I would convert the fasta file to a format with one line per record (I have already posted the FastaToTbl and TblToFasta scripts I use for this before), and then look for a specific pattern:
FastaToTbl file.fa | grep 'BKT028387' | TblToFasta > clostridium.fa
FastaToTbl file.fa | grep 'OBRC8' | TblToFasta > peptoanaerobacter.fa
I have downloaded a few sequences using the same command you described in your previous question, and it looks like the headers are not standardized. For example, while you have many that are in the format of $species strain $strain, like these:
Clostridioides difficile strain 7496-D/ST9
Clostridioides difficile strain 5616-DH/ST42,
Peptoanaerobacter stomatis strain OBRC8
Romboutsia maritimum strain CCRI-22766
Tepidibacter mesophilus strain JCM
Others don't have the word strain and just give the strain:
Peptostreptococcus anaerobius 653-L contig00088,
Peptoclostridium acidaminophilum DSM 3953
So, as a first step, you could deal with the ones that do have the word strain as the 4th word of the header line (the 1st is the seqID which I have not included in the examples above) and the actual strain as the 5th and get those out of the way:
FastaToTbl foo.fa |
awk '($4=="strain"){gsub("/","_"); print $0 >> $2"_"$3"_"$5".tbl"}'
That will look for lines whose 4th field is strain, then it will replace any / in the line with _ (there's a strain called CF/ST37 and that cannot be in a filename) and print into a file whose name is the 2nd, 3rd and 5th fields of the line concatenated. On my test file, this produced the following files (as you can see, some are wrong since there is a comma after the strain, but that's because they're not standardized):
$ ls *tbl
Clostridioides_difficile_5479-NonSp_ST229,.tbl Clostridioides_difficile_6589-DH_ST42.tbl Clostridioides_difficile_7457-NonSp_novelST,.tbl
Clostridioides_difficile_5479-NonSp_ST229.tbl Clostridioides_difficile_6592-G_ST8,.tbl Clostridioides_difficile_7457-NonSp_novelST.tbl
Clostridioides_difficile_5480-E_ST6,.tbl Clostridioides_difficile_6592-G_ST8.tbl Clostridioides_difficile_7458-N_ST10,.tbl
Clostridioides_difficile_5480-E_ST6.tbl Clostridioides_difficile_6593-Y_ST110,.tbl Clostridioides_difficile_7458-N_ST10.tbl
Clostridioides_difficile_5482-L_ST55,.tbl Clostridioides_difficile_6593-Y_ST110.tbl Clostridioides_difficile_7459-G_ST8,.tbl
Clostridioides_difficile_5482-L_ST55.tbl Clostridioides_difficile_6595-AL_ST58,.tbl Clostridioides_difficile_7459-G_ST8.tbl
Clostridioides_difficile_5485-Y_ST2,.tbl Clostridioides_difficile_6595-AL_ST58.tbl Clostridioides_difficile_7462-DH_ST42,.tbl
Clostridioides_difficile_5485-Y_ST2.tbl Clostridioides_difficile_6596-D_ST9,.tbl Clostridioides_difficile_7462-DH_ST42.tbl
Clostridioides_difficile_5488-DH_ST42,.tbl Clostridioides_difficile_6596-D_ST9.tbl Clostridioides_difficile_7463-E_ST6,.tbl
Clostridioides_difficile_5488-DH_ST42.tbl Clostridioides_difficile_6599-NonSp_ST103,.tbl Clostridioides_difficile_7463-E_ST6.tbl
Clostridioides_difficile_5489-M_ST15,.tbl Clostridioides_difficile_6599-NonSp_ST103.tbl Clostridioides_difficile_7464-Y_ST110,.tbl
Clostridioides_difficile_5489-M_ST15.tbl Clostridioides_difficile_6600-G_ST8,.tbl Clostridioides_difficile_7464-Y_ST110.tbl
Clostridioides_difficile_5490-CF_ST37,.tbl Clostridioides_difficile_6600-G_ST8.tbl Clostridioides_difficile_7466-DH_ST42,.tbl
Clostridioides_difficile_5490-CF_ST37.tbl Clostridioides_difficile_6606-BK_ST11,.tbl Clostridioides_difficile_7466-DH_ST42.tbl
Clostridioides_difficile_5493-DH_ST42,.tbl Clostridioides_difficile_6606-BK_ST11.tbl Clostridioides_difficile_7467-DH_ST42,.tbl
