How to filter "productive" amino acid sequences

Question

[sil_bioinfo]

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

[GenoMax]

Please do not delete posts once they have at least one comment or an answer.

[GenoMax]

don't have methionine

At beginning of sequence?

[sil_bioinfo]

in general, around all the sequence

Answer 1

[GenoMax]

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

[sil_bioinfo]

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.