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| -rw-r--r-- | .gitignore | 2 | ||||
| -rw-r--r-- | LICENSE | 201 | ||||
| -rw-r--r-- | README.md | 162 | ||||
| -rw-r--r-- | bh20seqanalyzer/main.py | 131 | ||||
| -rw-r--r-- | bh20sequploader/bh20seq-schema.yml | 36 | ||||
| -rw-r--r-- | bh20sequploader/main.py | 56 | ||||
| -rw-r--r-- | bh20sequploader/qc_metadata.py | 21 | ||||
| -rw-r--r-- | example/metadata.yaml | 17 | ||||
| -rw-r--r-- | example/sequence.fasta | 214 | ||||
| -rw-r--r-- | gittaggers.py | 36 | ||||
| -rw-r--r-- | setup.py | 46 |
11 files changed, 922 insertions, 0 deletions
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We also recommend that a + file or class name and description of purpose be included on the + same "printed page" as the copyright notice for easier + identification within third-party archives. + + Copyright {yyyy} {name of copyright owner} + + Licensed under the Apache License, Version 2.0 (the "License"); + you may not use this file except in compliance with the License. + You may obtain a copy of the License at + + http://www.apache.org/licenses/LICENSE-2.0 + + Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. diff --git a/README.md b/README.md new file mode 100644 index 0000000..a6fe052 --- /dev/null +++ b/README.md @@ -0,0 +1,162 @@ +# Sequence uploader + +This repository provides a sequence uploader for the COVID-19 Virtual Biohackathon's Public Sequence Resource project. You can use it to upload the genomes of SARS-CoV-2 samples to make them publicly and freely available to other researchers. + +To get started, first [install the uploader](#installation), and use the `bh20-seq-uploader` command to [uplaod your data](#usage). + +# Installation + +There are several ways to install the uploader. The most portable is with a [virtualenv](#installation-with-virtualenv). + +## Installation with `virtualenv` + +1. **Prepare your system.** You need to make sure you have Python, and the ability to install modules such as `pycurl` and `pyopenssl`. On Ubuntu 18.04, you can run: + +```sh +sudo apt update +sudo apt install -y virtualenv git libcurl4-openssl-dev build-essential python3-dev libssl-dev +``` + +2. **Create and enter your virtualenv.** Go to some memorable directory and make and enter a virtualenv: + +```sh +virtualenv --python python3 venv +. venv/bin/activate +``` + +Note that you will need to repeat the `. venv/bin/activate` step from this directory to enter your virtualenv whenever you want to use the installed tool. + +3. **Install the tool.** Once in your virtualenv, install this project: + +```sh +pip3 install git+https://github.com/arvados/bh20-seq-resource.git@master +``` + +4. **Test the tool.** Try running: + +```sh +bh20-seq-uploader --help +``` + +It should print some instructions about how to use the uploader. + +**Make sure you are in your virtualenv whenever you run the tool!** If you ever can't run the tool, and your prompt doesn't say `(venv)`, try going to the directory where you put the virtualenv and running `. venv/bin/activate`. It only works for the current terminal window; you will need to run it again if you open a new terminal. + +## Installation with `pip3 --user` + +If you don't want to have to enter a virtualenv every time you use the uploader, you can use the `--user` feature of `pip3` to install the tool for your user. + +1. **Prepare your system.** Just as for the `virtualenv` method, you need to install some dependencies. On Ubuntu 18.04, you can run: + +```sh +sudo apt update +sudo apt install -y virtualenv git libcurl4-openssl-dev build-essential python3-dev libssl-dev +``` + +2. **Install the tool.** You can run: + +```sh +pip3 install --user git+https://github.com/arvados/bh20-seq-resource.git@master +``` + +3. **Make sure the tool is on your `PATH`.** THe `pip3` command will install the uploader in `.local/bin` inside your home directory. Your shell may not know to look for commands there by default. To fix this for the terminal you currently have open, run: + +```sh +export PATH=$PATH:$HOME/.local/bin +``` + +To make this change permanent, assuming your shell is Bash, run: + +```sh +echo 'export PATH=$PATH:$HOME/.local/bin' >>~/.bashrc +``` + +4. **Test the tool.