Hello,
I have a fasta file with different amino acid sequences, for example:
>abc
HSTSDSAQTMFPVALLLLAAGSCVKGEQLTQPTSVTVQPGQRLTITCQVSYSLGTYFTAW
IRQPAGKGLEWIGMRSTGASYYKDSLKNKFSIDLDTSSKTVTLNGQNVQPEDTAVYYCAR
APSRGFDYWGKGTMVTITSATPKGPTVFPL
>def
TARQIQHKPCFL*LCCCWQLDHV*RVNS*HSRPL*LCSQVNV*PSPVRSLILLVPTSQLG
SDSLQEKDWSGLE*DLLELHTTKIH*RTSSVST*TLPAKL*L*MDRMCSLKTLLCITVPE
RPVGVLTTGGKAPWSPSPRPPQRDQLCFL*
>ghi
GSQHVRFSTNHVSCSSAAVGSWIMCEG*TVDTADLCDCAARSTSDHHLSGLLFSW*LLHS
LDQTACRKRTGVDWEQIYWSCILQRFIKEQVQYRLRHFQQNCDSKWTECAA*RHCCVLLC
QTTGSGSWLLGERHHGHHHLGHPKGTNCVSS
and I want to filter out the sequences that are "productive" from the "non-productive" ones.
Additional info: I had translated every DNA sequence to amino acid sequence in all 6 frames.
By "non-productive" I mean those that don't translate into proteins (don't have the amino acid M and/or have too many stop codons). I would like to filter out these non-productive sequences in a fasta file.
As for the "productive" ones, I would also like to save every "productive" sequence only with the complete frame in another fasta file.
Is there any software tool where I can do this? If there isn't, I'm trying to do it in python... but I'm stuck... Any ideas you can come up with are welcome.
Thank you in advance
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sil_bioinfo •
If you are simply looking to filter out sequences that contain a stop (*) then you can do the following:
Code to linearize fasta courtesy of @Pierre.
$ awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' < test.fasta | grep -v "*" | tr "\t" "\n" | fold -w 60
>abc
HSTSDSAQTMFPVALLLLAAGSCVKGEQLTQPTSVTVQPGQRLTITCQVSYSLGTYFTAW
IRQPAGKGLEWIGMRSTGASYYKDSLKNKFSIDLDTSSKTVTLNGQNVQPEDTAVYYCAR
APSRGFDYWGKGTMVTITSATPKGPTVFPL
Hi, I would like to filter out sequences that, for example, don't have a methionine (M) and/or have a lot of stop codons (*) in the middle, not just one. These sequences would be the "non-productive" ones, and I would like to create a fasta file with these sequences too.
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At beginning of sequence?
in general, around all the sequence
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