LASTZ does not accept/like "-" (dash) in Fasta file

Question

[biomagician]

Dear all,

I have tried the following command:

lastz output/genome/ref/seq/chromosome.I.fa output/assembly/celegans/hgap/bristol/contig.fa --notransition --step=20 --nogapped --format=maf > output/AvsB.maf

but LASTZ complains about the dash in my fasta file:

FAILURE: bad fasta character in output/assembly/celegans/hgap/bristol/contig.fa, >contig: -

Does anybody know how to get round this problem?

Best,

C.

[st.ph.n]

Can you post a couple examples of your header lines?

This will remove all dashes: sed -i 's/-//g' myfasta.fa

[biomagician]

What are header lines? Do you mean the header of the FASTA file? There is only one sequence in the file, so only one header: >contig

[firatuyulur]

-i in sed will make a change in the original file, I'd rather go without -i for this case because we dont know what is needed to be done specifically.

why is this post in job section anyways?

[Philipp Bayer]

Just moved it into the 'Question' section :)

[st.ph.n]

That's why I asked to see some header lines, unless the dash is in the sequences. The OP can also make a copy of the file, or sub-sample to test on.

[biomagician]

The output of sed is too long, is this what you want?:

>contig
ggaatattgttatttcagaaaatagctaaatgtgatttctgtaattttgcctgccaaatt
cgtgaaatgcaataaaaatctaatatccctcatcagtgcgatttccgaatcagtatattt
ttacgtaatagcttctttgacatcaataagtatttgcctatatgactttagacttgaaat
tggctattaatgccaatttcatgatatctagccactttagtataattgtttttagttttt
ggcaaaactattgtctaaacagatattcgtgttttcaannnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnacggccttgatgtgcnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnaggctgacgannnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnctttgnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn--------------------
------------------------------------------------------------
------------------------------------------------------------

and it goes on for much longer.

[WouterDeCoster]

Well how did those '-' end up there in the first place...

[biomagician]

It's the output of the HGAP assembler. I don't know why HGAP returns gaps in a contig.

[Rohit]

You can use sed to replace the file first, sed -e '/^[agctn]/ s/-/n/g' file1.fa >file2.fa

Additionally you have to use the --ambiguous=n and query.fa[unmask] options since you have lower-case letters.

[st.ph.n]

The output of sed is too long, is this what you want?

you need to put it into a new file, sed -i 's/-//g' myfasta.fa > nodash.fasta, otherwise it prints to stdout.

[WouterDeCoster]

it prints to stdout.

Not with -i ...

[Rohit]

I agree, this would destroy the original file - horrible experiences with sed -i and grep > (instead of grep '>')

Answer 1

[biomagician]

Thanks to all. In the end, I revised my HGAP pipeline and the output of HGAP does not contain dashes, so I don't have this problem anymore. I was able to create a MAF file for visualisation in GMAJ. Thanks. C.