Hello,
I have multiple fasta sequences that are like this:
>2p__scaffold_2__5799__6580__-__778568__0.00__0.00
GCTGGCGACGGATCTAGGCTCAGCGCAGAAGCAACTGAGAGTCGGCGATGAGCAGCCGGA
GCTGGCGACGGATCTAGGCTCAGCGCAGAAGCAA
>2p__scaffold_2__5799__6580__+__778569__0.00__0.00
GCTGGCGACGGATCTAGGCTCAGCGCAGAAGCAACTGAGAGTCGGCGATGAGC
>1p__scaffold_2__11235__11438__-__830827__0.00__0.00
GCTGGCGACGGATCTAGGCTCAGCGCAGAAGCAACTGAGAGTCGGCGATGAGCAGCCGGA
GCTTCAATCCAGGGGATCGAGGAGATCCAAAGCAGCAGAAGCGGCTCGACGATGGTGAGG
ATTCGGGATCGGATTCAGCGCTCGTCGGGACTGG
>1p__scaffold_2__33129__34129__+__811706__0.00__0.00
GCTGGCGACGGATCTA
And I want to keep just the "> + ID" (numbers after __+/-__ and before __0.00_0.00)
So I expect an output like this:
>778568
GCTGGCGACGGATCTAGGCTCAGCGCAGAAGCAACTGAGAGTCGGCGATGAGCAGCCGGA
GCTGGCGACGGATCTAGGCTCAGCGCAGAAGCAA
>778569
GCTGGCGACGGATCTAGGCTCAGCGCAGAAGCAACTGAGAGTCGGCGATGAGC
I searched for it and tried this:
sed 's@.*__-__@@' input.fa > output.fa
That removed __-__ and everything before it, including the ">" that I wanted to keep.
I also tried this to remove everything between ">" and __-__
sed -e 's/\>//' -e 's/\__-__.*//' input.fa > output.fa
But this removed everything after __-__
And this, that removed __0.00_0.00
sed 's/__0.00.*$//' input.fa > output.fa
Thank you for your help.
•
written
by
Harumi •
4 answers
Try the following regular expression:
$ awk '{ if ($0 ~ /^>/) { match($1, /[+|-]__[0-9]+__/, m); print ">"substr(m[0], 4, length(m[0]) - 5); } else { print $0; } }' input.fa > output.fa
Then:
$ less output.fa
>778568
GCTGGCGACGGATCTAGGCTCAGCGCAGAAGCAACTGAGAGTCGGCGATGAGCAGCCGGA
GCTGGCGACGGATCTAGGCTCAGCGCAGAAGCAA
>778569
GCTGGCGACGGATCTAGGCTCAGCGCAGAAGCAACTGAGAGTCGGCGATGAGC
>830827
GCTGGCGACGGATCTAGGCTCAGCGCAGAAGCAACTGAGAGTCGGCGATGAGCAGCCGGA
GCTTCAATCCAGGGGATCGAGGAGATCCAAAGCAGCAGAAGCGGCTCGACGATGGTGAGG
ATTCGGGATCGGATTCAGCGCTCGTCGGGACTGG
>811706
GCTGGCGACGGATCTA
You're quite welcome!
you will miss out on the __+__ cases with this one ;)
Thank you for your help!
I tried:
sed 's/.*__[\+-]__/>/' | sed 's/__.*//' input.fa > output.fa
But it took a long time processing so I canceled.
When I tried:
sed 's/.*__[\+-]__/>/' input.fa > output.fa | sed 's/__.*//' output.fa > output2.fa
The output was empty.
Why does this happen?
Thank you again!!
You need to put the input file before the '|' symbol, so like this:
sed 's/.*__[\+-]__/>/' input.fa | sed 's/__.*//' > output.fa
otherwise it is just waiting for input (== why it is taking so long)
the second is a wrong syntax and will indeed never work. The data stream stopped at ' > output.fa' so any pipe or such behind it will not do anything (and create empty file as you mention)
a little late to the party:
$ sed '/>/ s/^.*__\(\w\+\)__.*/>\1/g' file.fa
or
$ sed '/>/ s/^\(\W\).*__\(\w\+\)__.*/\1\2/g' file.fa
>778568
GCTGGCGACGGATCTAGGCTCAGCGCAGAAGCAACTGAGAGTCGGCGATGAGCAGCCGGA
GCTGGCGACGGATCTAGGCTCAGCGCAGAAGCAA
>778569
GCTGGCGACGGATCTAGGCTCAGCGCAGAAGCAACTGAGAGTCGGCGATGAGC
>830827
GCTGGCGACGGATCTAGGCTCAGCGCAGAAGCAACTGAGAGTCGGCGATGAGCAGCCGGA
GCTTCAATCCAGGGGATCGAGGAGATCCAAAGCAGCAGAAGCGGCTCGACGATGGTGAGG
ATTCGGGATCGGATTCAGCGCTCGTCGGGACTGG
>811706
GCTGGCGACGGATCTA
a little late to the party:
Always very welcome, though.
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