TCGTATGCCGTCTTCTGCTT
+      - GATCGGAAGAGCACACGT
+      - CGCCTTGGCCGTACAGCAG
+      - ACAGGTTCAGAGTTCTA
+      - CTGTAGGCACCATCAAT
+      - TCGTATGCCGTCTTCTG
+      - CACTCGGGCACCAAGGA
+      - CCTTGGCACCCGAGAATT
+      - GATCGGAAGAGCGTCGT
+      - CTGATGGCGCGAGGGAG
+      - GATCGGAAGAGCACACG
+      - AATGATACGGCGACCAC
+      - GATCGGAAGAGCTCGTA
+      - CAAGCAGAAGACGGCAT
+      - TGATCGGAAGAGCACAC
+      - CTGTCTCTTATACACATCT
+      - ACAGGTTCAGAGTTCTA
+      - CAAGCAGAAGACGGCAT
+      - ACTCTTTCCCTACA
+      - GATCGGAAGAGCGGTT
+      - AGATCGGAAGAGCAC
+      - AGATCGGAAGAGC
+      - TGTAGGCACCATC
+      - GATCGTCGGACT
+      - CTGTCTCTTATA
+      - CGCCTTGGCCGT
+      - TGGAATTCTCGG
+      - AAAAAAAAAA
+quality_markers:
+  adapter_match_threshold: 0.3

getRPF/architectures/ena_riboseq_standard.yaml

@@ -0,0 +1,24 @@
+seqspec_version: "0.3.0"
+assay_id: "ena_riboseq_standard"
+name: "ENA Standard RiboSeq"
+description: "Standard ENA dataset (ERR10323209)"
+library_kit: "ENA ribosome profiling dataset ERR10323209"
+modalities: ["rna"]
+sequence_spec:
+  - region_id: rpf
+    region_type: cdna
+    sequence_type: joined
+    min_len: 25
+    max_len: 80
+  - region_id: adapter_1
+    region_type: adapter
+    sequence: GGAATTCTCGGGTGCCAAGG
+    min_len: 20
+    max_len: 20
+  - region_id: adapter_2
+    region_type: adapter
+    sequence: TGGAATTCTCGGGTGCCAAGG
+    min_len: 21
+    max_len: 21
+quality_markers:
+  adapter_match_threshold: 0.5

getRPF/architectures/err605046_stau1_riboseq.yaml

@@ -0,0 +1,28 @@
+seqspec_version: "0.3.0"
+assay_id: "err605046_stau1_riboseq"
+name: "ERR605046 STAU1"
+description: "Specific STAU1 ribosome profiling dataset (ERR605046)"
+library_kit: "ERR605046 STAU1 ribosome profiling dataset"
+modalities: ["rna"]
+sequence_spec:
+  - region_id: prefix
+    region_type: unknown
+    min_len: 1
+    max_len: 1
+  - region_id: rpf
+    region_type: cdna
+    sequence_type: joined
+    min_len: 15
+    max_len: 45
+  - region_id: adapter_1
+    region_type: adapter
+    sequence: AGATCGGAAGAGC
+    min_len: 13
+    max_len: 13
+  - region_id: adapter_2
+    region_type: adapter
+    sequence: GATCGGAAGAGC
+    min_len: 12
+    max_len: 12
+quality_markers:
+  adapter_match_threshold: 0.2

getRPF/architectures/generic_umi_protocol.yaml

@@ -0,0 +1,24 @@
+seqspec_version: "0.3.0"
+assay_id: "generic_umi_protocol"
+name: "Generic UMI Protocol"
+description: "Common generic structure with 6nt UMI"
+library_kit: "Common UMI-based protocol"
+modalities: ["rna"]
+sequence_spec:
+  - region_id: umi
+    region_type: umi
+    sequence_type: random
+    min_len: 6
+    max_len: 6
+  - region_id: rpf
+    region_type: cdna
+    sequence_type: joined
+    min_len: 25
+    max_len: 35
+  - region_id: adapter
+    region_type: adapter
+    sequence: TGGAATTCTCGGGTGCCAAGG
+    min_len: 21
+    max_len: 21
+quality_markers:
+  umi_complexity_min: 0.75