Clostridioides_difficile_5493-DH_ST42.tbl Clostridioides_difficile_6607-DH_ST42,.tbl Clostridioides_difficile_7467-DH_ST42.tbl
Clostridioides_difficile_5495-AF_ST41,.tbl Clostridioides_difficile_6607-DH_ST42.tbl Clostridioides_difficile_7468-NonSp_ST97,.tbl
Clostridioides_difficile_5495-AF_ST41.tbl Clostridioides_difficile_6610-N_ST10,.tbl Clostridioides_difficile_7468-NonSp_ST97.tbl
Clostridioides_difficile_5497-Y_ST2,.tbl Clostridioides_difficile_6610-N_ST10.tbl Clostridioides_difficile_7471-BI_ST1,.tbl
Clostridioides_difficile_5497-Y_ST2.tbl Clostridioides_difficile_6612-DH_ST28,.tbl Clostridioides_difficile_7471-BI_ST1.tbl
Clostridioides_difficile_5500-DH_ST42,.tbl Clostridioides_difficile_6612-DH_ST28.tbl Clostridioides_difficile_7472-Y_ST2,.tbl
Clostridioides_difficile_5500-DH_ST42.tbl Clostridioides_difficile_6613-NonSp_ST3,.tbl Clostridioides_difficile_7472-Y_ST2.tbl
Clostridioides_difficile_5504-L_ST55,.tbl Clostridioides_difficile_6613-NonSp_ST3.tbl Clostridioides_difficile_7473-DH_ST42,.tbl
Clostridioides_difficile_5504-L_ST55.tbl Clostridioides_difficile_6614-AL_ST34,.tbl Clostridioides_difficile_7473-DH_ST42.tbl
Clostridioides_difficile_5505-Y_ST2,.tbl Clostridioides_difficile_6614-AL_ST34.tbl Clostridioides_difficile_7476-Y_ST2,.tbl
Clostridioides_difficile_5505-Y_ST2.tbl Clostridioides_difficile_6615-NonSp_ST11,.tbl Clostridioides_difficile_7476-Y_ST2.tbl
Clostridioides_difficile_5537-D_ST9,.tbl Clostridioides_difficile_6615-NonSp_ST11.tbl Clostridioides_difficile_7478-NonSp_novelST,.tbl
Clostridioides_difficile_5537-D_ST9.tbl Clostridioides_difficile_6616-NonSp_novelST,.tbl Clostridioides_difficile_7478-NonSp_novelST.tbl
Clostridioides_difficile_5538-BK_ST11,.tbl Clostridioides_difficile_6616-NonSp_novelST.tbl Clostridioides_difficile_7479-NonSp_ST3,.tbl
Clostridioides_difficile_5538-BK_ST11.tbl Clostridioides_difficile_6617-A_ST43,.tbl Clostridioides_difficile_7479-NonSp_ST3.tbl
Clostridioides_difficile_5539-Y_ST2,.tbl Clostridioides_difficile_6617-A_ST43.tbl Clostridioides_difficile_7480-M_ST15,.tbl
Clostridioides_difficile_5539-Y_ST2.tbl Clostridioides_difficile_6618-NonSp_ST53,.tbl Clostridioides_difficile_7480-M_ST15.tbl
Clostridioides_difficile_5541-CF_ST37,.tbl Clostridioides_difficile_6618-NonSp_ST53.tbl Clostridioides_difficile_7481-NonSp_ST59,.tbl
Clostridioides_difficile_5541-CF_ST37.tbl Clostridioides_difficile_6619-CF_ST37,.tbl Clostridioides_difficile_7481-NonSp_ST59.tbl
Clostridioides_difficile_5542-Y_ST2,.tbl Clostridioides_difficile_6619-CF_ST37.tbl Clostridioides_difficile_7482-DH_ST42,.tbl
Clostridioides_difficile_5542-Y_ST2.tbl Clostridioides_difficile_6621-NonSp_ST10,.tbl Clostridioides_difficile_7482-DH_ST42.tbl
Clostridioides_difficile_5547-DH_ST42,.tbl Clostridioides_difficile_6621-NonSp_ST10.tbl Clostridioides_difficile_7486-A_ST43,.tbl
Clostridioides_difficile_5547-DH_ST42.tbl Clostridioides_difficile_6622-CF_ST37,.tbl Clostridioides_difficile_7486-A_ST43.tbl
Clostridioides_difficile_5548-Y_ST2,.tbl Clostridioides_difficile_6622-CF_ST37.tbl Clostridioides_difficile_7488-NonSp_ST103,.tbl
Clostridioides_difficile_5548-Y_ST2.tbl Clostridioides_difficile_6623-NonSp_ST54,.tbl Clostridioides_difficile_7488-NonSp_ST103.tbl
Clostridioides_difficile_5549-NonSp_ST21,.tbl Clostridioides_difficile_6623-NonSp_ST54.tbl Clostridioides_difficile_7491-DH_ST42,.tbl
Clostridioides_difficile_5549-NonSp_ST21.tbl Clostridioides_difficile_6625-Y_ST2,.tbl Clostridioides_difficile_7491-DH_ST42.tbl
Clostridioides_difficile_5550-AH_ST67,.tbl Clostridioides_difficile_6625-Y_ST2.tbl Clostridioides_difficile_7492-CF_ST37,.tbl
Clostridioides_difficile_5550-AH_ST67.tbl Clostridioides_difficile_6626-Y_ST110,.tbl Clostridioides_difficile_7492-CF_ST37.tbl
