Change ID in multiple FASTA files - loops

Question

I need to rename multiple sequences in multiple fasta files and I found this script in order to do so for a single ID:
original_file = "./original.fasta"
corrected_file = "./corrected.fasta"
with open(original_file) as original, open(corrected_file, 'w') as corrected:
records = SeqIO.parse(original_file, 'fasta')
for record in records:
print record.id
if record.id == 'foo':
record.id = 'bar'
record.description = 'bar' # <- Add this line
print record.id
SeqIO.write(record, corrected, 'fasta')
Each fasta file corresponds to a single organism, but it is not specified in the IDs. I have the original fasta files (because these have been translated) with the same filenames but different directories and include in their IDs the name of each organism.
I wanted to figure out how to loop through all these fasta files and rename each ID in each file with the corresponding organism name.

Answer 1

ok my effort, got to use my own input folders/files since they where not specified in question
/old folder contains files :
MW628877.1.fasta :
>MW628877.1 Streptococcus agalactiae strain RYG82 DNA gyrase subunit A (gyrA) gene, complete cds
ATGCAAGATAAAAATTTAGTAGATGTTAATCTAACTAGTGAAATGAAAACGAGTTTTATCGATTACGCCA
TGAGTGTCATTGTTGCTCGTGCACTTCCAGATGTTAGAGATGGTTTAAAACCTGTTCATCGTCGTATTTT
>KY347969.1 Neisseria gonorrhoeae strain 1448 DNA gyrase subunit A (gyrA) gene, partial cds
CGGCGCGTACCGTACGCGATGCACGAGCTGAAAAATAACTGGAATGCCGCCTACAAAAAATCGGCGCGCA
TCGTCGGCGACGTCATCGGTAAATACCACCCCCACGGCGATTTCGCAGTTTACGGCACCATCGTCCGTAT
MG995190.1.fasta :
>MG995190.1 Mycobacterium tuberculosis strain UKR100 GyrA (gyrA) gene, complete cds
ATGACAGACACGACGTTGCCGCCTGACGACTCGCTCGACCGGATCGAACCGGTTGACATCCAGCAGGAGA
TGCAGCGCAGCTACATCGACTATGCGATGAGCGTGATCGTCGGCCGCGCGCTGCCGGAGGTGCGCGACGG
and an /empty folder.
/new folder contains files :
MW628877.1.fasta :
>MW628877.1
MQDKNLVDVNLTSEMKTSFIDYAMSVIVARALPDVRDGLKPVHRRI
>KY347969.1
RRVPYAMHELKNNWNAAYKKSARIVGDVIGKYHPHGDFAVYGTIVR
MG995190.1.fasta :
>MG995190.1
MTDTTLPPDDSLDRIEPVDIQQEMQRSYIDYAMSVIVGRALPEVRD
my code is :
from Bio import SeqIO
from os import scandir
old = './old'
new = './new'
old_ids_dict = {}
for filename in scandir(old):
if filename.is_file():
print(filename)
for seq_record in SeqIO.parse(filename, "fasta"):
old_ids_dict[seq_record.id] = ' '.join(seq_record.description.split(' ')[1:3])
print('_____________________')
print('old ids ---> ',old_ids_dict)
print('_____________________')
for filename in scandir(new):
if filename.is_file():
sequences = []
for seq_record in SeqIO.parse(filename, "fasta"):
if seq_record.id in old_ids_dict.keys():
print('### ', seq_record.id,' ', old_ids_dict[seq_record.id])
seq_record.id += '.'+old_ids_dict[seq_record.id]
seq_record.description = ''
print('-->', seq_record.id)
print(seq_record)
sequences.append(seq_record)
SeqIO.write(sequences, filename, 'fasta')
check how it works, it actually overwrites both files in new folder,
as pointed out by #Vovin in his comment it needs to be adapted per your files template from-to.
I am sure there is more than a way to do this, probably better and more pythonic than may way, I am learning too. Let us know