how to save your edited headers in original fasta files? - python

hi i'am trying to edit the header of my fasta files using seqkit and i have been able to do it but i'm not able to save it!
the command i am using to edit multiple fasta files with respect to their filename and doing it with refseq-
for i in $(find -name \genomid); do seqkit replace -p "^(.+?) (.+?)$" --replacement '{kv}' -k proid_unique *.faa; done
The directory having all my fasta files is like this-
PATH:
~/PANGENOMICS/DATA1/test
FILES in the directory:
GCF_000016305.1_ASM1630v1_protein.faa
GCF_000220485.1_ASM22048v1_protein.faa
GCF_900635735.1_32875_B01_protein.faa
proid_unique
genomid
i am finding filenames using a csv file list- genomid
GCF_900635735.1_32875_B01_protein.faa:WP_151362402.1:WP_151362402.1#0940
GCF_900635735.1_32875_B01_protein.faa:WP_151362403.1:WP_151362403.1#0940
GCF_900635735.1_32875_B01_protein.faa:WP_151362404.1:WP_151362404.1#0940
GCF_900635735.1_32875_B01_protein.faa:WP_151362405.1:WP_151362405.1#0940
GCF_900635735.1_32875_B01_protein.faa:WP_151362406.1:WP_151362406.1#0940
GCF_900635735.1_32875_B01_protein.faa:WP_151362407.1:WP_151362407.1#0940
GCF_900635735.1_32875_B01_protein.faa:WP_151362408.1:WP_151362408.1#0940
GCF_900635735.1_32875_B01_protein.faa:WP_151362409.1:WP_151362409.1#0940
GCF_900635735.1_32875_B01_protein.faa:WP_151362410.1:WP_151362410.1#0940
GCF_900635735.1_32875_B01_protein.faa:WP_151362411.1:WP_151362411.1#0940
GCF_900635735.1_32875_B01_protein.faa:WP_151362412.1:WP_151362412.1#0940
GCF_900635735.1_32875_B01_protein.faa:WP_151362413.1:WP_151362413.1#0940
GCF_900635735.1_32875_B01_protein.faa:WP_151362414.1:WP_151362414.1#0940
the file (proid_unique) i used as key-value file to edit the fasta headers look like this-
WP_151362399.1 WP_151362399.1#0940
WP_151362400.1 WP_151362400.1#0940
WP_151362401.1 WP_151362401.1#0940
WP_151362402.1 WP_151362402.1#0940
WP_151362409.1 WP_151362409.1#0940
WP_151362410.1 WP_151362410.1#0940
WP_151362411.1 WP_151362411.1#0940
WP_151362412.1 WP_151362412.1#0940
WP_151362413.1 WP_151362413.1#0940
WP_151362414.1 WP_151362414.1#0940
WP_094096600.1 WP_094096600.1#0945
WP_016530940.1 WP_016530940.1#0950
WP_000940121.1 WP_000940121.1#0951
WP_012540940.1 WP_012540940.1#0951
example of input-
>WP_151362411.1 YoaH family protein [Klebsiella pneumoniae]
MYAPQCSRSKRCFAGLPSLSHEQQQQAVERIHELMAQGISSGQAIALVAEELRATHTGEQ
IVARFEDEDEDE
>WP_151362412.1 gamma-glutamylcyclotransferase [Klebsiella pneumoniae]
MLEAIGGEWRPGYVTGTFYARGWGAAADFPGIVLDAHGPRVNGYLFLSDRLARTGPCWTT
LRRGYDRVPVEVTTDDGQQISAWIYQLQPRG
>WP_151362413.1 acid resistance repetitive basic protein Asr [Klebsiella pneumoniae]
MKKVLALVVAAAMGLSSVAFAADAASTTPSAAASHTTVHHKKHHKAAAKPAAEQKAQAAK
KHHKTAAKTGSRAESAGCKETS
>WP_151362414.1 ABC transporter permease [Klebsiella pneumoniae]
MKRAPWYLRLATWGGVIFLHFPLLIIAIYAFNTEDAAFSFPPQGLTLRWFSEAAGRSDIL
QAVTLSLKIAALSTAIALVLGTLAAGALWRSAFFGKNAVSLLLLLPIALPGIITGLALLT
AFKAVGLEPGLLTIVVGHATFCVVVVFNNVIARFRRTSWSMVEASMDLGATGWQTFRYVV
LPNLGSALLAGGMLAFALSFDEIIVTTFTAGHERTLPLWLLNQLGRPRDVPVTNVVALLV
MLVTTIPILGAWWLTRDGDSDAGNGK
example of output- expected and correct with above command
>WP_151362411.1#0940
MYAPQCSRSKRCFAGLPSLSHEQQQQAVERIHELMAQGISSGQAIALVAEELRATHTGEQ
IVARFEDEDEDE
>WP_151362412.1#0940
MLEAIGGEWRPGYVTGTFYARGWGAAADFPGIVLDAHGPRVNGYLFLSDRLARTGPCWTT
LRRGYDRVPVEVTTDDGQQISAWIYQLQPRG
>WP_151362413.1#0940
MKKVLALVVAAAMGLSSVAFAADAASTTPSAAASHTTVHHKKHHKAAAKPAAEQKAQAAK
KHHKTAAKTGSRAESAGCKETS
>WP_151362414.1#0940
MKRAPWYLRLATWGGVIFLHFPLLIIAIYAFNTEDAAFSFPPQGLTLRWFSEAAGRSDIL
QAVTLSLKIAALSTAIALVLGTLAAGALWRSAFFGKNAVSLLLLLPIALPGIITGLALLT
AFKAVGLEPGLLTIVVGHATFCVVVVFNNVIARFRRTSWSMVEASMDLGATGWQTFRYVV
LPNLGSALLAGGMLAFALSFDEIIVTTFTAGHERTLPLWLLNQLGRPRDVPVTNVVALLV
MLVTTIPILGAWWLTRDGDSDAGNGK
i am getting the required/expected result but this editing is not saving with this command, can someone help me figure out that how to save those editing in the original files bcz when i open those files again they were same as before with no edited header?
Python alternative of the above command used would also be helpful

Assuming:
The relevant files are proid_unique and *.faa files in current
directory.
We want to replace *.faa files by editing the header lines
according to the key-value pairs described in proid_unique.
We can forget about genomid file so far.
As I'm not familiar with seqkit command, here is an python alternative:
#!/usr/bin/python
import glob
import os
with open('proid_unique') as f: # open the key-value file
m = {k : v for k, v in [line.split() for line in f]}
# create a dictionary of key-value pairs to edit
for fasta in glob.glob('*.faa'):
org = fasta + '.O' # backup filename appending '.O' suffix
os.rename(fasta, org) # rename the file
with open(org) as f, open(fasta, 'w') as w:
# open files to read and write
for line in f: # process line by line
line = line.rstrip() # remove a newline character
if line.startswith('>'): # header line
header = line.split()[0] # extract the substring before a whitespace
if header[1:] in m: # if the header is a key in the dictionary
line = '>' + m[header[1:]]
# then replace the line
w.write(line + '\n') # overwrite to the fasta file
It back-ups the old *.faa files as *.faa.O.
If my assumption is incorrect, please let me know.

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