comparison export.py @ 10:d72192ec8e39 draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"

9:29ce13734a5c

#!/usr/bin/env python
from __future__ import print_function

import argparse
import json
import sys

from BCBio import GFF

from Bio import SeqIO

from webapollo import CnOrGuess, GuessCn, PermissionCheck, WAAuth, WebApolloInstance

try:
    import StringIO as io
except ImportError:
    import io


def export(org_cn, seqs):
    org_data = wa.organisms.findOrganismByCn(org_cn)

    data = io.StringIO()

    kwargs = dict(
        exportType='GFF3',
        seqType='genomic',
        exportGff3Fasta=True,
        output="text",
        exportFormat="text",
        organism=org_cn,
    )

    if len(seqs) > 0:
        data.write(wa.io.write(
            exportAllSequences=False,
            sequences=seqs,
            **kwargs
        ).encode('utf-8'))
    else:
        data.write(wa.io.write(
            exportAllSequences=True,
            sequences=[],
            **kwargs
        ).encode('utf-8'))

    # Seek back to start
    data.seek(0)

    records = list(GFF.parse(data))
    if len(records) == 0:
        print("Could not find any sequences or annotations for this organism + reference sequence")
        sys.exit(2)
    else:
        for record in records:
            record.annotations = {}
            record.features = sorted(record.features, key=lambda x: x.location.start)
            if args.gff:
                GFF.write([record], args.gff)
            record.description = ""
            if args.fasta:
                SeqIO.write([record], args.fasta, 'fasta')

    return org_data


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Sample script to add an attribute to a feature via web services')
    WAAuth(parser)
    CnOrGuess(parser)
    parser.add_argument('--gff', type=argparse.FileType('w'))
    parser.add_argument('--fasta', type=argparse.FileType('w'))
    parser.add_argument('--json', type=argparse.FileType('w'))
    parser.add_argument('email', help='User Email')
    args = parser.parse_args()

    wa = WebApolloInstance(args.apollo, args.username, args.password)

    org_cn_list, seqs = GuessCn(args, wa)

    # User must have an apollo account, if not, create it
    gx_user = wa.users.assertOrCreateUser(args.email)

    org_data = []
    for org_cn in org_cn_list:
        # User must have read permission on organism
        if not PermissionCheck(gx_user, org_cn, "READ"):
            continue
        indiv_org_data = export(org_cn, seqs)
        org_data.append(indiv_org_data)
    args.json.write(json.dumps(org_data, indent=2))

10:d72192ec8e39

#!/usr/bin/env python
from __future__ import print_function

import argparse
import json
import time

from apollo import accessible_organisms
from apollo.util import CnOrGuess, GuessCn

from arrow.apollo import get_apollo_instance

from webapollo import UserObj, handle_credentials

if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Script to export data from Apollo via web services')
    CnOrGuess(parser)
    parser.add_argument('--gff', type=argparse.FileType('w'))
    parser.add_argument('--fasta_pep', type=argparse.FileType('w'))
    parser.add_argument('--fasta_cds', type=argparse.FileType('w'))
    parser.add_argument('--fasta_cdna', type=argparse.FileType('w'))
    parser.add_argument('--vcf', type=argparse.FileType('w'))
    parser.add_argument('--json', type=argparse.FileType('w'))
    parser.add_argument('email', help='User Email')
    args = parser.parse_args()

    wa = get_apollo_instance()

    # User must have an apollo account, if not, create it
    gx_user = UserObj(**wa.users._assert_or_create_user(args.email))
    handle_credentials(gx_user)

    org_cns, seqs = GuessCn(args, wa)
    if not isinstance(org_cns, list):
        org_cns = [org_cns]

    all_orgs = wa.organisms.get_organisms()
    if 'error' in all_orgs:
        all_orgs = []
    all_orgs = [org['commonName'] for org in all_orgs]

    org_data = []
    for org_cn in org_cns:
        if org_cn not in all_orgs:
            raise Exception("Could not find organism %s" % org_cn)

        orgs = accessible_organisms(gx_user, [org_cn], 'READ')
        if not orgs:
            raise Exception("You do not have read permission on organism %s" % org_cn)

        org = wa.organisms.show_organism(org_cn)

        uuid_gff = wa.io.write_downloadable(org['commonName'], 'GFF3', export_gff3_fasta=True, sequences=seqs)
        if 'error' in uuid_gff or 'uuid' not in uuid_gff:
            raise Exception("Apollo failed to prepare the file for download: %s" % uuid_gff)
        args.gff.write(wa.io.download(uuid_gff['uuid'], output_format="text"))

        time.sleep(1)

        uuid_vcf = wa.io.write_downloadable(org['commonName'], 'VCF', sequences=seqs)
        if 'error' in uuid_vcf or 'uuid' not in uuid_vcf:
            raise Exception("Apollo failed to prepare the file for download: %s" % uuid_vcf)
        args.vcf.write(wa.io.download(uuid_vcf['uuid'], output_format="text"))

        time.sleep(1)

        uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='cdna')
        if 'error' in uuid_fa or 'uuid' not in uuid_fa:
            raise Exception("Apollo failed to prepare the file for download: %s" % uuid_fa)
        args.fasta_cdna.write(wa.io.download(uuid_fa['uuid'], output_format="text"))

        time.sleep(1)

        uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='cds')
        if 'error' in uuid_fa or 'uuid' not in uuid_fa:
            raise Exception("Apollo failed to prepare the file for download: %s" % uuid_fa)
        args.fasta_cds.write(wa.io.download(uuid_fa['uuid'], output_format="text"))

        time.sleep(1)

        uuid_fa = wa.io.write_downloadable(org['commonName'], 'FASTA', sequences=seqs, seq_type='peptide')
        if 'error' in uuid_fa or 'uuid' not in uuid_fa:
            raise Exception("Apollo failed to prepare the file for download: %s" % uuid_fa)
        args.fasta_pep.write(wa.io.download(uuid_fa['uuid'], output_format="text"))

        org_data.append(org)

    args.json.write(json.dumps(org_data, indent=2))