** Try running: + +```sh +bh20-seq-uploader --help +``` + +It should print some instructions about how to use the uploader. + +## Installation from Source for Development + +If you plan to contribute to the project, you may want to install an editable copy from source. With this method, changes to the source code are automatically reflected in the installed copy of the tool. + +1. **Prepare your system.** On Ubuntu 18.04, you can run: + +```sh +sudo apt update +sudo apt install -y virtualenv git libcurl4-openssl-dev build-essential python3-dev libssl-dev +``` + +2. **Clone and enter the repository.** You can run: + +```sh +git clone https://github.com/arvados/bh20-seq-resource.git +cd bh20-seq-resource +``` + +3. **Create and enter a virtualenv.** Go to some memorable directory and make and enter a virtualenv: + +```sh +virtualenv --python python3 venv +. venv/bin/activate +``` + +Note that you will need to repeat the `. venv/bin/activate` step from this directory to enter your virtualenv whenever you want to use the installed tool. + +4. **Install the checked-out repository in editable mode.** Once in your virtualenv, install with this special pip command: + +```sh +pip3 install -e . +``` + +5. **Test the tool.** Try running: + +```sh +bh20-seq-uploader --help +``` + +It should print some instructions about how to use the uploader. + +## Installation with GNU Guix + +Another way to install this tool is inside a [GNU Guix Environment](https://guix.gnu.org/manual/en/html_node/Invoking-guix-environment.html), which can handle installing dependencies for you even when you don't have root access on an Ubuntu system. + +1. **Set up and enter a container with the necessary dependencies.** After installing Guix as `~/opt/guix/bin/guix`, run: + +```sh +~/opt/guix/bin/guix environment -C guix --ad-hoc git python openssl python-pycurl nss-certs +``` + +2. **Install the tool.** From there you can follow the [user installation instructions](#installation-with-pip3---user). In brief: + +```sh +pip3 install --user git+https://github.com/arvados/bh20-seq-resource.git@master +``` + +# Usage + +Run the uploader with a FASTA file and accompanying metadata file in [JSON-LD format](https://json-ld.org/): + +```sh +bh20-seq-uploader example/sequence.fasta example/metadata.json +``` + +## Workflow for Generating a Pangenome + +All these uploaded sequences are being fed into a workflow to generate a [pangenome](https://academic.oup.com/bib/article/19/1/118/2566735) for the virus. You can replicate this workflow yourself. + +Get your SARS-CoV-2 sequences from GenBank in `seqs.fa`, and then run: + +```sh +minimap2 -cx asm20 -X seqs.fa seqs.fa >seqs.paf +seqwish -s seqs.fa -p seqs.paf -g seqs.gfa +odgi build -g seqs.gfa -s -o seqs.odgi +odgi viz -i seqs.odgi -o seqs.png -x 4000 -y 500 -R -P 5 +``` + +For more information on building pangenome models, [see this wiki page](https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Pangenome#pangenome-model-from-available-genomes). + + diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py new file mode 100644 index 0000000..78e32c9 --- /dev/null +++ b/bh20seqanalyzer/main.py @@ -0,0 +1,131 @@ +import argparse +import arvados +import arvados.collection +import time +import subprocess +import tempfile +import json +import logging +import ruamel.yaml +from bh20sequploader.qc_metadata import qc_metadata + +logging.basicConfig(format="[%(asctime)s] %(levelname)s %(message)s", datefmt="%Y-%m-%d %H:%M:%S", + level=logging.INFO) +logging.getLogger("googleapiclient.discovery").setLevel(logging.WARN) + +def validate_upload(api, collection, validated_project): + col = arvados.collection.Collection(collection["uuid"]) + + # validate the collection here. Check metadata, etc. + valid = True + + if "sequence.fasta" not in col: + valid = False + logging.warn("Upload '%s' missing sequence.fasta", collection["name"]) + if "metadata.yaml" not in col: + logging.warn("Upload '%s' missing metadata.yaml", collection["name"]) + valid = False + else: + metadata_content = ruamel.yaml.round_trip_load(col.open("metadata.yaml")) + valid = qc_metadata(metadata_content) and valid + + dup = api.collections().list(filters=[["owner_uuid", "=", validated_project], + ["portable_data_hash", "=", col.portable_data_hash()]]).execute() + if dup["items"]: + # This exact collection has been