getRPF/architectures/ingolia_2009.yaml

@@ -0,0 +1,19 @@
+seqspec_version: "0.3.0"
+assay_id: "ingolia_2009"
+name: "Ingolia 2009 Protocol"
+description: "Original Ingolia et al. Science 2009 yeast protocol"
+library_kit: "Ingolia et al. Science 2009"
+modalities: ["rna"]
+sequence_spec:
+  - region_id: rpf
+    region_type: cdna
+    sequence_type: joined
+    min_len: 28
+    max_len: 35
+  - region_id: adapter
+    region_type: adapter
+    sequence: CTGTAGGCACCATCAAT
+    min_len: 17
+    max_len: 17
+quality_markers:
+  adapter_match_threshold: 0.85

getRPF/architectures/mcglincy_ingolia_2017.yaml

@@ -0,0 +1,41 @@
+seqspec_version: "0.3.0"
+assay_id: "mcglincy_ingolia_2017"
+name: "McGlincy & Ingolia 2017 Protocol"
+description: "McGlincy & Ingolia (2017) protocol with 5nt UMI and 5nt Barcode (3' Linker). Includes 8 specific barcoded linkers."
+library_kit: "Ingolia Lab - Nature Protocols 2017"
+modalities: ["rna"]
+sequence_spec:
+  - region_id: rpf
+    region_type: cdna
+    sequence_type: joined
+    min_len: 26
+    max_len: 34
+    onlist: null
+  - region_id: umi
+    region_type: umi
+    sequence_type: random
+    min_len: 5
+    max_len: 5
+  - region_id: barcode
+    region_type: barcode
+    sequence_type: fixed
+    min_len: 5
+    max_len: 5
+  - region_id: adapter
+    region_type: adapter
+    # Listing all 8 barcoded linkers (Barcode + Constant Adapter)
+    # The 5nt UMI (NNNNN) precedes these.
+    sequence_type: list
+    sequences:
+      - ATCGTAGATCGGAAGAGCACACGTCTGAA
+      - AGCTAAGATCGGAAGAGCACACGTCTGAA
+      - CGTAAAGATCGGAAGAGCACACGTCTGAA
+      - CTAGAAGATCGGAAGAGCACACGTCTGAA
+      - GATCAAGATCGGAAGAGCACACGTCTGAA
+      - GCATAAGATCGGAAGAGCACACGTCTGAA
+      - TAGACAGATCGGAAGAGCACACGTCTGAA
+      - TCTAGAGATCGGAAGAGCACACGTCTGAA
+quality_markers:
+  umi_complexity_min: 0.8
+  rpf_start: 0
+  rpf_end: -1

getRPF/architectures/observed_atgtacac_3p_adapter.yaml

@@ -0,0 +1,33 @@
+# Auto-generated observed adapter/UMI structure.
+# Encodes protocol shape only; accession-level validation metadata is external to getRPF.
+# Adapter sequences are normalized to DNA alphabet (U -> T) for matching sequencing reads.
+seqspec_version: 0.3.0
+assay_id: observed_atgtacac_3p_adapter
+name: Observed ATGTACAC 3p adapter
+description: Observed adapter/UMI structure from 6 matched public run(s); RPF length
+  intentionally broad.
+library_kit: Observed public Ribo-seq protocol cluster
+modalities:
+- rna
+sequence_spec:
+- region_id: rpf
+  region_type: cdna
+  sequence_type: joined
+  min_len: 15
+  max_len: 40
+- region_id: adapter_3p
+  region_type: adapter
+  sequence: ATGTACACGGAGTCGACCCGCAACGCGA
+  min_len: 28
+  max_len: 28
+quality_markers:
+  confidence: observed_protocol
+  matched_run_count: 6
+  rpf_length_policy: broad_15_40_dynamic_boundaries_not_encoded
+  adapter_alphabet: DNA_normalized
+  example_gsms:
+  - GSM1331342
+  - GSM1331344
+  - GSM1331346
+  - GSM1331348
+  source_type: observed_public_run_cluster

