#!/usr/bin/env python3
#
# Create a single YAML/FASTA from genbank XML
#
#   transform-genbank-xml2yamlfa --out ~/tmp/pubseq file(s)
#
# Also writes a validation file in the outdir named state.json
#
# Where --in can be a file or a directory
# ----------------------------------------------------------------------

# See also directory .guix-run and README.md

import argparse
import gzip
import os
import sys
import types
import xml.etree.ElementTree as ET
from utils import chunks
import genbank

parser = argparse.ArgumentParser()
parser.add_argument('--out', type=str, help='Directory to write to',
required=True)
parser.add_argument('files', nargs='+', help='file(s)')
args = parser.parse_args()

dir = args.out
if not os.path.exists(dir):
    raise Exception(f"Directory {dir} does not exist")

states = {}

for xmlfn in args.files:
    print(f"--- Reading {xmlfn}")
    with gzip.open(xmlfn, 'r') as f:
        xml = f.read().decode()
        tree = ET.fromstring(xml)
        for gb in tree.findall('./GBSeq'):
            valid = None
            error = None
            meta = {}
            id = gb.find("GBSeq_locus").text
            basename = dir+"/"+id
            print(f"    parsing {id}")
            try:
                valid,meta = genbank.get_metadata(id,gb)
                if valid:
                    fa = basename+".fa"
                    seq = genbank.get_sequence(id,gb)
                    print(f"    writing {fa}")
                    with open(fa,"w") as f2:
                        f2.write(f"> {id}\n")
                        f2.write(seq)
                    # print(seq)
            except genbank.GBError as e:
                error = f"{e} for {id}"
                print(error,file=sys.stderr)
                valid = False
            state = {}
            state['valid'] = valid
            if error:
                state['error'] = error
            if meta['warnings']:
                state['warnings'] = meta['warnings']
            states[id] = state

print(states)