Seqkit Replace

Question

[pablo]

Hi,

I would like to replace my FASTA headers according to a matching file.

I have :

head my.fasta
>CM020909.1:14117
aTTTTTGTCCCCAatattaggccctatgttctcacatttcacaatttttt[C/T]ccccaaaattaggccctatgttcccacatttcaagatttattttttccaa
>CM020909.1:148127
TTACTTTGTAGTAGCTTTTACTTTGTAGCTAGAGGCTTGGCTGTGCTGTT[T/A]GGGCTTTTACTGTAGTGGCTTGGGTTGGTAGTGACTTTGAAGGAGGTTAA
>CM020909.1:254785
CGTCCATCTTCTCCAGAGCTCTTTAAAGCCAAAGCGTTTTGGGGGACAGC[A/T]GCACAAAGAGCCAATCAAACGCCACAAAAGGCAGAGAACCGGACACCTGG
>CM020909.1:362180
ccaaaaatgatcGCCGCTGGtcgggagggggaggggacgggggAGGTGGG[T/G]AATTTGGCTTAAACACACAATTCAAAGAGGGGAACGTTGTTAAACAAACG
>CM020909.1:469928
agggtaactaatcattctttacccttctgaaaaagtgtaactacccttct[G/C]aaaaacagtaactaatcattaactacctatttttttgtgtaccttattat

And the corresponding file :

head correspondances.txt
CM020909.1      CHR1
CM020910.1      CHR2
CM020911.1      CHR3
CM020912.1      CHR4
CM020913.1      CHR5
CM020914.1      CHR6
CM020915.1      CHR7
CM020916.1      CHR8
CM020917.1      CHR9
CM020918.1      CHR10

I use this but does not work :

seqkit replace -k correspondances.txt -p "^(.+?) (.+)$" -r "{kv}:\$2" my.fasta

I need to keep the position after the " : " , to get something like that for the first sequence : >CHR1:14117

Any help?

Answer 1

[shenwei356]

"^(.+?) (.+)$" should be "^(.+?):(.+)$". It's a colon not space in the middle of CM020909.1:14117. :)

[pablo]

Thanks a lot, that was pretty easy actually. I take this opportunity to ask you another thing : in my FASTA file, I have some headers which do not match any line of my correspondances.txt . With the seqkit replace command , that creates for these headers something like this ">:643" (rather than >CM020933.1:643) . Is there an option to do not edit those headers ?

[shenwei356]

add -K.

  -K, --keep-key                 keep the key as value when no value found for the key (only for
                                 sequence name)
  -U, --keep-untouch             do not change anything when no value found for the key (only for
                                 sequence name)

the logic is (code):

if v, ok = kvs[k]; ok {                             # replace with value
    r = reKV.ReplaceAll(r, []byte(v))
} else if keepUntouch {                             # -U, --keep-untouch
    doNotChange = true
} else if keepKey {                                 # -K, --keep-key
    r = reKV.ReplaceAll(r, found[keyCaptIdx])
} else {                                            # -m, --key-miss-repl
    r = reKV.ReplaceAll(r, []byte(keyMissRepl))
}

[pablo]

Perfect, thanks a lot!