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-rw-r--r--bh20seqanalyzer/main.py14
-rw-r--r--bh20sequploader/bh20seq-schema.yml1
-rw-r--r--bh20sequploader/bh20seq-shex.rdf2
-rw-r--r--bh20sequploader/main.py8
-rw-r--r--scripts/dict_ontology_standardization/ncbi_speciesman_source.csv2
-rwxr-xr-xscripts/foreach.sh18
-rwxr-xr-x[-rw-r--r--]scripts/from_genbank_to_fasta_and_yaml.py33
-rw-r--r--workflows/pangenome-generate/merge-metadata.cwl46
-rw-r--r--workflows/pangenome-generate/merge-metadata.py33
-rw-r--r--workflows/pangenome-generate/minimap2.cwl2
-rw-r--r--workflows/pangenome-generate/relabel-seqs.cwl33
-rw-r--r--workflows/pangenome-generate/relabel-seqs.py24
12 files changed, 168 insertions, 48 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index 193a268..8d0f562 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -214,14 +214,26 @@ def main():
parser.add_argument('--fastq-workflow-uuid', type=str, default='lugli-7fd4e-2zp9q4jo5xpif9y', help='')
parser.add_argument('--latest-result-collection', type=str, default='lugli-4zz18-z513nlpqm03hpca', help='')
+ parser.add_argument('--kickoff', action="store_true")
args = parser.parse_args()
api = arvados.api()
- logging.info("Starting up, monitoring %s for uploads" % (args.uploader_project))
+
schema_ref = upload_schema(api, args.workflow_def_project)
+ if args.kickoff:
+ logging.info("Starting a single analysis run")
+ start_pangenome_analysis(api,
+ args.pangenome_analysis_project,
+ args.pangenome_workflow_uuid,
+ args.validated_project,
+ schema_ref)
+ return
+
+ logging.info("Starting up, monitoring %s for uploads" % (args.uploader_project))
+
while True:
move_fastq_to_fasta_results(api, args.fastq_project, args.uploader_project)
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 75308ab..1ceebe2 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -106,6 +106,7 @@ $graph:
jsonldPredicate:
_id: http://purl.obolibrary.org/obo/OBI_0001479
_type: "@id"
+ noLinkCheck: true
sample_storage_conditions:
doc: Information about storage of a specified type, e.g. frozen specimen, paraffin, fresh ....
type: string?
diff --git a/bh20sequploader/bh20seq-shex.rdf b/bh20sequploader/bh20seq-shex.rdf
index 59ee71b..31e714f 100644
--- a/bh20sequploader/bh20seq-shex.rdf
+++ b/bh20sequploader/bh20seq-shex.rdf
@@ -50,7 +50,7 @@ PREFIX wikidata: <http://www.wikidata.org/entity/>
:technologyShape {
obo:OBI_0600047 IRI {0,2} ;
- obo:FLU_0000848 xsd:integer ?;
+ obo:FLU_0000848 xsd:double ?;
efo:EFO_0002699 xsd:string ?;
}
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index 49d012d..4c4711d 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -44,7 +44,8 @@ def main():
with col.open(target, "w") as f:
r = args.sequence.read(65536)
- print(r[0:20])
+ seqlabel = r[1:r.index("\n")]
+ print(seqlabel)
while r:
f.write(r)
r = args.sequence.read(65536)
@@ -62,13 +63,14 @@ def main():
external_ip = urllib.request.urlopen('https://ident.me').read().decode('utf8')
properties = {
+ "sequence_label": seqlabel,
"upload_app": "bh20-seq-uploader",
"upload_ip": external_ip,
"upload_user": "%s@%s" % (getpass.getuser(), socket.gethostname())
}
- col.save_new(owner_uuid=UPLOAD_PROJECT, name="Uploaded by %s from %s" %
- (properties['upload_user'], properties['upload_ip']),
+ col.save_new(owner_uuid=UPLOAD_PROJECT, name="%s uploaded by %s from %s" %
+ (seqlabel, properties['upload_user'], properties['upload_ip']),
properties=properties, ensure_unique_name=True)
print("Done")
diff --git a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
index 2905588..909cf37 100644
--- a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
+++ b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
@@ -1,4 +1,4 @@
-nasopharyngeal swab, http://purl.obolibrary.org/obo/NCIT_C155831
+nasopharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155831
nasopharyngeal exudate,http://purl.obolibrary.org/obo/NCIT_C155831
respiratory swab,http://purl.obolibrary.org/obo/NCIT_C155831