uploaded before. + valid = False + logging.warn("Upload '%s' is duplicate" % collection["name"]) + + if valid: + logging.info("Added '%s' to validated sequences" % collection["name"]) + # Move it to the "validated" project to be included in the next analysis + api.collections().update(uuid=collection["uuid"], body={"owner_uuid": validated_project}).execute() + else: + # It is invalid, delete it. + logging.warn("Deleting '%s'" % collection["name"]) + api.collections().delete(uuid=collection["uuid"]).execute() + + return valid + +def start_analysis(api, + analysis_project, + workflow_uuid, + validated_project): + + project = api.groups().create(body={ + "group_class": "project", + "name": "Pangenome analysis", + "owner_uuid": analysis_project, + }, ensure_unique_name=True).execute() + + validated = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", validated_project]]) + + with tempfile.NamedTemporaryFile() as tmp: + inputobj = { + "inputReads": [] + } + for v in validated: + inputobj["inputReads"].append({ + "class": "File", + "location": "keep:%s/sequence.fasta" % v["portable_data_hash"] + }) + tmp.write(json.dumps(inputobj, indent=2).encode('utf-8')) + tmp.flush() + cmd = ["arvados-cwl-runner", + "--submit", + "--no-wait", + "--debug", + "--project-uuid=%s" % project["uuid"], + "arvwf:%s" % workflow_uuid, + tmp.name] + logging.info("Running %s" % ' '.join(cmd)) + comp = subprocess.run(cmd, capture_output=True) + if comp.returncode != 0: + logging.error(comp.stderr.decode('utf-8')) + + +def copy_most_recent_result(api, analysis_project, latest_result_uuid): + most_recent_analysis = api.groups().list(filters=[['owner_uuid', '=', analysis_project]], + order="created_at desc", limit=1).execute() + for m in most_recent_analysis["items"]: + cr = api.container_requests().list(filters=[['owner_uuid', '=', m["uuid"]], + ["requesting_container_uuid", "=", None]]).execute() + if cr["items"] and cr["items"][0]["output_uuid"]: + wf = cr["items"][0] + src = api.collections().get(uuid=wf["output_uuid"]).execute() + dst = api.collections().get(uuid=latest_result_uuid).execute() + if src["portable_data_hash"] != dst["portable_data_hash"]: + logging.info("Copying latest result from '%s' to %s", m["name"], latest_result_uuid) + api.collections().update(uuid=latest_result_uuid, + body={"manifest_text": src["manifest_text"], + "description": "latest result from %s %s" % (m["name"], wf["uuid"])}).execute() + break + + +def main(): + parser = argparse.ArgumentParser(description='Analyze collections uploaded to a project') + parser.add_argument('--uploader-project', type=str, default='lugli-j7d0g-n5clictpuvwk8aa', help='') + parser.add_argument('--analysis-project', type=str, default='lugli-j7d0g-y4k4uswcqi3ku56', help='') + parser.add_argument('--validated-project', type=str, default='lugli-j7d0g-5ct8p1i1wrgyjvp', help='') + parser.add_argument('--workflow-uuid', type=str, default='lugli-7fd4e-mqfu9y3ofnpnho1', help='') + parser.add_argument('--latest-result-uuid', type=str, default='lugli-4zz18-z513nlpqm03hpca', help='') + args = parser.parse_args() + + api = arvados.api() + + logging.info("Starting up, monitoring %s for uploads" % (args.uploader_project)) + + while True: + new_collections = api.collections().list(filters=[['owner_uuid', '=', args.uploader_project]]).execute() + at_least_one_new_valid_seq = False + for c in new_collections["items"]: + at_least_one_new_valid_seq = validate_upload(api, c, args.validated_project) or at_least_one_new_valid_seq + + if at_least_one_new_valid_seq: + start_analysis(api, args.analysis_project, + args.workflow_uuid, + args.validated_project) + + copy_most_recent_result(api, args.analysis_project, args.latest_result_uuid) + + time.sleep(10) diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml new file mode 100644 index 0000000..6e0973a --- /dev/null +++ b/bh20sequploader/bh20seq-schema.yml @@ -0,0 +1,36 @@ +$graph: + +- name: sampleInformationSchema + type: record + fields: + location: string + host: string + sequenceTechnology: string + assemblyMethod: string + +- name: InstituteInformationSchema + type: record + fields: + OriginatingLab: string + SubmittingLab: string + +- name: SubmitterInformationSchema + type: record + fields: + Submitter: string + submissionDate: string + +- name: