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

import sys
import textwrap

from Bio import GenBank

assert sys.version_info[:2] >= (2, 4)


def make_fasta(rec):
    '''Creates fasta format from a record'''
    gi = rec.annotations.get('gi', '')
    org = rec.annotations.get('organism', '')
    date = rec.annotations.get('date', '')
    head = '>gi:%s, id:%s, org:%s, date:%s\n' % (gi, rec.id, org, date)
    body = '\n'.join(textwrap.wrap(rec.seq.data, width=80))
    return head, body


if __name__ == '__main__':
    mode = sys.argv[1]
    text = sys.argv[2]
    output_file = sys.argv[3]

    print('Searching for %s <br>' % text)

    # check if inputs are all numbers
    try:
        gi_list = text.split()
        [int(_) for _ in gi_list]
    except ValueError:
        gi_list = GenBank.search_for(text, max_ids=10)

    fp = open(output_file, 'wt')
    record_parser = GenBank.FeatureParser()
    ncbi_dict = GenBank.NCBIDictionary(mode, 'genbank', parser=record_parser)
    for gid in gi_list:
        res = ncbi_dict[gid]
        head, body = make_fasta(res)
        fp.write(head + body + '\n')
        print(head)
    fp.close()