comparison export.py @ 5:7610987e0c48 draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 29795b77c0d5c7894219b018a92c5ee7818096c3

4:23ead6905145

#!/usr/bin/env python
import sys
import StringIO
import json
import argparse
from Bio import SeqIO
from BCBio import GFF
from webapollo import WAAuth, WebApolloInstance, CnOrGuess, GuessCn


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

    data = StringIO.StringIO()

    kwargs = dict(
        exportType='GFF3',
        seqType='genomic',
        exportGff3Fasta=True,

    # 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 = {}
            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)

5:7610987e0c48

#!/usr/bin/env python
import sys
try:
    import StringIO as io
except ImportError:
    import io

import json
import argparse
from Bio import SeqIO
from BCBio import GFF
from webapollo import WAAuth, WebApolloInstance, CnOrGuess, GuessCn


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

    data = io.StringIO()

    kwargs = dict(
        exportType='GFF3',
        seqType='genomic',
        exportGff3Fasta=True,

    # 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)