It looks like a lot of work. I'm trying it. Thank you for your advice.
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How to find the longest common sequence for a cluster of sequences in a fasta file using python?
I have a fasta file in which sequences are clustered and sorted by IDs. I want to find the longest sequence for each cluster and write them to a new file. How do I do it with python?
Here is the format of my fasta file:
>abc var1
kdfafaljflasjfalsjfaljfs
>abc var2
lasuowiejwaljflaj
>abc var3
lajflasjfowijflasjfopiefjjkfldfjqop
>dce var1
owiepqfpufaplddfpqoiwejlkdf
>dce var2
qopwelsmdfljfaldjfaopif
>red var1
alsdfowejfsladfjojflsdfjsdfjaslfjk
>red var2
lsdfjjqowjelsaflasflfnkdaflasfj
>red var3
kahfiqwuefkasdnkashdfiqfkasjdfh
>red var4
akhqioweadhauisydklsdfksdyiofjasldfhihladfni
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2 answers
Check out the Python module pyfaidx: https://github.com/mdshw5/pyfaidx
It makes doing this sort of thing super easy. You may have to experiment a bit to figure out how to do exactly what you are wanting to, but with pyfaidx, you have a nice interface to access each sequence in your file and get information about each sequence, i.e. length, name, etc.
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dbrowne.up •
pyfaidx will not work on this type of FASTA because the indexing process splits each sequence name on whitespace, so you'd end up with non-unique identifiers. This was a design decision to match the samtools behavior.
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Matt Shirley
Thanks for pointing it out, Matt. I noticed that too. However, the integrated faidx commandline tool is really handy for doing other things with your fasta file.
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Ram
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Hey folks,
I found a solution from another post. Here is the link for those who are in the same boat with me.
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