how to change the sequence ID and order of sequences in a file to match an alignment output file

>maker-scaffold10x_338_pilon-snap-gene-0.71-mRNA-1 MHLKNGDPKPTIKPNQCTLFGFRFCPYVDRVRMVLQYYNVPHDNVWIHLYSKPDWYLELY PVGKVPLLITKEGKTIVESDAIIRYLDETIGNKSLMSLCGEAEFERAGKLASKLMAQSHG ILFGASVAEANASAYRDVCQEINDTIKGPYLLGDKLTLADFLLFSHVNHFEPIMARLDGL APSDVHDLKATDQYRTKWPRLTTFLDVMRRLPCVLTVREPSQKLALFAETYRQGQPNPDL >augustus_masked-scf7180006947290-processed-gene-0.5-mRNA-1 MSEIRSLNIFDANSQNSSEFRRNIPDFLRPYECYRCVIGKKKPDDVEYICRYSLSCLGDC AKEKDYARYLEMKPCIFLQVNKVYGWIPDIVGENLLVKCFGKVGLIKIILNSITPEIVFN YFGIKYDKVLINLQDKPEWFLKMYPEGKVPFIIDKQRQLGDSEIIIRDYDSKNNNKLITA CGEEKFSETKDLISSFFGLCYTILFKDNKISDENADLFLKALEKVEAKIVGPFMWGDQLS LADVILFTHLNMFECSLSRIEGIHPDQVKDGYPNAAREASFVKIPAYLKQMRNHSAVKDV YVHPNDISKYAVGLRIGKPNPEGDN >DILT_0000424901-mRNA-1 MGWVLGGDGSFLPTGCANHGDPEPSVNPENVTLYDMQFCPYCQRVRYTLDYHKIPYDRIL IDLMSKPSWYLKMYPVGKVPLLLYRGKTMAESDVIMKYCDQMKGAKASLLSVCGEEGFKR ALNLTSSVSLLLIALLRYKLLFSPDVTRADADSLKAALSNLDKAIQGPYLMDLLPFLTFE GKELSLADLALFPFLHAWDLLISRLKDVGDDSDESAEPVAPRWPNVLKYCQLMNQKPFIM KTAFRDDEFSKYMDTRLQAARP >MS3_04642.1 MHLKRSDPKPLIDPNRLTLIGFRFCPYVDRVRLILSYYKIDYDLINVSLASKPEWFLKMY PIGKVPLLLLPNEQKLPESDEIIRHIDKLYGSETLLSHCGIEEFEKVKELITGISRPSYM IMCVQEINLCDVSLYRAACNKINDAIKGPYFTGSELSLADLILFPHLHRFEVVMGRITGK KPEEINELNINDELRKEFPKLTEFLDTMRKQSFVIDVTIPYRIHVQYAASVLSGHANPDI E

>maker-scaffold10x_338_pilon-snap-gene-0.71-mRNA-1 ATGCATCTGAAAAACGGTGACCCAAAACCTACCATCAAGCCTAATCAATGTACTCTATTT GGTTTTCGATTCTGTCCCTATGTGGATCGTGTCAGAATGGTACTCCAATATTACAACGTC CCGCATGATAATGTTTGGATACATTTATACTCAAAACCGGATTGGTATCTGGAATTATAT CCGGTCGGCAAAGTACCTCTTTTGATTACCAAAGAGGGGAAGACAATTGTGGAATCGGAT GCGATTATACGGTATTTGGACGAAACGATCGGAAACAAGTCTCTGATGTCTTTGTGTGGT GAAGCGGAGTTTGAGCGGGCCGGGAAATTGGCGTCTAAACTCATGGCTCAATCGCATGGT ATTTTATTCGGCGCCAGTGTCGCGGAAGCTAATGCGTCTGCGTATCGTGACGTCTGTCAA GAAATAAATGATACAATCAAGGGACCATACTTGTTGGGCGACAAGTTGACATTGGCCGAT TTTCTGTTATTCTCTCATGTGAACCACTTCGAACCGATCATGGCTCGTTTAGACGGTCTA GCACCCAGTGACGTTCATGATCTGAAAGCGACCGATCAGTACAGGACGAAATGGCCCCGG TTGACCACCTTCTTGGATGTTATGCGTCGTTTGCCCTGTGTGCTTACCGTACGTGAGCCG TCCCAAAAGCTTGCCCTTTTTGCGGAAACATATCGTCAAGGTCAACCAAATCCGGATCTA TGA >augustus_masked-scf7180006947290-processed-gene-0.5-mRNA-1 ATGAGTGAAATACGGAGTTTAAACATTTTCGATGCCAACAGCCAGAACTCA....... >DILT_0000424901-mRNA-1 ATGGGCTGGGTATTAGGTGGCGACGGCTCCTTCTTACCCACCGGTTGTGCTAA....... >MS3_04642.1 ATGCACCTCAAACGAAGTGACCCTAAACCACTGATTGATCCTAATC..........

