gb2peg.py

import sys
from Bio import SeqIO
import Bio


sequence = ""
gene_loci = list()

c_start = 0
for record in SeqIO.parse(sys.argv[1], 'genbank'):
    if c_start == 0:
        sequence = str(record.seq)
    else:
        c_start = len(sequence)
        sequence = "N" + str(record.sequence)
    for feature in record.features:
        if feature.type == 'CDS':
            if isinstance(feature.location , Bio.SeqFeature.FeatureLocation):
                #print(feature)
                #print(type(feature.location))
                strand = feature.location.strand
                start = int(feature.location.start)
                end = int(feature.location.end)
                #print("!# ",start,end, strand, end-start, (end-start)%3)
                if start > end:
                    print(start,end, strand)
                    t = start
                    start = end
                    end = t
                gene_loci.append( (start,end,strand) )

                # loci = (start,end,strand)
                # print(loci, (loci[1]-loci[0])%3  )
                # gene_seq = sequence[loci[0]:loci[1]]
                # print( len(gene_seq)%3 )
                # print( str(Seq(gene_seq).translate(table=4)) )
                # print(feature.qualifiers['translation'])
                # #print(feature.translate(seq, cds=False))

sequence = sequence.upper()
gene_loci = sorted(gene_loci)


off =  open(sys.argv[2],'w')
off.write(sequence+"\n")
for locus in gene_loci:
    off.write(str(locus[0])+" "+str(locus[1])+" "+str(locus[2])+"\n")
off.flush()
off.close()