getRPF/architectures/observed_ctgtaggc_3p_adapter.yaml

@@ -0,0 +1,39 @@
+# Auto-generated observed adapter/UMI structure.
+# Encodes protocol shape only; accession-level validation metadata is external to getRPF.
+# Adapter sequences are normalized to DNA alphabet (U -> T) for matching sequencing reads.
+seqspec_version: 0.3.0
+assay_id: observed_ctgtaggc_3p_adapter
+name: Observed CTGTAGGC 3p adapter
+description: Observed adapter/UMI structure from 613 matched public run(s); RPF length
+  intentionally broad.
+library_kit: Observed public Ribo-seq protocol cluster
+modalities:
+- rna
+sequence_spec:
+- region_id: rpf
+  region_type: cdna
+  sequence_type: joined
+  min_len: 15
+  max_len: 40
+- region_id: adapter_3p
+  region_type: adapter
+  sequence: CTGTAGGCACCATCAAT
+  min_len: 17
+  max_len: 17
+quality_markers:
+  confidence: observed_protocol
+  matched_run_count: 613
+  rpf_length_policy: broad_15_40_dynamic_boundaries_not_encoded
+  adapter_alphabet: DNA_normalized
+  example_gsms:
+  - GSM1184592
+  - GSM1184594
+  - GSM1184596
+  - GSM1184598
+  - GSM1184600
+  - GSM1184602
+  - GSM1187134
+  - GSM1187135
+  - GSM1187138
+  - GSM1187139
+  source_type: observed_public_run_cluster

getRPF/architectures/observed_ctgtaggc_variant_3p_adapter.yaml

@@ -0,0 +1,33 @@
+# Auto-generated observed adapter/UMI structure.
+# Encodes protocol shape only; accession-level validation metadata is external to getRPF.
+# Adapter sequences are normalized to DNA alphabet (U -> T) for matching sequencing reads.
+seqspec_version: 0.3.0
+assay_id: observed_ctgtaggc_variant_3p_adapter
+name: Observed CTGTAGGC variant 3p adapter
+description: Observed adapter/UMI structure from 4 matched public run(s); RPF length
+  intentionally broad.
+library_kit: Observed public Ribo-seq protocol cluster
+modalities:
+- rna
+sequence_spec:
+- region_id: rpf
+  region_type: cdna
+  sequence_type: joined
+  min_len: 15
+  max_len: 40
+- region_id: adapter_3p
+  region_type: adapter
+  sequence: ACTGTAGGCACCATCAATC
+  min_len: 19
+  max_len: 19
+quality_markers:
+  confidence: observed_protocol
+  matched_run_count: 4
+  rpf_length_policy: broad_15_40_dynamic_boundaries_not_encoded
+  adapter_alphabet: DNA_normalized
+  example_gsms:
+  - GSM3068264
+  - GSM3068265
+  - GSM3068266
+  - GSM3068267
+  source_type: observed_public_run_cluster