VirusDetailSchema + type: record + fields: + VirusName: string + AccessionId: string + +- name: MainSchema + type: record + documentRoot: true + fields: + sampleInformation: sampleInformationSchema + InstituteInformation: InstituteInformationSchema + SubmitterInformation: SubmitterInformationSchema + VirusDetail: VirusDetailSchema diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py new file mode 100644 index 0000000..8b8fefe --- /dev/null +++ b/bh20sequploader/main.py @@ -0,0 +1,56 @@ +import argparse +import time +import arvados +import arvados.collection +import json +import urllib.request +import socket +import getpass +from .qc_metadata import qc_metadata + +ARVADOS_API_HOST='lugli.arvadosapi.com' +ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462' +UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa' + +def main(): + parser = argparse.ArgumentParser(description='Upload SARS-CoV-19 sequences for analysis') + parser.add_argument('sequence', type=argparse.FileType('r'), help='sequence FASTA') + parser.add_argument('metadata', type=argparse.FileType('r'), help='sequence metadata json') + args = parser.parse_args() + + api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True) + + qc_metadata(args.metadata.name) + + col = arvados.collection.Collection(api_client=api) + + print("Reading FASTA") + with col.open("sequence.fasta", "w") as f: + r = args.sequence.read(65536) + print(r[0:20]) + while r: + f.write(r) + r = args.sequence.read(65536) + + print("Reading metadata") + with col.open("metadata.yaml", "w") as f: + r = args.metadata.read(65536) + print(r[0:20]) + while r: + f.write(r) + r = args.metadata.read(65536) + + external_ip = urllib.request.urlopen('https://ident.me').read().decode('utf8') + + properties = { + "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']), + properties=properties, ensure_unique_name=True) + +if __name__ == "__main__": + main() diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py new file mode 100644 index 0000000..78b31b2 --- /dev/null +++ b/bh20sequploader/qc_metadata.py @@ -0,0 +1,21 @@ +import schema_salad.schema +import logging +import pkg_resources + +def qc_metadata(metadatafile): + schema_resource = pkg_resources.resource_stream(__name__, "bh20seq-schema.yml") + cache = {"https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml": schema_resource.read().decode("utf-8")} + (document_loader, + avsc_names, + schema_metadata, + metaschema_loader) = schema_salad.schema.load_schema("https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml", cache=cache) + + if not isinstance(avsc_names, schema_salad.avro.schema.Names): + print(avsc_names) + return False + + try: + doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True) + return True + except: + return False diff --git a/example/metadata.yaml b/example/metadata.yaml new file mode 100644 index 0000000..587d0be --- /dev/null +++ b/example/metadata.yaml @@ -0,0 +1,17 @@ +sampleInformation: + location: "USA" + host : "Homo Sapiens" + sequenceTechnology: "Sanger" + assemblyMethod: "CLC Genomics" + +InstituteInformation: + OriginatingLab: "Erik's kitchen" + SubmittingLab: "National Institute for Viral Disease Control and Prevention, China CDC" + +SubmitterInformation: + Submitter: "National Institute for Viral Disease Control and Prevention, China CDC" + submissionDate: "04-04-2020" + +VirusDetail: + VirusName: "hCoV-19/USA/identifer/2020" + AccessionId: "EPI_ISL_Random" diff --git a/example/sequence.fasta b/example/sequence.fasta new file mode 100644 index 0000000..3c4c0ef --- /dev/null +++ b/example/sequence.fasta @@ -0,0 +1,214 @@ +>AF324493.2 HIV-1 vector pNL4-3, complete sequence +TGGAAGGGCTAATTTGGTCCCAAAAAAGACAAGAGATCCTTGATCTGTGGATCTACCACACACAAGGCTA +CTTCCCTGATTGGCAGAACTACACACCAGGGCCAGGGATCAGATATCCACTGACCTTTGGATGGTGCTTC +AAGTTAGTACCAGTTGAACCAGAGCAAGTAGAAGAGGCCAATGAAGGAGAGAACAACAGCTTGTTACACC +CTATGAGCCAGCATGGGATGGAGGACCCGGAGGGAGAAGTATTAGTGTGGAAGTTTGACAGCCTCCTAGC +ATTTCGTCACATGGCCCGAGAGCTGCATCCGGAGTACTACAAAGACTGCTGACATCGAGCTTTCTACAAG +GGACTTTCCGCTGGGGACTTTCCAGGGAGGTGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGAT +GCTACATATAAGCAGCTGCTTTTTGCCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGC +TCTCTGGCTAACTAGGGAACCCACTGCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTCAAAGTAGTGTG +TGCCCGTCTGTTGTGTGACTCTGGTAACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCT +AGCAGTGGCGCCCGAACAGGGACTTGAAAGCGAAAGTAAAGCCAGAGGAGATCTCTCGACGCAGGACTCG +GCTTGCTGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACTGGTGAGTACGCCAAAAATTTTGACTAGC +GGAGGCTAGAAGGAGAGAGATGGGTGCGAGAGCGTCGGTATTAAGCGGGGGAGAATTAGATAAATGGGAA +AAAATTCGGTTAAGGCCAGGGGGAAAGAAACAATATAAACTAAAACATATAGTATGGGCAAGCAGGGAGC +TAGAACGATTCGCAGTTAATCCTGGCCTTTTAGAGACATCAGAAGGCTGTAGACAAATACTGGGACAGCT +ACAACCATCCCTTCAGACAGGATCAGAAGAACTTAGATCATTATATAATACAATAGCAGTCCTCTATTGT +GTGCATCAAAGGATAGATGTAAAAGACACCAAGGAAGCCTTAGATAAGATAGAGGAAGAGCAAAACAAAA +GTAAGAAAAAGGCACAGCAAGCAGCAGCTGACACAGGAAACAACAGCCAGGTCAGCCAAAATTACCCTAT +AGTGCAGAACCTCCAGGGGCAAATGGTACATCAGGCCATATCACCTAGAACTTTAAATGCATGGGTAAAA +GTAGTAGAAGAGAAGGCTTTCAGCCCAGAAGTAATACCCATGTTTTCAGCATTATCAGAAGGAGCCACCC +CACAAGATTTAAATACCATGCTAAACACAGTGGGGGGACATCAAGCAGCCATGCAAATGTTAAAAGAGAC +CATCAATGAGGAAGCTGCAGAATGGGATAGATTGCATCCAGTGCATGCAGGGCCTATTGCACCAGGCCAG +ATGAGAGAACCAAGGGGAAGTGACATAGCAGGAACTACTAGTACCCTTCAGGAACAAATAGGATGGATGA +CACATAATCCACCTATCCCAGTAGGAGAAATCTATAAAAGATGGATAATCCTGGGATTAAATAAAATAGT +AAGAATGTATAGCCCTACCAGCATTCTGGACATAAGACAAGGACCAAAGGAACCCTTTAGAGACTATGTA +GACCGATTCTATAAAACTCTAAGAGCCGAGCAAGCTTCACAAGAGGTAAAAAATTGGATGACAGAAACCT +TGTTGGTCCAAAATGCGAACCCAGATTGTAAGACTATTTTAAAAGCATTGGGACCAGGAGCGACACTAGA +AGAAATGATGACAGCATGTCAGGGAGTGGGGGGACCCGGCCATAAAGCAAGAGTTTTGGCTGAAGCAATG +AGCCAAGTAACAAATCCAGCTACCATAATGATACAGAAAGGCAATTTTAGGAACCAAAGAAAGACTGTTA +AGTGTTTCAATTGTGGCAAAGAAGGGCACATAGCCAAAAATTGCAGGGCCCCTAGGAAAAAGGGCTGTTG +GAAATGTGGAAAGGAAGGACACCAAATGAAAGATTGTACTGAGAGACAGGCTAATTTTTTAGGGAAGATC +TGGCCTTCCCACAAGGGAAGGCCAGGGAATTTTCTTCAGAGCAGACCAGAGCCAACAGCCCCACCAGAAG +AGAGCTTCAGGTTTGGGGAAGAGACAACAACTCCCTCTCAGAAGCAGGAGCCGATAGACAAGGAACTGTA +TCCTTTAGCTTCCCTCAGATCACTCTTTGGCAGCGACCCCTCGTCACAATAAAGATAGGGGGGCAATTAA +AGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAATTTGCCAGGAAGATGGAA +ACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATC +TGCGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGT +TGACTCAGATTGGCTGCACTTTAAATTTTCCCATTAGTCCTATTGAGACTGTACCAGTAAAATTAAAGCC +AGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATT +TGTACAGAAATGGAAAAGGAAGGAAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTAT +TTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAAC +TCAAGATTTCTGGGAAGTTCAATTAGGAATACCACATCCTGCAGGGTTAAAACAGAAAAAATCAGTAACA +GTACTGGATGTGGGCGATGCATATTTTTCAGTTCCCTTAGATAAAGACTTCAGGAAGTATACTGCATTTA +CCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAA +AGGATCACCAGCAATATTCCAGTGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGAC +ATAGTCATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAA +AAATAGAGGAACTGAGACAACATCTGTTGAGGTGGGGATTTACCACACCAGACAAAAAACATCAGAAAGA +ACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCA +GAAAAGGACAGCTGGACTGTCAATGACATACAGAAATTAGTGGGAAAATTGAATTGGGCAAGTCAGATTT +ATGCAGGGATTAAAGTAAGGCAATTATGTAAACTTCTTAGGGGAACCAAAGCACTAACAGAAGTAGTACC +ACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGGGAGATTCTAAAAGAACCGGTACATGGAGTG +TATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAA +TTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAGTATGCAAGAATGAAGGGTGCCCACACTAATGA +TGTGAAACAATTAACAGAGGCAGTACAAAAAATAGCCACAGAAAGCATAGTAATATGGGGAAAGACTCCT +AAATTTAAATTACCCATACAAAAGGAAACATGGGAAGCATGGTGGACAGAGTATTGGCAAGCCACCTGGA +TTCCTGAGTGGGAGTTTGTCAATACCCCTCCCTTAGTGAAGTTATGGTACCAGTTAGAGAAAGAACCCAT +AATAGGAGCAGAAACTTTCTATGTAGATGGGGCAGCCAATAGGGAAACTAAATTAGGAAAAGCAGGATAT +GTAACTGACAGAGGAAGACAAAAAGTTGTCCCCCTAACGGACACAACAAATCAGAAGACTGAGTTACAAG +CAATTCATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTGACAGACTCACAATATGCATTGGG +AATCATTCAAGCACAACCAGATAAGAGTGAATCAGAGTTAGTCAGTCAAATAATAGAGCAGTTAATAAAA +AAGGAAAAAGTCTACCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAAT +TGGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGAAGAACATGAGAA +ATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTACCACCTGTAGTAGCAAAAGAAATAGTA +GCCAGCTGTGATAAATGTCAGCTAAAAGGGGAAGCCATGCATGGACAAGTAGACTGTAGCCCAGGAATAT +GGCAGCTAGATTGTACACATTTAGAAGGAAAAGTTATCTTGGTAGCAGTTCATGTAGCCAGTGGATATAT +AGAAGCAGAAGTAATTCCAGCAGAGACAGGGCAAGAAACAGCATACTTCCTCTTAAAATTAGCAGGAAGA +TGGCCAGTAAAAACAGTACATACAGACAATGGCAGCAATTTCACCAGTACTACAGTTAAGGCCGCCTGTT +GGTGGGCGGGGATCAAGCAGGAATTTGGCATTCCCTACAATCCCCAAAGTCAAGGAGTAATAGAATCTAT +GAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAA +ATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAG +TAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCG +GGTTTATTACAGGGACAGCAGAGATCCAGTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGG +GCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATCAGGGATT +ATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAACACATGGAAAAGAT +TAGTAAAACACCATATGTATATTTCAAGGAAAGCTAAGGACTGGTTTTATAGACATCACTATGAAAGTAC +TAATCCAAAAATAAGTTCAGAAGTACACATCCCACTAGGGGATGCTAAATTAGTAATAACAACATATTGG +GGTCTGCATACAGGAGAAAGAGACTGGCATTTGGGTCAGGGAGTCTCCATAGAATGGAGGAAAAAGAGAT +ATAGCACACAAGTAGACCCTGACCTAGCAGACCAACTAATTCATCTGCACTATTTTGATTGTTTTTCAGA +ATCTGCTATAAGAAATACCATATTAGGACGTATAGTTAGTCCTAGGTGTGAATATCAAGCAGGACATAAC +AAGGTAGGATCTCTACAGTACTTGGCACTAGCAGCATTAATAAAACCAAAACAGATAAAGCCACCTTTGC +CTAGTGTTAGGAAACTGACAGAGGACAGATGGAACAAGCCCCAGAAGACCAAGGGCCACAGAGGGAGCCA +TACAATGAATGGACACTAGAGCTTTTAGAGGAACTTAAGAGTGAAGCTGTTAGACATTTTCCTAGGATAT +GGCTCCATAACTTAGGACAACATATCTATGAAACTTACGGGGATACTTGGGCAGGAGTGGAAGCCATAAT +AAGAATTCTGCAACAACTGCTGTTTATCCATTTCAGAATTGGGTGTCGACATAGCAGAATAGGCGTTACT +CGACAGAGGAGAGCAAGAAATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAG +CCTAAAACTGCTTGTACCAATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATGACAA +AAGCCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGAC +TCATCAAGCTTCTCTATCAAAGCAGTAAGTAGTACATGTAATGCAACCTATAATAGTAGCAATAGTAGCA +TTAGTAGTAGCAATAATAATAGCAATAGTTGTGTGGTCCATAGTAATCATAGAATATAGGAAAATATTAA +GACAAAGAAAAATAGACAGGTTAATTGATAGACTAATAGAAAGAGCAGAAGACAGTGGCAATGAGAGTGA +AGGAGAAGTATCAGCACTTGTGGAGATGGGGGTGGAAATGGGGCACCATGCTCCTTGGGATATTGATGAT +CTGTAGTGCTACAGAAAAATTGTGGGTCACAGTCTATTATGGGGTACCTGTGTGGAAGGAAGCAACCACC +ACTCTATTTTGTGCATCAGATGCTAAAGCATATGATACAGAGGTACATAATGTTTGGGCCACACATGCCT +GTGTACCCACAGACCCCAACCCACAAGAAGTAGTATTGGTAAATGTGACAGAAAATTTTAACATGTGGAA +AAATGACATGGTAGAACAGATGCATGAGGATATAATCAGTTTATGGGATCAAAGCCTAAAGCCATGTGTA +AAATTAACCCCACTCTGTGTTAGTTTAAAGTGCACTGATTTGAAGAATGATACTAATACCAATAGTAGTA +GCGGGAGAATGATAATGGAGAAAGGAGAGATAAAAAACTGCTCTTTCAATATCAGCACAAGCATAAGAGA +TAAGGTGCAGAAAGAATATGCATTCTTTTATAAACTTGATATAGTACCAATAGATAATACCAGCTATAGG +TTGATAAGTTGTAACACCTCAGTCATTACACAGGCCTGTCCAAAGGTATCCTTTGAGCCAATTCCCATAC +ATTATTGTGCCCCGGCTGGTTTTGCGATTCTAAAATGTAATAATAAGACGTTCAATGGAACAGGACCATG +TACAAATGTCAGCACAGTACAATGTACACATGGAATCAGGCCAGTAGTATCAACTCAACTGCTGTTAAAT +GGCAGTCTAGCAGAAGAAGATGTAGTAATTAGATCTGCCAATTTCACAGACAATGCTAAAACCATAATAG +TACAGCTGAACACATCTGTAGAAATTAATTGTACAAGACCCAACAACAATACAAGAAAAAGTATCCGTAT +CCAGAGGGGACCAGGGAGAGCATTTGTTACAATAGGAAAAATAGGAAATATGAGACAAGCACATTGTAAC +ATTAGTAGAGCAAAATGGAATGCCACTTTAAAACAGATAGCTAGCAAATTAAGAGAACAATTTGGAAATA +ATAAAACAATAATCTTTAAGCAATCCTCAGGAGGGGACCCAGAAATTGTAACGCACAGTTTTAATTGTGG +AGGGGAATTTTTCTACTGTAATTCAACACAACTGTTTAATAGTACTTGGTTTAATAGTACTTGGAGTACT +GAAGGGTCAAATAACACTGAAGGAAGTGACACAATCACACTCCCATGCAGAATAAAACAATTTATAAACA +TGTGGCAGGAAGTAGGAAAAGCAATGTATGCCCCTCCCATCAGTGGACAAATTAGATGTTCATCAAATAT +TACTGGGCTGCTATTAACAAGAGATGGTGGTAATAACAACAATGGGTCCGAGATCTTCAGACCTGGAGGA +GGCGATATGAGGGACAATTGGAGAAGTGAATTATATAAATATAAAGTAGTAAAAATTGAACCATTAGGAG +TAGCACCCACCAAGGCAAAGAGAAGAGTGGTGCAGAGAGAAAAAAGAGCAGTGGGAATAGGAGCTTTGTT +CCTTGGGTTCTTGGGAGCAGCAGGAAGCACTATGGGCGCAGCGTCAATGACGCTGACGGTACAGGCCAGA +CAATTATTGTCTGATATAGTGCAGCAGCAGAACAATTTGCTGAGGGCTATTGAGGCGCAACAGCATCTGT +TGCAACTCACAGTCTGGGGCATCAAACAGCTCCAGGCAAGAATCCTGGCTGTGGAAAGATACCTAAAGGA +TCAACAGCTCCTGGGGATTTGGGGTTGCTCTGGAAAACTCATTTGCACCACTGCTGTGCCTTGGAATGCT +AGTTGGAGTAATAAATCTCTGGAACAGATTTGGAATAACATGACCTGGATGGAGTGGGACAGAGAAATTA +ACAATTACACAAGCTTAATACACTCCTTAATTGAAGAATCGCAAAACCAGCAAGAAAAGAATGAACAAGA +ATTATTGGAATTAGATAAATGGGCAAGTTTGTGGAATTGGTTTAACATAACAAATTGGCTGTGGTATATA +AAATTATTCATAATGATAGTAGGAGGCTTGGTAGGTTTAAGAATAGTTTTTGCTGTACTTTCTATAGTGA +ATAGAGTTAGGCAGGGATATTCACCATTATCGTTTCAGACCCACCTCCCAATCCCGAGGGGACCCGACAG +GCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAGAGACAGAGACAGATCCATTCGATTAGTGAACGGATCC +TTAGCACTTATCTGGGACGATCTGCGGAGCCTGTGCCTCTTCAGCTACCACCGCTTGAGAGACTTACTCT +TGATTGTAACGAGGATTGTGGAACTTCTGGGACGCAGGGGGTGGGAAGCCCTCAAATATTGGTGGAATCT +CCTACAGTATTGGAGTCAGGAACTAAAGAATAGTGCTGTTAACTTGCTCAATGCCACAGCCATAGCAGTA +GCTGAGGGGACAGATAGGGTTATAGAAGTATTACAAGCAGCTTATAGAGCTATTCGCCACATACCTAGAA +GAATAAGACAGGGCTTGGAAAGGATTTTGCTATAAGATGGGTGGCAAGTGGTCAAAAAGTAGTGTGATTG +GATGGCCTGCTGTAAGGGAAAGAATGAGACGAGCTGAGCCAGCAGCAGATGGGGTGGGAGCAGTATCTCG +AGACCTAGAAAAACATGGAGCAATCACAAGTAGCAATACAGCAGCTAACAATGCTGCTTGTGCCTGGCTA +GAAGCACAAGAGGAGGAAGAGGTGGGTTTTCCAGTCACACCTCAGGTACCTTTAAGACCAATGACTTACA +AGGCAGCTGTAGATCTTAGCCACTTTTTAAAAGAAAAGGGGGGACTGGAAGGGCTAATTCACTCCCAAAG +AAGACAAGATATCCTTGATCTGTGGATCTACCACACACAAGGCTACTTCCCTGATTGGCAGAACTACACA +CCAGGGCCAGGGGTCAGATATCCACTGACCTTTGGATGGTGCTACAAGCTAGTACCAGTTGAGCCAGATA +AGGTAGAAGAGGCCAATAAAGGAGAGAACACCAGCTTGTTACACCCTGTGAGCCTGCATGGAATGGATGA +CCCTGAGAGAGAAGTGTTAGAGTGGAGGTTTGACAGCCGCCTAGCATTTCATCACGTGGCCCGAGAGCTG +CATCCGGAGTACTTCAAGAACTGCTGACATCGAGCTTGCTACAAGGGACTTTCCGCTGGGGACTTTCCAG +GGAGGCGTGGCCTGGGCGGGACTGGGGAGTGGCGAGCCCTCAGATGCTGCATATAAGCAGCTGCTTTTTG +CCTGTACTGGGTCTCTCTGGTTAGACCAGATCTGAGCCTGGGAGCTCTCTGGCTAACTAGGGAACCCACT +GCTTAAGCCTCAATAAAGCTTGCCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTGTTGTGTGACTCTGGT +AACTAGAGATCCCTCAGACCCTTTTAGTCAGTGTGGAAAATCTCTAGCACCCAGGAGGTAGAGGTTGCAG +TGAGCCAAGATCGCGCCACTGCATTCCAGCCTGGGCAAGAAAACAAGACTGTCTAAAATAATAATAATAA +GTTAAGGGTATTAAATATATTTATACATGGAGGTCATAAAAATATATATATTTGGGCTGGGCGCAGTGGC +TCACACCTGCGCCCGGCCCTTTGGGAGGCCGAGGCAGGTGGATCACCTGAGTTTGGGAGTTCCAGACCAG +CCTGACCAACATGGAGAAACCCCTTCTCTGTGTATTTTTAGTAGATTTTATTTTATGTGTATTTTATTCA +CAGGTATTTCTGGAAAACTGAAACTGTTTTTCCTCTACTCTGATACCACAAGAATCATCAGCACAGAGGA +AGACTTCTGTGATCAAATGTGGTGGGAGAGGGAGGTTTTCACCAGCACATGAGCAGTCAGTTCTGCCGCA +GACTCGGCGGGTGTCCTTCGGTTCAGTTCCAACACCGCCTGCCTGGAGAGAGGTCAGACCACAGGGTGAG +GGCTCAGTCCCCAAGACATAAACACCCAAGACATAAACACCCAACAGGTCCACCCCGCCTGCTGCCCAGG +CAGAGCCGATTCACCAAGACGGGAATTAGGATAGAGAAAGAGTAAGTCACACAGAGCCGGCTGTGCGGGA +GAACGGAGTTCTATTATGACTCAAATCAGTCTCCCCAAGCATTCGGGGATCAGAGTTTTTAAGGATAACT +TAGTGTGTAGGGGGCCAGTGAGTTGGAGATGAAAGCGTAGGGAGTCGAAGGTGTCCTTTTGCGCCGAGTC +AGTTCCTGGGTGGGGGCCACAAGATCGGATGAGCCAGTTTATCAATCCGGGGGTGCCAGCTGATCCATGG +AGTGCAGGGTCTGCAAAATATCTCAAGCACTGATTGATCTTAGGTTTTACAATAGTGATGTTACCCCAGG +AACAATTTGGGGAAGGTCAGAATCTTGTAGCCTGTAGCTGCATGACTCCTAAACCATAATTTCTTTTTTG +TTTTTTTTTTTTTATTTTTGAGACAGGGTCTCACTCTGTCACCTAGGCTGGAGTGCAGTGGTGCAATCAC +AGCTCACTGCAGCCTCAACGTCGTAAGCTCAAGCGATCCTCCCACCTCAGCCTGCCTGGTAGCTGAGACT +ACAAGCGACGCCCCAGTTAATTTTTGTATTTTTGGTAGAGGCAGCGTTTTGCCGTGTGGCCCTGGCTGGT +CTCGAACTCCTGGGCTCAAGTGATCCAGCCTCAGCCTCCCAAAGTGCTGGGACAACCGGGGCCAGTCACT +GCACCTGGCCCTAAACCATAATTTCTAATCTTTTGGCTAATTTGTTAGTCCTACAAAGGCAGTCTAGTCC +CCAGGCAAAAAGGGGGTTTGTTTCGGGAAAGGGCTGTTACTGTCTTTGTTTCAAACTATAAACTAAGTTC +CTCCTAAACTTAGTTCGGCCTACACCCAGGAATGAACAAGGAGAGCTTGGAGGTTAGAAGCACGATGGAA +TTGGTTAGGTCAGATCTCTTTCACTGTCTGAGTTATAATTTTGCAATGGTGGTTCAAAGACTGCCCGCTT +CTGACACCAGTCGCTGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCTCT +TCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTCAA +AGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCA +AAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCAT +CACAAAAATCGACGCTCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCC +CTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCC +TTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCC +AAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGCGCCTTATCCGGTAACTATCGTCTTG +AGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCGAG +GTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGAACAGTATTT +GGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAA +CCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGA +AGATCCTTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTC +ATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAA +GTATATATGAGTAAACTTGGTCTGACAGTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTG +TCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACGGGAGGGCTTACCA +TCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGCTCCAGATTTATCAGCAATAAACC +AGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAATTG +TTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACAGGC +ATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTA +CATGATCCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAGTT +GGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGA +TGCTTTTCTGTGACTGGTGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCT +CTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACTTTAAAAGTGCTCATCATTGGAAA +ACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGT +GCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCAAA +ATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATATTA +TTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAA +ATAGGGGTTCCGCGCACATTTCCCCGAAAAGTGCCACCTGACGTCTAAGAAACCATTATTATCATGACAT +TAACCTATAAAAATAGGCGTATCACGAGGCCCTTTCGTCTCGCGCGTTTCGGTGATGACGGTGAAAACCT +CTGACACATGCAGCTCCCGGAGACGGTCACAGCTTGTCTGTAAGCGGATGCCGGGAGCAGACAAGCCCGT +CAGGGCGCGTCAGCGGGTGTTGGCGGGTGTCGGGGCTGGCTTAACTATGCGGCATCAGAGCAGATTGTAC +TGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATGCGTAAGGAGAAAATACCGCATCAGGCGCCA +TTCGCCATTCAGGCTGCGCAACTGTTGGGAAGGGCGATCGGTGCGGGCCTCTTCGCTATTACGCCAGGGG +AGGCAGAGATTGCAGTAAGCTGAGATCGCAGCACTGCACTCCAGCCTGGGCGACAGAGTAAGACTCTGTC +TCAAAAATAAAATAAATAAATCAATCAGATATTCCAATCTTTTCCTTTATTTATTTATTTATTTTCTATT +TTGGAAACACAGTCCTTCCTTATTCCAGAATTACACATATATTCTATTTTTCTTTATATGCTCCAGTTTT +TTTTAGACCTTCACCTGAAATGTGTGTATACAAAATCTAGGCCAGTCCAGCAGAGCCTAAAGGTAAAAAA +TAAAATAATAAAAAATAAATAAAATCTAGCTCACTCCTTCACATCAAAATGGAGATACAGCTGTTAGCAT +TAAATACCAAATAACCCATCTTGTCCTCAATAATTTTAAGCGCCTCTCTCCACCACATCTAACTCCTGTC +AAAGGCATGTGCCCCTTCCGGGCGCTCTGCTGTGCTGCCAACCAACTGGCATGTGGACTCTGCAGGGTCC +CTAACTGCCAAGCCCCACAGTGTGCCCTGAGGCTGCCCCTTCCTTCTAGCGGCTGCCCCCACTCGGCTTT +GCTTTCCCTAGTTTCAGTTACTTGCGTTCAGCCAAGGTCTGAAACTAGGTGCGCACAGAGCGGTAAGACT +GCGAGAGAAAGAGACCAGCTTTACAGGGGGTTTATCACAGTGCACCCTGACAGTCGTCAGCCTCACAGGG +GGTTTATCACATTGCACCCTGACAGTCGTCAGCCTCACAGGGGGTTTATCACAGTGCACCCTTACAATCA +TTCCATTTGATTCACAATTTTTTTAGTCTCTACTGTGCCTAACTTGTAAGTTAAATTTGATCAGAGGTGT +GTTCCCAGAGGGGAAAACAGTATATACAGGGTTCAGTACTATCGCATTTCAGGCCTCCACCTGGGTCTTG +GAATGTGTCCCCCGAGGGGTGATGACTACCTCAGTTGGATCTCCACAGGTCACAGTGACACAAGATAACC +AAGACACCTCCCAAGGCTACCACAATGGGCCGCCCTCCACGTGCACATGGCCGGAGGAACTGCCATGTCG +GAGGTGCAAGCACACCTGCGCATCAGAGTCCTTGGTGTGGAGGGAGGGACCAGCGCAGCTTCCAGCCATC +CACCTGATGAACAGAACCTAGGGAAAGCCCCAGTTCTACTTACACCAGGAAAGGC + diff --git a/gittaggers.py b/gittaggers.py new file mode 100644 index 0000000..e91cf0f --- /dev/null +++ b/gittaggers.py @@ -0,0 +1,36 @@ +import subprocess +import time +import pkg_resources +from setuptools.command.egg_info import egg_info + +SETUPTOOLS_VER = pkg_resources.get_distribution( + "setuptools").version.split('.') + +RECENT_SETUPTOOLS = int(SETUPTOOLS_VER[0]) > 40 or ( + int(SETUPTOOLS_VER[0]) == 40 and int(SETUPTOOLS_VER[1]) > 0) or ( + int(SETUPTOOLS_VER[0]) == 40 and int(SETUPTOOLS_VER[1]) == 0 and + int(SETUPTOOLS_VER[2]) > 0) + +class EggInfoFromGit(egg_info): + """Tag the build with git commit timestamp. + + If a build tag has already been set (e.g., "egg_info -b", building + from source package), leave it alone. + """ + + def git_timestamp_tag(self): + gitinfo = subprocess.check_output( + ['git', 'log', '--first-parent', '--max-count=1', + '--format=format:%ct', '.']).strip() + return time.strftime('.%Y%m%d%H%M%S', time.gmtime(int(gitinfo))) + + def tags(self): + if self.tag_build is None: + try: + self.tag_build = self.git_timestamp_tag() + except subprocess.CalledProcessError: + pass + return egg_info.tags(self) + + if RECENT_SETUPTOOLS: + vtags = property(tags) diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..48c25aa --- /dev/null +++ b/setup.py @@ -0,0 +1,46 @@ +#!/usr/bin/env python3 +import os +import sys + +import setuptools.command.egg_info as egg_info_cmd +from setuptools import setup + +SETUP_DIR = os.path.dirname(__file__) +README = os.path.join(SETUP_DIR, "README.md") + +try: + import gittaggers + + tagger = gittaggers.EggInfoFromGit +except ImportError: + tagger = egg_info_cmd.egg_info + +install_requires = ["arvados-python-client", "schema-salad"] + +needs_pytest = {"pytest", "test", "ptr"}.intersection(sys.argv) +pytest_runner = ["pytest < 6", "pytest-runner < 5"] if needs_pytest else [] + +setup( + name="bh20-seq-uploader", + version="1.0", + description="Biohackathon sequence uploader", + long_description=open(README).read(), + long_description_content_type="text/x-rst", + author="Peter Amstutz", + author_email="peter.amstutz@curii.com", + license="Apache 2.0", + packages=["bh20sequploader", "bh20seqanalyzer"], + package_data={"bh20sequploader": ["bh20seq-schema.yml"]}, + install_requires=install_requires, + setup_requires=[] + pytest_runner, + tests_require=["pytest<5"], + entry_points={ + "console_scripts": [ + "bh20-seq-uploader=bh20sequploader.main:main", + "bh20-seq-analyzer=bh20seqanalyzer.main:main" + ] + }, + zip_safe=True, + cmdclass={"egg_info": tagger}, + python_requires=">=3.5, <4", +) |