naso-pharyngeal exudate,http://purl.obolibrary.org/obo/NCIT_C155831
diff --git a/scripts/foreach.sh b/scripts/foreach.sh
new file mode 100755
index 0000000..35b07b8
--- /dev/null
+++ b/scripts/foreach.sh
@@ -0,0 +1,18 @@
+#!/bin/sh
+rm -rf validated fasta_and_yaml_*
+mkdir -p validated
+./from_genbank_to_fasta_and_yaml.py
+fasta_files=$(find fasta_and_yaml_20200421/ -name "*.fasta")
+for f in $fasta_files ; do
+ yaml=$(echo $f | rev | cut -c7- | rev).yaml
+ echo $f
+ echo $yaml
+ if bh20-seq-uploader --validate $f $yaml ; then
+ sz=$(stat --format=%s $f)
+ if test $sz -gt 20000 ; then
+ mv $f $yaml validated
+ else
+ echo "Fasta file too small"
+ fi
+ fi
+done
diff --git a/scripts/from_genbank_to_fasta_and_yaml.py b/scripts/from_genbank_to_fasta_and_yaml.py
index 91562d0..00c0012 100644..100755
--- a/scripts/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/from_genbank_to_fasta_and_yaml.py
@@ -1,8 +1,10 @@
+#!/usr/bin/env python3
+
from Bio import Entrez
Entrez.email = 'another_email@gmail.com'
import xml.etree.ElementTree as ET
-import yaml
+import json
import os
from datetime import date
@@ -29,7 +31,7 @@ for term in term_list:
# Remove the version in the id
tmp_list = [x.split('.')[0] for x in tmp_list]
-
+
print(term, len(tmp_list))
tmp_list=tmp_list
# tmp_list = tmp_list[0:2] # restricting to small run
@@ -49,11 +51,11 @@ print(term_list + ['NCBI Virus'], len(id_set))
def chunks(lst, n):
for i in range(0, len(lst), n):
yield lst[i:i + n]
-
+
num_ids_for_request = 100
if not os.path.exists(dir_metadata_today):
os.makedirs(dir_metadata_today)
-
+
for i, id_x_list in enumerate(chunks(list(id_set), num_ids_for_request)):
path_metadata_xxx_xml = os.path.join(dir_metadata_today, 'metadata_{}.xml'.format(i))
print('Requesting {} ids --> {}'.format(len(id_x_list), path_metadata_xxx_xml))
@@ -63,7 +65,7 @@ if not os.path.exists(dir_metadata_today):
Entrez.efetch(db='nuccore', id=id_x_list, retmode='xml').read()
)
-
+
term_to_uri_dict = {}
for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_xxx_csv) for name_xxx_csv in os.listdir(dir_dict_ontology_standardization) if name_xxx_csv.endswith('.csv')]:
@@ -74,7 +76,7 @@ for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_x
if len(line.split(',')) > 2:
term, uri = line.strip('\n').split('",')
term = term.strip('"')
- else:
+ else:
term, uri = line.strip('\n').split(',')
term_to_uri_dict[term] = uri
@@ -125,12 +127,15 @@ if not os.path.exists(dir_fasta_and_yaml_today):
):
if info_to_check in GBSeq_comment_text:
tech_info_to_parse = GBSeq_comment_text.split('{} :: '.format(info_to_check))[1].split(' ;')[0]
-
+
if field_in_yaml == 'sequencing_coverage':
# A regular expression would be better!
- info_for_yaml_dict['technology'][field_in_yaml] = ';'.join(
- [x.strip('(average)').strip("reads/nt").replace(',', '.').strip(' xX>') for x in tech_info_to_parse.split(';')]
- )
+ try:
+ info_for_yaml_dict['technology'][field_in_yaml] = float(
+ tech_info_to_parse.strip('(average)').strip("reads/nt").replace(',', '.').strip(' xX>'))
+ except ValueError:
+ print(accession_version, "Couldn't make sense of Coverage '%s'" % tech_info_to_parse)
+ pass
elif field_in_yaml == 'sample_sequencing_technology':
new_seq_tec_list = []
for seq_tec in tech_info_to_parse.split(';'):
@@ -139,7 +144,7 @@ if not os.path.exists(dir_fasta_and_yaml_today):
seq_tec = term_to_uri_dict[seq_tec]
else:
print(accession_version, 'missing technologies:', seq_tec)
-
+
new_seq_tec_list.append(seq_tec)
for n, seq_tec in enumerate(new_seq_tec_list):
@@ -147,7 +152,7 @@ if not os.path.exists(dir_fasta_and_yaml_today):
else:
info_for_yaml_dict['technology'][field_in_yaml] = tech_info_to_parse
-
+
#term_to_uri_dict
for GBFeature in GBSeq.iter('GBFeature'):
@@ -211,7 +216,7 @@ if not os.path.exists(dir_fasta_and_yaml_today):
info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_"+GBQualifier_value_text.split('taxon:')[1]
- #Remove technology key if empty!