getRPF/architectures/observed_dual_ligation_adapter_pair.yaml

@@ -0,0 +1,44 @@
+# Auto-generated observed adapter/UMI structure.
+# Encodes protocol shape only; accession-level validation metadata is external to getRPF.
+# Adapter sequences are normalized to DNA alphabet (U -> T) for matching sequencing reads.
+seqspec_version: 0.3.0
+assay_id: observed_dual_ligation_adapter_pair
+name: Observed dual ligation adapter pair
+description: Observed adapter/UMI structure from 10 matched public run(s); RPF length
+  intentionally broad.
+library_kit: Observed public Ribo-seq protocol cluster
+modalities:
+- rna
+sequence_spec:
+- region_id: adapter_5p
+  region_type: adapter
+  sequence: GTTCAGAGTTCTACAGTCCGACGATC
+  min_len: 26
+  max_len: 26
+- region_id: rpf
+  region_type: cdna
+  sequence_type: joined
+  min_len: 15
+  max_len: 40
+- region_id: adapter_3p
+  region_type: adapter
+  sequence: TCGTATGCCGTCTTCTGCTTG
+  min_len: 21
+  max_len: 21
+quality_markers:
+  confidence: observed_protocol
+  matched_run_count: 10
+  rpf_length_policy: broad_15_40_dynamic_boundaries_not_encoded
+  adapter_alphabet: DNA_normalized
+  example_gsms:
+  - GSM1047584
+  - GSM1047585
+  - GSM1047586
+  - GSM1047587
+  - GSM1047591
+  - GSM1115204
+  - GSM1115207
+  - GSM1115210
+  - GSM1115213
+  - GSM1115216
+  source_type: observed_public_run_cluster

getRPF/architectures/observed_ingolia_variant_atct_adapter.yaml

@@ -0,0 +1,32 @@
+# Auto-generated observed adapter/UMI structure.
+# Encodes protocol shape only; accession-level validation metadata is external to getRPF.
+# Adapter sequences are normalized to DNA alphabet (U -> T) for matching sequencing reads.
+seqspec_version: 0.3.0
+assay_id: observed_ingolia_variant_atct_adapter
+name: Observed ATCT adapter variant
+description: Observed adapter/UMI structure from 3 matched public run(s); RPF length
+  intentionally broad.
+library_kit: Observed public Ribo-seq protocol cluster
+modalities:
+- rna
+sequence_spec:
+- region_id: rpf
+  region_type: cdna
+  sequence_type: joined
+  min_len: 15
+  max_len: 40
+- region_id: adapter_3p
+  region_type: adapter
+  sequence: ATCTCGTATGCCGTCTTCTGCTTGAAA
+  min_len: 27
+  max_len: 27
+quality_markers:
+  confidence: observed_protocol
+  matched_run_count: 3
+  rpf_length_policy: broad_15_40_dynamic_boundaries_not_encoded
+  adapter_alphabet: DNA_normalized
+  example_gsms:
+  - GSM3168233
+  - GSM3168235
+  - GSM3168236
+  source_type: observed_public_run_cluster

getRPF/architectures/observed_nextera_template_switch_6n_adapter.yaml

@@ -0,0 +1,35 @@
+# Auto-generated observed adapter/UMI structure.
+# Encodes protocol shape only; accession-level validation metadata is external to getRPF.
+# Adapter sequences are normalized to DNA alphabet (U -> T) for matching sequencing reads.
+seqspec_version: 0.3.0
+assay_id: observed_nextera_template_switch_6n_adapter
+name: Observed 6N template-switch adapter
+description: Observed adapter/UMI structure from 6 matched public run(s); RPF length
+  intentionally broad.
+library_kit: Observed public Ribo-seq protocol cluster
+modalities:
+- rna
+sequence_spec:
+- region_id: rpf
+  region_type: cdna
+  sequence_type: joined
+  min_len: 15
+  max_len: 40
+- region_id: adapter_3p
+  region_type: adapter
+  sequence: NNNNNNCACTCGGGCACCAAGGA
+  min_len: 23
+  max_len: 23
+quality_markers:
+  confidence: observed_protocol
+  matched_run_count: 6
+  rpf_length_policy: broad_15_40_dynamic_boundaries_not_encoded
+  adapter_alphabet: DNA_normalized
+  example_gsms:
+  - GSM3168387
+  - GSM3168389
+  - GSM3168390
+  - GSM3168391
+  - GSM3168392
+  - GSM3168393
+  source_type: observed_public_run_cluster

