Skip to main content
Bioinformatics

Return to Answer

added 11933 characters in body
Source Link
terdon ♦
terdon ♦
  • 10.6k
  • 5
  • 23
  • 48

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.

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.

Source Link
terdon ♦
terdon ♦
  • 10.6k
  • 5
  • 23
  • 48

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