# idlist, idlist will be an emtpy list if none is provided
idlist = get_id_list(args)
# read the sequences and store all that match the IDs
# duplicates in sequence files will be stored twice
n_match = {} # per file number of sequences in list
n_notmatch = {} # per file number of sequences not in list
n_sequence = {} # per file number of sequences
n_found = {} # per ID, number of times found in all files
n_file = 0
n_total = 0
n_written = 0
out = sys.stdout
for fastafile in glob.glob(args.input_filename):
fasta = Fasta()
fasta.open(fastafile)
if args.outsuffix:
outfile = os.path.basename(fastafile) + f'{args.outsuffix}'
out = opensafe(outfile, 'w')
if not out:
# if file can't be opened use stdout
out = sys.stdout
n_sequence[fastafile] = 0
n_match[fastafile] = 0
n_notmatch[fastafile] = 0
n_file += 1
while fasta.next():
n_sequence[fastafile] += 1
n_total += 1
# --------------------------------------------------------------------------------------------------
# main
# --------------------------------------------------------------------------------------------------
if __name__ == '__main__':
# open files
gtffile = sys.argv[1]
try:
gtf = open(gtffile, 'r')
except:
sys.stderr.write('Unable to open GTF file ({})\n'.format(gtffile))
exit(1)
seq = {}
fasta = Fasta()
fasta.open(sys.argv[2])
sys.stderr.write('Reading Fasta {}...\n'.format(sys.argv[2]))
nseq = 0
while fasta.next():
seq[fasta.id] = fasta.seq
nseq += 1
sys.stderr.write('\n{} Sequences read from {}\n'.format(nseq, sys.argv[2]))
for s in seq:
sys.stderr.write('\t{} len={}\n'.format(s, len(seq[s])))
sys.stderr.write('\ngtf2fasta\n')
sys.stderr.write('\tGTF: {}\n'.format(gtffile))
sys.stderr.write('\tFasta: {}\n'.format(sys.argv[2]))
features = ('gene', 'pseudogene', 'tRNA')