CLUSTAL W (1.81) multiple sequence alignment augustus_masked-scf7180006947290 MSEIRSLNIFDANSQNSSEFRRNIPD-FLRPYECYRCVIGKKKPDDVEYICRYSLSCLGD DILT_0000424901-mRNA-1 ---MGWVLGGDGSFLPTGCANHGDPEPSVNPENV-------------------------- maker-scaffold10x_338_pilon-snap -----------------MHLKNGDPKPTIKPNQC-------------------------- MS3_04642.1 -----------------MHLKRSDPKPLIDPNRL-------------------------- ... *. : * augustus_masked-scf7180006947290 CAKEKDYARYLEMKPCIFLQVNKVYGWIPDIVGENLLVKCFGKVGLIKIILNSITPEIVF DILT_0000424901-mRNA-1 --------TLYDMQFCPYCQRVR----------------------------------YTL maker-scaffold10x_338_pilon-snap --------TLFGFRFCPYVDRVR----------------------------------MVL MS3_04642.1 --------TLIGFRFCPYVDRVR----------------------------------LIL :. * : : . : augustus_masked-scf7180006947290 NYFGIKYDKVLINLQDKPEWFLKMYPEGKVPFIIDK-QRQLGDSEIIIRDYDSKNNNK-- DILT_0000424901-mRNA-1 DYHKIPYDRILIDLMSKPSWYLKMYPVGKVPLLLYR-GKTMAESDVIMKYCDQMKGAKAS maker-scaffold10x_338_pilon-snap QYYNVPHDNVWIHLYSKPDWYLELYPVGKVPLLITKEGKTIVESDAIIRYLDETIGNK-S MS3_04642.1 SYYKIDYDLINVSLASKPEWFLKMYPIGKVPLLLLPNEQKLPESDEIIRHIDKLYGSE-T .*. : :* : : * .**.*:*::** ****::: . : :*: *:. *. . :

>augustus_masked-scf7180006947290 ATGAGTGAAATACGGAGTTTAAACATTTTCGATGCCAACAGCCAGAACTCATCAGAATTT AGACGTAATATTCCAGATTTCCTGAGACCCTATGAGTGTTATCGCTGTGTTATCGGGAAA AAGAAGCCGGATGATGTTGAATACATTTGCAGATATTCTCTGTCATGTTTAGGTGATTGT GCAAAAGAAAAGGACTATGCAAGGTATCTGGAAATGAAACCCTGCATTTTTCTTCAAGTC AATAAAGTTTATGGCTGGATTCCAGACATTGTTGGTGAAAATTTACTCGTGAAATGTTTC GGAAAGGTCGGTTTAATTAAAATTATATTAAATAGTATAACACCTGAAATTGTATTCAAC TACTTCGGGATCAAATATGACAAGGTTCTAATAAATCTACAGGATAAACCTGAATGGTTT CTCAAAATGTACCCTGAAGGCAAGGTTCCATTCATCATTGATAAACAGAGACAACTTGGT GACTCTGAGATTATCATTCGAGACTATGACTCAAAGAACAATAATAAATTGATTACTGCC TGTGGCGAAGAAAAGTTTTCTGAAACTAAAGATCTCATCTCAAGCTTCTTTGGCCTTTGC TATACCATTCTCTTCAAGGATAATAAAATTTCCGATGAGAATGCTGATCTCTTCTTGAAA GCTCTCGAGAAGGTTGAAGCGAAAATTGTTGGCCCCTTCATGTGGGGAGATCAACTATCT CTAGCCGATGTAATTCTCTTCACACATTTGAACATGTTCGAGTGCTCTTTATCGAGAATC GAGGGAATTCATCCTGACCAAGTGAAAGATGGTTATCCCAATGCCGCAAGGGAAGCTAGC TTCGTCAAGATTCCCGCCTATCTGAAGCAAATGAGAAATCACTCTGCAGTTAAAGATGTC TACGTTCATCCTAATGATATTTCCAAGTACGCTGTCGGTTTAAGAATTGGAAAGCCAAAT CCGGAAGGCGATAACTAG >DILT_0000424901-mRNA-1 ATGGGCTGGGTATTAGGTGGCGACGGCTCCTTCTTACCCACCGG....... >maker-scaffold10x_338_pilon-snap ATGCATCTGAAAAACGGTGACCCAAAACCTACCA.......... >MS3_04642.1 ATGCACCTCAAACGAAGTGACCCTAAACCACTGATTGATCCTAAT.........

6 months ago by

shenwei356 ♦ 4.7k

China

shenwei356 ♦ 4.7k wrote:

It seems that you want sort sequences in FASTA format in a custom order. Here's a quick solution without writing script.

seqkit sort can sort FASTA, but it lacks the ability of sorting in custom order, luckily, which can be provided by csvtk sort:

An example:

$ cat seqs.fa 
>a
actg
>b
ACTG
>c
cagt
>d
CAGT

Using seqkit fx2tab to convert FASTA/Q into tabular format, and seqkit tab2fx convert it back to FASTA/Q.

