Assuming file1 is:
contig1 134
contig2 354
contig3 345
Your script would look like
import re
contigDict={}
with open('file1') as c1:
text=c1.readlines()
for line in text:
key,value = line.split()
contigDict[key]=value
with open('file2') as c2:
scrambled_text=c2.read()
contigs = re.findall(r'contig\d+',scrambled_text)
output = {}
for contig in contigs:
output[contig]=contigDict[contig]
with open('file3',w) as w:
for key in output.keys():
w.write(key+'\t'+output[key]+'\n')