How can I perform multiple re.sub() on a file? - regex

Question

I am attempting to perform multiple regex alterations of a file but I'm not sure how to do this while retaining the previous alterations. I have found several ways to do this but I'm new to coding and couldn't get them to work in my code.
import re
import sys
if len(sys.argv) != 3:
sys.exit('Error: One input and one output file is required')
fasta = open(sys.argv[1],'r')
output = open(sys.argv[2],'r+')
output1 = re.sub(r'^>\w+\|(\d+)\|.*LOXAF.*', r'>Loxodonta africana, \1, MW =',fasta)
output2 = re.sub(r'^>\w+\|(\d+)\|.*DUGDU.*', r'>Dendrohyrax dorsalis, \1, MW =',output1)
output3 = re.sub(r'(^[A-Z].*)\n', r'\1',output2)
print(output3)
Ideally, I would write all of the regex to the output file instead of just printing it. I put an example of changes I'd like to make below (I cut the number and length of sequences down for simplicity).
>gi|75074720|sp|Q9TA19.1|NU5M_LOXAF RecName: Full=NADH-ubiquinone oxidoreductase chain 5; AltName: Full=NADH dehydrogenase subunit 5
MKVINLIPTLMLTSLIILTLPIITTLLQNNKTNCFLYITKTAVTYAFAISLIPTLLFIQSNQEAYISNWH
WMTIHTLKLSMSFKLDFFSLTFMPIALFITWSIM
>gi|75068112|sp|Q9TA29.1|NU1M_LOXAF RecName: Full=NADH-ubiquinone oxidoreductase chain 1; AltName: Full=NADH dehydrogenase subunit 1
MFLINVLTVTLPILLAVAFLTLVERKALGYMQLRKGPNVVGPYGLLQPIADAIKLFTKEPIYPQTSSKFL
FTVAPILALTLALTVWAPLPMPYPLINLNLSL
>gi|24418335|sp|Q8W9N2.1|ATP8_DUGDU RecName: Full=ATP synthase protein 8; AltName: Full=A6L; AltName: Full=F-ATPase subunit 8
MPQLDTTTWFITILSMLITLFILFQTKLLNYTYPLNALPISPNVTNHLTPWKMKWTKTYLPLSLPLQ
Output:
>Loxodonta africana, 75074720, MW =
MKVINLIPTLMLTSLIILTLPIITTLLQNNKTNCFLYITKTAVTYAFAISLIPTLLFIQSNQEAYISNWHWMTIHTLKLSMSFKLDFFSLTFMPIALFITWSIM
>Loxodonta africana, 75068112, MW =
MFLINVLTVTLPILLAVAFLTLVERKALGYMQLRKGPNVVGPYGLLQPIADAIKLFTKEPIYPQTSSKFLFTVAPILALTLALTVWAPLPMPYPLINLNLSL
>Dendrohyrax dorsalis, 24418335, MW =
MPQLDTTTWFITILSMLITLFILFQTKLLNYTYPLNALPISPNVTNHLTPWKMKWTKTYLPLSLPLQ
Thanks for all of your help!

Answer 1

fasta files can be very large. It isn't a good idea to load the whole file into a variable. I suggest to work line by line (less memory usage).
A fasta file is something with a format and not a wild text file, so understanding and using this format will help you to extract the informations you want without to use 3 blind regex replacements.
Suggestion:
import re
import sys
from itertools import takewhile
if len(sys.argv) != 3:
sys.exit('Error: One input and one output file is required')
with open(sys.argv[1], 'r') as fi, open(sys.argv[2], 'r+') as fo:
species = {
'LOXAF': 'Loxodonta africana',
'DUGDU': 'Dendrohyrax dorsalis'
}
sep = re.compile(r'[|_ ]');
recF = ">{}, {}, MW =\n{}"
def getSeq(f):
return ''.join([line.rstrip() for line in takewhile(lambda x: x!="\n", f)])
for line in fi:
if line.startswith('>'):
parts = sep.split(line, 6)
print(recF.format(species[parts[5]], parts[1], getSeq(fi)), file=fo)

Answer 2

You can try something like this:
import re
import sys
if len(sys.argv) != 3:
sys.exit('Error: One input and one output file is required')
else:
fasta = open(sys.argv[1],'r')
fasta_content = fasta.read()
print(fasta)
output = open(sys.argv[2],'w')
output1 = re.sub(r'>\w+\|(\d+)\|.*LOXAF.*', r'>Loxodonta africana, \1, MW =',fasta_content)
print(output1)
output2 = re.sub(r'>\w+\|(\d+)\|.*DUGDU.*', r'>Dendrohyrax dorsalis, \1, MW =',output1)
print(output2)
output3 = re.sub(r'([A-Z]+)\n', r'\1',output2)
print(output3)
output.write(output3)
output.close()
fasta.close()
First of all you need to operate on the text, so read() is needed.
To write to output file you can use output.write(), but when opening you have to have 'w' option
Regex here didn't work because in each regex you have start of string (^) and it applies only to the beginning of the text (unless you read line by line) but with read() you get whole text as single string.