+ # Remove technology key if empty!
if (info_for_yaml_dict['technology']=={}):
del info_for_yaml_dict['technology']
@@ -219,4 +224,4 @@ if not os.path.exists(dir_fasta_and_yaml_today):
fw.write('>{}\n{}'.format(accession_version, GBSeq_sequence.text.upper()))
with open(os.path.join(dir_fasta_and_yaml_today, '{}.yaml'.format(accession_version)), 'w') as fw:
- yaml.dump(info_for_yaml_dict, fw, default_flow_style=False)
+ json.dump(info_for_yaml_dict, fw, indent=2)
diff --git a/workflows/pangenome-generate/merge-metadata.cwl b/workflows/pangenome-generate/merge-metadata.cwl
index fcefe32..4d9c808 100644
--- a/workflows/pangenome-generate/merge-metadata.cwl
+++ b/workflows/pangenome-generate/merge-metadata.cwl
@@ -5,16 +5,48 @@ hints:
dockerPull: commonworkflowlanguage/cwltool_module
inputs:
metadata: File[]
- metadataSchema: File
subjects: string[]
- dups: File?
- originalLabels: File
+ metadataSchema:
+ type: File
+ inputBinding: {position: 2}
+ originalLabels:
+ type: File
+ inputBinding: {position: 3}
+ dups:
+ type: File?
+ inputBinding: {position: 4}
+ script:
+ type: File
+ inputBinding: {position: 1}
+ default: {class: File, location: merge-metadata.py}
outputs:
merged: stdout
stdout: mergedmetadata.ttl
requirements:
+ InlineJavascriptRequirement: {}
InitialWorkDirRequirement:
- listing:
- - entry: {$include: merge-metadata.py}
- entryname: merge-metadata.py
-baseCommand: [python3, merge-metadata.py]
+ listing: |
+ ${
+ var i = 0;
+ var b = 1;
+ var out = [];
+ for (; i < inputs.metadata.length; i++) {
+ var block = [];
+ var sub = [];
+ for (; i < (b*150) && i < inputs.metadata.length; i++) {
+ block.push(inputs.metadata[i]);
+ sub.push(inputs.subjects[i]);
+ }
+ out.push({
+ entryname: "block"+b,
+ entry: JSON.stringify(block)
+ });
+ out.push({
+ entryname: "subs"+b,
+ entry: JSON.stringify(sub)
+ });
+ b++;
+ }
+ return out;
+ }
+baseCommand: python
diff --git a/workflows/pangenome-generate/merge-metadata.py b/workflows/pangenome-generate/merge-metadata.py
index bfec781..65d08a6 100644
--- a/workflows/pangenome-generate/merge-metadata.py
+++ b/workflows/pangenome-generate/merge-metadata.py
@@ -2,12 +2,27 @@ import re
import schema_salad.schema
import schema_salad.jsonld_context
import json
+import sys
+import os
+import logging
+
+metadataSchema = sys.argv[1]
+originalLabels = sys.argv[2]
+dups = None
+if len(sys.argv) == 4:
+ dups = sys.argv[3]
+
+def readitems(stem):
+ items = []
+ b = 1
+ while os.path.exists("%s%i" % (stem, b)):
+ with open("%s%i" % (stem, b)) as f:
+ items.extend(json.load(f))
+ b += 1
+ return items
-metadataSchema = '$(inputs.metadataSchema.path)'
-metadata = $(inputs.metadata)
-subjects = $(inputs.subjects)
-dups = json.loads('''$(inputs.dups)''')
-originalLabels = $(inputs.originalLabels)
+metadata = readitems("block")
+subjects = readitems("subs")
(document_loader,
avsc_names,
@@ -20,17 +35,15 @@ for i, m in enumerate(metadata):
g = schema_salad.jsonld_context.makerdf(subjects[i], doc, document_loader.ctx)
print(g.serialize(format="ntriples").decode("utf-8"))
-import logging
-
if dups:
- sameseqs = open(dups["path"], "rt")
+ sameseqs = open(dups, "rt")
for d in sameseqs:
logging.warn(d)
- g = re.match(r"\\d+\\t(.*)", d)
+ g = re.match(r"\d+\t(.*)", d)
logging.warn("%s", g.group(1))
sp = g.group(1).split(",")
for n in sp[1:]:
