How to reverse complement the DNA sequences for given inverse/reverse coordinates?
Since you tagged python, here is a solution that solves this in a single script using Biopython:

import sys
from Bio import SeqIO

d = {}
with open('id.txt') as f:
    for line in f:
        contig, coords = line.split(':')
        start, end = map(int, coords.split('-'))
        d[contig] = start, end

for record in SeqIO.parse('genome.fasta', 'fasta'):
    start, end = d[record.id]
    if start &gt; end:
        record.seq = record.seq[end - 1: start].reverse_complement()
    else:
        record.seq = record.seq[start - 1: end]
    SeqIO.write(record, sys.stdout, 'fasta')


Output on your example:

&gt;Contig1
CTTGATGGCC
&gt;Contig2
AGCGCT
&gt;Contig3
GATCAGCGC