I have a fasta file with different amino acid sequences, for
example : example.fasta
:
>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.
An example using biopython
and a threshold on the number of stop codons.
# pip install biopython
from Bio import SeqIO
seqs = SeqIO.parse(open('example.fasta'), 'fasta')
productive = {}
for s in seqs:
productive.setdefault(s.count('*')<3, []).append(s)
print(productive)
Output:
{True: [SeqRecord(seq=Seq('HSTSDSAQTMFPVALLLLAAGSCVKGEQLTQPTSVTVQPGQRLTITCQVSYSLG...FPL'), id='abc', name='abc', description='abc', dbxrefs=[])],
False: [SeqRecord(seq=Seq('TARQIQHKPCFL*LCCCWQLDHV*RVNS*HSRPL*LCSQVNV*PSPVRSLILLV...FL*'), id='def', name='def', description='def', dbxrefs=[]),
SeqRecord(seq=Seq('GSQHVRFSTNHVSCSSAAVGSWIMCEG*TVDTADLCDCAARSTSDHHLSGLLFS...VSS'), id='ghi', name='ghi', description='ghi', dbxrefs=[])]}
You can add a mode complex logic by replacing s.count('*')<3
by a custom function:
from Bio import SeqIO
seqs = SeqIO.parse(open('test/stackoverflow/example.fasta'), 'fasta')
def is_productive(s) -> bool:
# does the sequence start with M and contain less than 3 stops?
return s.seq.startswith('M') and (s.count('*')<3)
productive = {}
for s in seqs:
productive.setdefault(is_productive(s), []).append(s)
with open('productive_seqs.fasta', 'w') as fw:
SeqIO.write(productive.get(True, []), fw, 'fasta')
with open('nonproductive_seqs.fasta', 'w') as fw:
SeqIO.write(productive.get(False, []), fw, 'fasta')
Output:
# productive_seqs.fasta
>abc
HSTSDSAQTMFPVALLLLAAGSCVKGEQLTQPTSVTVQPGQRLTITCQVSYSLGTYFTAW
IRQPAGKGLEWIGMRSTGASYYKDSLKNKFSIDLDTSSKTVTLNGQNVQPEDTAVYYCAR
APSRGFDYWGKGTMVTITSATPKGPTVFPL
# nonproductive_seqs.fasta
>def
TARQIQHKPCFL*LCCCWQLDHV*RVNS*HSRPL*LCSQVNV*PSPVRSLILLVPTSQLG
SDSLQEKDWSGLE*DLLELHTTKIH*RTSSVST*TLPAKL*L*MDRMCSLKTLLCITVPE
RPVGVLTTGGKAPWSPSPRPPQRDQLCFL*
>ghi
GSQHVRFSTNHVSCSSAAVGSWIMCEG*TVDTADLCDCAARSTSDHHLSGLLFSW*LLHS
LDQTACRKRTGVDWEQIYWSCILQRFIKEQVQYRLRHFQQNCDSKWTECAA*RHCCVLLC
QTTGSGSWLLGERHHGHHHLGHPKGTNCVSS
Note that if you only need the files, you can directly write the sequence in the loop:
from Bio import SeqIO
seqs = SeqIO.parse(open('test/stackoverflow/example.fasta'), 'fasta')
def is_productive(s):
return s.seq.startswith('M') and (s.count('*')<3)
with open('productive_seqs.fasta', 'w') as fw1, open('nonproductive_seqs.fasta', 'w') as fw2:
for s in seqs:
SeqIO.write(s, fw1 if is_productive(s) else fw2, 'fasta')