Clostridioides_difficile_5551-CF_ST37,.tbl Clostridioides_difficile_6626-Y_ST110.tbl Clostridioides_difficile_7494-E_ST6,.tbl
Clostridioides_difficile_5551-CF_ST37.tbl Clostridioides_difficile_6628-AL_ST58,.tbl Clostridioides_difficile_7494-E_ST6.tbl
Clostridioides_difficile_5552-DH_ST42,.tbl Clostridioides_difficile_6628-AL_ST58.tbl Clostridioides_difficile_7496-D_ST9,.tbl
Clostridioides_difficile_5552-DH_ST42.tbl Clostridioides_difficile_6629-NonSp_novelST,.tbl Clostridioides_difficile_7496-D_ST9.tbl
Clostridioides_difficile_5553-L_ST55,.tbl Clostridioides_difficile_6629-NonSp_novelST.tbl Clostridioides_difficile_7497-NonSp_novelST,.tbl
Clostridioides_difficile_5553-L_ST55.tbl Clostridioides_difficile_6631-DH_ST42,.tbl Clostridioides_difficile_7497-NonSp_novelST.tbl
Clostridioides_difficile_5555-DH_ST42,.tbl Clostridioides_difficile_6631-DH_ST42.tbl Clostridioides_difficile_7498-M_ST15,.tbl
Clostridioides_difficile_5555-DH_ST42.tbl Clostridioides_difficile_6632-NonSp_ST3,.tbl Clostridioides_difficile_7498-M_ST15.tbl
Clostridioides_difficile_5557-DH_ST42,.tbl Clostridioides_difficile_6632-NonSp_ST3.tbl Clostridioides_difficile_7499-CF_ST37,.tbl
Clostridioides_difficile_5557-DH_ST42.tbl Clostridioides_difficile_6634-DH_ST42,.tbl Clostridioides_difficile_7499-CF_ST37.tbl
Clostridioides_difficile_5558-AH_ST67,.tbl Clostridioides_difficile_6634-DH_ST42.tbl Clostridioides_difficile_7501-BI_ST1,.tbl
Clostridioides_difficile_5558-AH_ST67.tbl Clostridioides_difficile_6635-BI_ST1,.tbl Clostridioides_difficile_7501-BI_ST1.tbl
Clostridioides_difficile_5559-DH_ST42,.tbl Clostridioides_difficile_6635-BI_ST1.tbl Clostridioides_difficile_7503-Y_ST2,.tbl
Clostridioides_difficile_5559-DH_ST42.tbl Clostridioides_difficile_6637-AL_ST58,.tbl Clostridioides_difficile_7503-Y_ST2.tbl
Clostridioides_difficile_5573-CF_ST37,.tbl Clostridioides_difficile_6637-AL_ST58.tbl Clostridioides_difficile_7505-Y_ST2,.tbl
Clostridioides_difficile_5573-CF_ST37.tbl Clostridioides_difficile_7450-DH_ST42,.tbl Clostridioides_difficile_7505-Y_ST2.tbl
Clostridioides_difficile_5616-DH_ST42,.tbl Clostridioides_difficile_7450-DH_ST42.tbl Clostridioides_difficile_NCKUH-21,.tbl
Clostridioides_difficile_5616-DH_ST42.tbl Clostridioides_difficile_7451-NonSp_ST2,.tbl Clostridioides_difficile_RC10,.tbl
Clostridioides_difficile_5754,.tbl Clostridioides_difficile_7451-NonSp_ST2.tbl Clostridioides_difficile_RC10.tbl
Clostridioides_difficile_5754.tbl Clostridioides_difficile_7452-Y_ST110,.tbl Clostridioides_difficile_RF17,.tbl
Clostridioides_difficile_6583-AH_ST67,.tbl Clostridioides_difficile_7452-Y_ST110.tbl Clostridioides_difficile_RF17.tbl
Clostridioides_difficile_6583-AH_ST67.tbl Clostridioides_difficile_7453-Y_ST2,.tbl Peptoanaerobacter_stomatis_OBRC8,.tbl
Clostridioides_difficile_6584-AQ_ST26,.tbl Clostridioides_difficile_7453-Y_ST2.tbl Peptoanaerobacter_stomatis_OBRC8.tbl
Clostridioides_difficile_6584-AQ_ST26.tbl Clostridioides_difficile_7455-A_ST43,.tbl Romboutsia_maritimum_CCRI-22766,.tbl
Clostridioides_difficile_6588-G_ST8,.tbl Clostridioides_difficile_7455-A_ST43.tbl Romboutsia_maritimum_CCRI-22766.tbl
Clostridioides_difficile_6588-G_ST8.tbl Clostridioides_difficile_7456-DH_ST42,.tbl Tepidibacter_mesophilus_JCM.tbl
Clostridioides_difficile_6589-DH_ST42,.tbl Clostridioides_difficile_7456-DH_ST42.tbl
Finally, you can convert these back to fasta with:
for f in *tbl; do TblToFasta $f > ${f/.tbl/.fa} && rm $f; done
This will only get those sequences whose naming scheme is as described above. But that's a start. You can then see what else you have and extract the rest manually or by finding a similar approach that matches those.