print("<%s> <http://biohackathon.org/bh20-seq-schema/has_duplicate_sequence> <%s> ." % (n.strip(), sp[0].strip()))
-orig = open(originalLabels["path"], "rt")
+orig = open(originalLabels, "rt")
print(orig.read())
diff --git a/workflows/pangenome-generate/minimap2.cwl b/workflows/pangenome-generate/minimap2.cwl
index bf19ef7..42d1dce 100644
--- a/workflows/pangenome-generate/minimap2.cwl
+++ b/workflows/pangenome-generate/minimap2.cwl
@@ -12,7 +12,7 @@ hints:
ResourceRequirement:
coresMin: 8
coresMax: 32
- ramMin: $(7 * 1024)
+ ramMin: $(9 * 1024)
outdirMin: $(Math.ceil(inputs.readsFA.size/(1024*1024*1024) + 20))
stdout: $(inputs.readsFA.nameroot).paf
baseCommand: minimap2
diff --git a/workflows/pangenome-generate/relabel-seqs.cwl b/workflows/pangenome-generate/relabel-seqs.cwl
index 2b780d4..c1f17a4 100644
--- a/workflows/pangenome-generate/relabel-seqs.cwl
+++ b/workflows/pangenome-generate/relabel-seqs.cwl
@@ -3,6 +3,10 @@ class: CommandLineTool
inputs:
readsFA: File[]
subjects: string[]
+ script:
+ type: File
+ default: {class: File, location: relabel-seqs.py}
+ inputBinding: {}
outputs:
relabeledSeqs:
type: File
@@ -15,11 +19,32 @@ outputs:
requirements:
InlineJavascriptRequirement: {}
InitialWorkDirRequirement:
- listing:
- - entry: {$include: relabel-seqs.py}
- entryname: relabel-seqs.py
+ listing: |
+ ${
+ var i = 0;
+ var b = 1;
+ var out = [];
+ for (; i < inputs.readsFA.length; i++) {
+ var block = [];
+ var sub = [];
+ for (; i < (b*150) && i < inputs.readsFA.length; i++) {
+ block.push(inputs.readsFA[i]);
+ sub.push(inputs.subjects[i]);
+ }
+ out.push({
+ entryname: "block"+b,
+ entry: JSON.stringify(block)
+ });
+ out.push({
+ entryname: "subs"+b,
+ entry: JSON.stringify(sub)
+ });
+ b++;
+ }
+ return out;
+ }
hints:
DockerRequirement:
dockerPull: commonworkflowlanguage/cwltool_module
stdout:
-baseCommand: [python, relabel-seqs.py]
+baseCommand: [python]
diff --git a/workflows/pangenome-generate/relabel-seqs.py b/workflows/pangenome-generate/relabel-seqs.py
index 1188ceb..6b022a0 100644
--- a/workflows/pangenome-generate/relabel-seqs.py
+++ b/workflows/pangenome-generate/relabel-seqs.py
@@ -1,5 +1,17 @@
-reads = $(inputs.readsFA)
-subjects = $(inputs.subjects)
+import os
+import json
+
+def readitems(stem):
+ items = []
+ b = 1
+ while os.path.exists("%s%i" % (stem, b)):
+ with open("%s%i" % (stem, b)) as f:
+ items.extend(json.load(f))
+ b += 1
+ return items
+
+reads = readitems("block")
+subjects = readitems("subs")
relabeled_fasta = open("relabeledSeqs.fasta", "wt")
original_labels = open("originalLabels.ttl", "wt")
@@ -7,12 +19,12 @@ original_labels = open("originalLabels.ttl", "wt")
for i, r in enumerate(reads):
with open(r["path"], "rt") as fa:
label = fa.readline()
- original_labels.write("<%s> <http://biohackathon.org/bh20-seq-schema/original_fasta_label> \\"%s\\" .\\n" % (subjects[i], label[1:].strip().replace('"', '\\\\"')))
- relabeled_fasta.write(">"+subjects[i]+"\\n")
+ original_labels.write("<%s> <http://biohackathon.org/bh20-seq-schema/original_fasta_label> \"%s\" .\n" % (subjects[i], label[1:].strip().replace('"', '\\"')))
+ relabeled_fasta.write(">"+subjects[i]+"\n")
data = fa.read(8096)
while data:
relabeled_fasta.write(data)
- endswithnewline = data.endswith("\\n")
+ endswithnewline = data.endswith("\n")
data = fa.read(8096)
if not endswithnewline:
- relabeled_fasta.write("\\n")
+ relabeled_fasta.write("\n")