getRPF/architectures/observed_polya_a10_tail.yaml

@@ -0,0 +1,39 @@
+# Auto-generated observed adapter/UMI structure.
+# Encodes protocol shape only; accession-level validation metadata is external to getRPF.
+# Adapter sequences are normalized to DNA alphabet (U -> T) for matching sequencing reads.
+seqspec_version: 0.3.0
+assay_id: observed_polya_a10_tail
+name: Observed poly-A A10 tail
+description: Observed adapter/UMI structure from 42 matched public run(s); RPF length
+  intentionally broad.
+library_kit: Observed public Ribo-seq protocol cluster
+modalities:
+- rna
+sequence_spec:
+- region_id: rpf
+  region_type: cdna
+  sequence_type: joined
+  min_len: 15
+  max_len: 40
+- region_id: adapter_3p
+  region_type: adapter
+  sequence: AAAAAAAAAA
+  min_len: 10
+  max_len: 10
+quality_markers:
+  confidence: observed_protocol
+  matched_run_count: 42
+  rpf_length_policy: broad_15_40_dynamic_boundaries_not_encoded
+  adapter_alphabet: DNA_normalized
+  example_gsms:
+  - GSM3118928
+  - GSM3118929
+  - GSM3118930
+  - GSM3118931
+  - GSM3118932
+  - GSM3118933
+  - GSM3118934
+  - GSM3118935
+  - GSM3118936
+  - GSM3118937
+  source_type: observed_public_run_cluster

getRPF/architectures/observed_protocols_README.md

@@ -0,0 +1,13 @@
+# Observed Protocol Architectures
+
+These seqspec YAML files encode adapter and UMI structures observed across public
+Ribo-seq runs. They are bundled as generic protocol-shape candidates for getRPF
+matching and adapter-evidence scoring.
+
+They do not encode accession-level expectations, external database validation,
+or dynamic RPF boundaries. Each observed protocol uses a broad RPF length range
+so that final output quality is decided from extracted read evidence rather than
+from the source metadata that suggested the adapter structure.
+
+Adapter strings are normalized to the DNA alphabet (`U` -> `T`) for matching
+sequencing reads.

getRPF/architectures/observed_small_rna_composite_3p_adapter.yaml

@@ -0,0 +1,39 @@
+# Auto-generated observed adapter/UMI structure.
+# Encodes protocol shape only; accession-level validation metadata is external to getRPF.
+# Adapter sequences are normalized to DNA alphabet (U -> T) for matching sequencing reads.
+seqspec_version: 0.3.0
+assay_id: observed_small_rna_composite_3p_adapter
+name: Observed small-RNA composite 3p adapter
+description: Observed adapter/UMI structure from 75 matched public run(s); RPF length
+  intentionally broad.
+library_kit: Observed public Ribo-seq protocol cluster
+modalities:
+- rna
+sequence_spec:
+- region_id: rpf
+  region_type: cdna
+  sequence_type: joined
+  min_len: 15
+  max_len: 40
+- region_id: adapter_3p
+  region_type: adapter
+  sequence: TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG
+  min_len: 63
+  max_len: 63
+quality_markers:
+  confidence: observed_protocol
+  matched_run_count: 75
+  rpf_length_policy: broad_15_40_dynamic_boundaries_not_encoded
+  adapter_alphabet: DNA_normalized
+  example_gsms:
+  - GSM1446834
+  - GSM1446838
+  - GSM1446846
+  - GSM1446847
+  - GSM1446854
+  - GSM1446855
+  - GSM1446856
+  - GSM1446857
+  - GSM1446866
+  - GSM1446867
+  source_type: observed_public_run_cluster