$ seqkit fx2tab seqs.fa 
a       actg
b       ACTG
c       cagt
d       CAGT

csvtk sort can sort in user-defined order, defined by order.txt:

$ cat order.txt 
c
b
d
a

All in one:

$ seqkit fx2tab seqs.fa  | csvtk sort -H -t -L 1:order.txt -k 1:u | seqkit tab2fx 
>c
cagt
>b
ACTG
>d
CAGT
>a
actg

ADD COMMENT • link written 6 months ago by shenwei356 ♦ 4.7k

shenwei356 : Do you need to add anything to the command to recognize fasta names that are truncated to first 32 characters? It looks like the alignment software is doing that.

ADD REPLY • link written 6 months ago by genomax ♦ 70k

thanks for your reply, but would for few sequences, I'm talking of when I have like 50 sequences (or more).

Also, Im not sure if truncating the sequence ID truncated to 32 characters makes Identifying unique, it appears it just truncates them, meaning in case of sequences where sequences have similar ID within the 32 characters, identifying them may be an issue.

thanks

ADD REPLY • link written 6 months ago by Kay • 0

According what you mentioned in another similar post, the MSA software can save aligment result in FASTA file, where sequence ids are not truncted. I also remember some MSA tools indeed support this, like clustalo/clustalw.

So, you can just output the sequence headers

seqkit seq -n alignment.fasta > order.txt

ADD REPLY • link written 6 months ago by shenwei356 ♦ 4.7k

thanks, figured another way to do it using a script.

ADD REPLY • link written 6 months ago by Kay • 0

Assuming alignment file is also in fasta file, and the sequence ID is not truncated. Is it possible to sort my nucleotides then to have something like:

>augustus_masked-scf7180006947290-processed-gene-0.5-mRNA-1
ATGAGTGAAATACGGAGTTTAAACATTTTCGATGCCAACAGCCAGAACTCATCAGAATTT
AGACGTAATATTCCAGATTTCCTGAGACCCTATGAGTGTTATCGCTGTGTTATCGGGAAA
AAGAAGCCGGATGATGTTGAATACATTTGCAGATATTCTCTGTCATGTTTAGGTGATTGT
GCAAAAGAAAAGGACTATGCAAGGTATCTGGAAATGAAACCCTGCATTTTTCTTCAAGTC
AATAAAGTTTATGGCTGGATTCCAGACATTGTTGGTGAAAATTTACTCGTGAAATGTTTC
GGAAAGGTCGGTTTAATTAAAATTATATTAAATAGTATAACACCTGAAATTGTATTCAAC
TACTTCGGGATCAAATATGACAAGGTTCTAATAAATCTACAGGATAAACCTGAATGGTTT
CTCAAAATGTACCCTGAAGGCAAGGTTCCATTCATCATTGATAAACAGAGACAACTTGGT
GACTCTGAGATTATCATTCGAGACTATGACTCAAAGAACAATAATAAATTGATTACTGCC
TGTGGCGAAGAAAAGTTTTCTGAAACTAAAGATCTCATCTCAAGCTTCTTTGGCCTTTGC
TATACCATTCTCTTCAAGGATAATAAAATTTCCGATGAGAATGCTGATCTCTTCTTGAAA
GCTCTCGAGAAGGTTGAAGCGAAAATTGTTGGCCCCTTCATGTGGGGAGATCAACTATCT
CTAGCCGATGTAATTCTCTTCACACATTTGAACATGTTCGAGTGCTCTTTATCGAGAATC
GAGGGAATTCATCCTGACCAAGTGAAAGATGGTTATCCCAATGCCGCAAGGGAAGCTAGC
TTCGTCAAGATTCCCGCCTATCTGAAGCAAATGAGAAATCACTCTGCAGTTAAAGATGTC
TACGTTCATCCTAATGATATTTCCAAGTACGCTGTCGGTTTAAGAATTGGAAAGCCAAAT
CCGGAAGGCGATAACTAG
>DILT_0000424901-mRNA-1
ATGGGCTGGGTATTAGGTGGCGACGGCTCCTTCTTACCCACCGG.......
>maker-scaffold10x_338_pilon-snap-gene-0.71-mRNA-1
ATGCATCTGAAAAACGGTGACCCAAAACCTACCA..........
>MS3_04642.1
ATGCACCTCAAACGAAGTGACCCTAAACCACTGATTGATCCTAAT.........

ADD REPLY • link written 6 months ago by Kay • 0

using this approach I will have to extract the new sequence ID from the alignment file and write it to a new file:

augustus_masked-scf7180006947290      
DILT_0000424901-mRNA-1                
maker-scaffold10x_338_pilon-snap
MS3_04642.1

and then use csvtk sort, what if I have many sequences?

ADD REPLY • link written 6 months ago by Kay • 0

The desired output looks like it is just sorted sorted by sequence name. Shouldn't be seqkit sort enough to do the job? Truncating the names could than be done by a little awk script.

fin swimmer

ADD REPLY • link written 6 months ago by finswimmer ♦ 12k

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