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-rw-r--r--bh20sequploader/bh20seq-schema.yml22
-rw-r--r--bh20sequploader/supporting_webuploader.yml28
-rw-r--r--scripts/from_genbank_to_fasta_and_yaml.py12
-rw-r--r--scripts/sequences.acc396
4 files changed, 282 insertions, 176 deletions
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 0520e36..4cd0865 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -84,6 +84,11 @@ $graph:
type: string?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/OBI_0001479
+ specimen_source2:
+ doc: A specimen that derives from an anatomical part or substance arising from an organism, e.g. tissue, organ
+ type: string?
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/OBI_0001479
collection_date:
doc: Date when the sample was taken
type: string?
@@ -139,6 +144,11 @@ $graph:
type: string
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/OBI_0600047
+ sample_sequencing_technology2:
+ doc: Technology that was used to sequence this sample (e.g Sanger, Nanopor MiniION)
+ type: string?
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/OBI_0600047
sequence_assembly_method:
doc: Protocol which provides instructions on the alignment of sequencing reads to reference genome
type: string?
@@ -146,9 +156,19 @@ $graph:
_id: http://www.ebi.ac.uk/efo/EFO_0002699
sequencing_coverage:
doc: Sequence coverage defined as the average number of reads representing a given nucleotide (e.g. 100x)
- type: int?
+ type: float?
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/FLU_0000848
+ sequencing_coverage2:
+ doc: If a second sequence technology was use you can submit its coverage here
+ type: float?
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/FLU_0000848
+ additional_technology_information:
+ doc: Field for additional technology information
+ type: string?
+ jsonldPredicate:
+ _id: http://semanticscience.org/resource/SIO_001167
- name: submitterSchema
type: record
diff --git a/bh20sequploader/supporting_webuploader.yml b/bh20sequploader/supporting_webuploader.yml
index 6b8946f..3650526 100644
--- a/bh20sequploader/supporting_webuploader.yml
+++ b/bh20sequploader/supporting_webuploader.yml
@@ -10,6 +10,34 @@ host_sex:
Female: http://purl.obolibrary.org/obo/NCIT_C27993
unknown: http://purl.obolibrary.org/obo/NCIT_C17998
+sample_sequencing_technology:
+ Illumina NextSeq 500: http://www.ebi.ac.uk/efo/EFO_0009173
+ Oxford Nanopore MinION: http://www.ebi.ac.uk/efo/EFO_0008632
+ Illumina MiSeq: http://www.ebi.ac.uk/efo/EFO_0004205
+ IonTorrent: http://purl.obolibrary.org/obo/NCIT_C125894
+ Oxford Nanopore Sequencing: http://purl.obolibrary.org/obo/NCIT_C146818
+ Sanger dideoxy sequencing: http://purl.obolibrary.org/obo/NCIT_C19641
+
+sample_sequencing_technology2:
+ Illumina NextSeq 500: http://www.ebi.ac.uk/efo/EFO_0009173
+ Oxford Nanopore MinION: http://www.ebi.ac.uk/efo/EFO_0008632
+ Illumina MiSeq: http://www.ebi.ac.uk/efo/EFO_0004205
+ IonTorrent: http://purl.obolibrary.org/obo/NCIT_C125894
+ Oxford Nanopore Sequencing: http://purl.obolibrary.org/obo/NCIT_C146818
+ Sanger dideoxy sequencing: http://purl.obolibrary.org/obo/NCIT_C19641
+
+specimen_source:
+ nasopharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155831
+ oropharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155835
+ sputum: http://purl.obolibrary.org/obo/NCIT_C13278
+ bronchoalveolar lavage fluid: http://purl.obolibrary.org/obo/NCIT_C13195
+
+specimen_source2:
+ nasopharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155831
+ oropharyngeal swab: http://purl.obolibrary.org/obo/NCIT_C155835
+ sputum: http://purl.obolibrary.org/obo/NCIT_C13278
+ bronchoalveolar lavage fluid: http://purl.obolibrary.org/obo/NCIT_C13195
+
host_species:
OLS-ontology: ncbitaxon
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index 0cc1a57..6a55b5e 100644
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -7,7 +7,7 @@ import os
path_ncbi_virus_accession = 'sequences.acc'
-date = '20200414'
+date = '20200415'
path_seq_fasta = 'seq_from_nuccore.{}.fasta'.format(date)
path_metadata_xml = 'metadata_from_nuccore.{}.xml'.format(date)
@@ -19,9 +19,15 @@ for term in term_list:
tmp_list = Entrez.read(
Entrez.esearch(db='nuccore', term=term, idtype='acc', retmax='10000')
)['IdList']
- print(term, len(tmp_list))
-
+
+ # Remove mRNAs, ncRNAs, Proteins, and predicted models (more information here: https://en.wikipedia.org/wiki/RefSeq)
+ tmp_list = [x for x in tmp_list if x[:2] not in ['NM', 'NR', 'NP', 'XM', 'XR', 'XP', 'WP']]
+
# Remove the version in the id
+ tmp_list = [x.split('.')[0] for x in tmp_list]
+
+ print(term, len(tmp_list))
+
id_set.update([x.split('.')[0] for x in tmp_list])
print(term_list, len(id_set))
diff --git a/scripts/sequences.acc b/scripts/sequences.acc
index 62bde2c..a420fb4 100644
--- a/scripts/sequences.acc
+++ b/scripts/sequences.acc
@@ -1,25 +1,159 @@
-MT325599
-MT325601
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+NC_045512
+MT334522
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MT325565
MT325566
MT326147
@@ -56,7 +190,6 @@ MT326121
MT326119
MT326109
MT326100
-MT325568
MT324679
MT325561
MT325571
@@ -95,31 +228,11 @@ MT326177
MT326184
MT326185
MT326187
-MT325572
-MT325575
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-MT326115
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-MT326131
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-MT325563
-MT326164
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+MT324681
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+MT328035
MT325569
MT326097
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@@ -177,146 +290,83 @@ MT326101
MT326099
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@@ -324,9 +374,12 @@ MT304485
MT304486
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@@ -366,7 +419,6 @@ MT293168
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@@ -376,7 +428,6 @@ MT293165
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@@ -426,6 +477,8 @@ MT293223
MT291826
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+MT281577
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@@ -645,8 +698,6 @@ MT253700
MT253705
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@@ -689,6 +740,8 @@ MT246472
MT246473
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+MT233526
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@@ -774,8 +827,8 @@ MT127113
MT127114
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-LC528233
LC528232
+LC528233
MT123290
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@@ -807,8 +860,8 @@ MT066159
MT066175
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LC523807
-LC523808
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+LC523808
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@@ -830,7 +883,6 @@ LC522350
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@@ -838,13 +890,14 @@ MT019533
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LR757995
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MT007544
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MN996530
MN996531
MN996527
@@ -856,22 +909,21 @@ MN988668
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MN970003
MN970004
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MN908947
generated by cgit v1.2.3 (git 2.45.2) at 2024-11-11 13:46:48 +0000