getRPF/architectures/observed_small_rna_tgga18_adapter.yaml

@@ -0,0 +1,33 @@
+# Auto-generated observed adapter/UMI structure.
+# Encodes protocol shape only; accession-level validation metadata is external to getRPF.
+# Adapter sequences are normalized to DNA alphabet (U -> T) for matching sequencing reads.
+seqspec_version: 0.3.0
+assay_id: observed_small_rna_tgga18_adapter
+name: Observed small-RNA TGGA 18 nt adapter
+description: Observed adapter/UMI structure from 4 matched public run(s); RPF length
+  intentionally broad.
+library_kit: Observed public Ribo-seq protocol cluster
+modalities:
+- rna
+sequence_spec:
+- region_id: rpf
+  region_type: cdna
+  sequence_type: joined
+  min_len: 15
+  max_len: 40
+- region_id: adapter_3p
+  region_type: adapter
+  sequence: TGGAATTCTCGGGTGCCA
+  min_len: 18
+  max_len: 18
+quality_markers:
+  confidence: observed_protocol
+  matched_run_count: 4
+  rpf_length_policy: broad_15_40_dynamic_boundaries_not_encoded
+  adapter_alphabet: DNA_normalized
+  example_gsms:
+  - GSM3563711
+  - GSM3563712
+  - GSM3563713
+  - GSM3563714
+  source_type: observed_public_run_cluster

getRPF/architectures/observed_small_rna_truseq_composite_adapter.yaml

@@ -0,0 +1,39 @@
+# Auto-generated observed adapter/UMI structure.
+# Encodes protocol shape only; accession-level validation metadata is external to getRPF.
+# Adapter sequences are normalized to DNA alphabet (U -> T) for matching sequencing reads.
+seqspec_version: 0.3.0
+assay_id: observed_small_rna_truseq_composite_adapter
+name: Observed small-RNA TruSeq composite adapter
+description: Observed adapter/UMI structure from 20 matched public run(s); RPF length
+  intentionally broad.
+library_kit: Observed public Ribo-seq protocol cluster
+modalities:
+- rna
+sequence_spec:
+- region_id: rpf
+  region_type: cdna
+  sequence_type: joined
+  min_len: 15
+  max_len: 40
+- region_id: adapter_3p
+  region_type: adapter
+  sequence: TGGAATTCTCGGGTGCCAAGGAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCG
+  min_len: 58
+  max_len: 58
+quality_markers:
+  confidence: observed_protocol
+  matched_run_count: 20
+  rpf_length_policy: broad_15_40_dynamic_boundaries_not_encoded
+  adapter_alphabet: DNA_normalized
+  example_gsms:
+  - GSM3396990
+  - GSM3396991
+  - GSM3396992
+  - GSM3396993
+  - GSM3396994
+  - GSM3396995
+  - GSM3396996
+  - GSM3396997
+  - GSM3396998
+  - GSM3396999
+  source_type: observed_public_run_cluster

getRPF/architectures/observed_truseq_18nt_3p_adapter.yaml

@@ -0,0 +1,31 @@
+# Auto-generated observed adapter/UMI structure.
+# Encodes protocol shape only; accession-level validation metadata is external to getRPF.
+# Adapter sequences are normalized to DNA alphabet (U -> T) for matching sequencing reads.
+seqspec_version: 0.3.0
+assay_id: observed_truseq_18nt_3p_adapter
+name: Observed TruSeq 18 nt 3p adapter
+description: Observed adapter/UMI structure from 2 matched public run(s); RPF length
+  intentionally broad.
+library_kit: Observed public Ribo-seq protocol cluster
+modalities:
+- rna
+sequence_spec:
+- region_id: rpf
+  region_type: cdna
+  sequence_type: joined
+  min_len: 15
+  max_len: 40
+- region_id: adapter_3p
+  region_type: adapter
+  sequence: AGATCGGAAGAGCACAC
+  min_len: 17
+  max_len: 17
+quality_markers:
+  confidence: observed_protocol
+  matched_run_count: 2
+  rpf_length_policy: broad_15_40_dynamic_boundaries_not_encoded
+  adapter_alphabet: DNA_normalized
+  example_gsms:
+  - GSM2327825
+  - GSM2327826
+  source_type: observed_public_run_cluster