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Select distinct sequences from fasta file and list

 
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Top Forums UNIX for Dummies Questions & Answers Select distinct sequences from fasta file and list
# 1  
Old 09-24-2014
Select distinct sequences from fasta file and list
Hi
How can I extract sequences from a fasta file with respect a certain criteria? The beginning of my file (containing in total more than 1000 sequences) looks like this:
Code:
>H8V34IS02I59VP 
SDACNDLTIALLQIAREVRVCNPTFSFRWHPQVKDEVMRECFDCIRQGLG
YPSMRNDPILIANCMNWHGHPLEEARQWVHQACMSPCPSTKHGFQPFRMA
SATANCAKIIEYALSNGYDPVVNMQMGPKIGDARDFT*L*TVIRGLGTTR
WSG
>H8V34IS02IRUQO 
SDACNDLTTAYMQAARLVRVCNPTFSFRYHPQVKDEVMREAFGCIRHGLG
YPNIKNDSVLIPNAMYWHGHPLEEARQWVNQACMSPCPPXKYGCQPNRMA
SAANCAKMIEYTLHTGMIM**TCRVGTEGRVIRAYFKDFGGVLTRYGVKQ
MEWLDVVLIVRFT
>H8V34IS02HTVT3 
SDACNGMTIALMQAARLVRTPNPTFAFRWHPKVKDEVMREIFECIRHGLG
YPAMRNDPILISNAMHWHRHPIEEARTWVHQACMSPCPTTKHGTQPMRMA
HATANCAKIMEYALWNGYDHVVNMQMGPRTGDARKFTDFEQLFDAWVKQX
DGC
>H8V34IS02HI4PS 
SDACNALTDCYLEAALVSRVSDPTFGFRYHSKVRTETLRRVFECIRHGLG
YPSIRNDDVLIPNIMHWFGHPLKEARRWLHQACMAPAPDTKWGAPSLRYP
QASIITGSKAISLAMFDGFDPLTGMQTGIKTGDCSKFETFDEFYDAWYEQ
PKAGFKQATGMEH
>H8V34IS02F9NL0 
SDACNDLTIALLQIAREVRVCNPTFSFRWHPQVKDEVMRECFDCIRQGLG
YPSMRNDPILIANCMNWHGHPLEEARQWVHQACMSPCPSTKHGFQPFRMA
SATANCAKIIEYALSNGYDPVVNMQMGPKIGDAGISDFEQLFEAWVQTDG
VA*WIL

I want to extract the sequences containing the motif FDCIR? Can it be done with grep? Or do I need a pearl script?
In a next step: How could I even extract sequences with respect to fullfilling two or more criteria?

Looking forward getting your suggestions.

Cheers, Marion.
Last edited by jim mcnamara; 09-24-2014 at 04:55 PM..
# 2  
Old 09-24-2014
Hi Marion Welcome to Forums, can we have expected output as well please.
# 3  
Old 09-24-2014
Have you tried
Code:
grep "FDCIR" file

?
Multiple matches:
Code:
grep -e "FDCIR" -e "ALSNG" file

or
Code:
grep "\
FDCIR
ALSNG" file

or
Code:
egrep "FDCIR|ALSNG" file

# 4  
Old 09-24-2014
Code:
#  Try awk (or nawk on Solaris)
awk ' />/ {arr[$0]=""; i=$0; next}
        {arr[i]=arr[i] $0}
        END {for( p in arr) { if ( index(arr[p], "FCDIR")>0 ) {print p, arr[p] }}}
       '   fasta_file > newfile

# 5  
Old 09-25-2014
Hi
Many thanks for the quick reply.
I tried but the output looks like
Code:
SDACNDLTDAILEASLNIRTPEPSLSFRYSPKINEKTRHLVFDNIAQGFGFPSIKHEEKN
GRVQRSDRRHTRGILEYQDAGAVSCIQILAQNQRKTRHLVFDNIAQGFGFPSIKHEEKTR
SDACNALTDAILEASLNIRTPEPSLSFRYSPKINEKTRHLVFDNIAQGFGFPSIKHEEKN
GRVQRSDRRHTRSILEYQNAGAVPFIQVLTQDQRKTRHLVFDNIAQGFGFPSIKHDEKNT
GRVQRSDRRHTRSILEYQDAGAVSCVQIFS*NQRKTRHLVFDNIAQGFGFPSIKHEEKTR
GRVQRSDRRHTRGILEYQDAGAVSCIQILAQNQRKTRHLVFDNIAQGFGFPSIKHEEKNT
GRVQRSDRRHTRSILEYQDTGAVPFIQVLTQDQRKTRHLVFDNIAQGFGFPSIKHEEKNT
GRVQRSDRRHTRSILEYQDTGAVPFIQVLTQDQRKTRHLVFDNIAQGFGFPSIKHEEKNH
SDACNDLTDAILEASLNIRTPEPSLAFRYSPKINEKTRHLVFDNIAQGFGFPSIKHEEKN
SDACNDLTDAILEASLNIRTPEPSLSFRYSPKINEKTRHLVFDNIAQGFGFPSIKHEEKN
SDACNDLTDAILEASLNIRTPEPSLSFRYSPKINEKTRHLVFDNIAQGFGFPSIKHEEKN
SDACNALTDAILEASLNIRTPEPSLAFRYSPKINEKTRHLVFDNIAQGFGFPSIKHEEKN
SDACNDLTDAILEASLNIRTPEPSLSFRYSPKINEKTRHLVFDNIAQGFGFPSIKHDEKN
SDACNALTDAILEASLNIRTPEPSLSFRYSPKINEKTRHLVFDNIAQGFGFRP*SMKKKT
SDACNALTDVILEASLNIRTPEPSLGFRYSPKINEKTRHLVFDNIAQGFGFPSIKRDEKN
SDACNDLTDAILEASLNIRTPEPSLSFRYSPKINEKTRHLVFDNIAQGFGFPSIKHDEKN
GRVQRSDRRHTRGILEYQDAGAVSCIQILAQNQRKTRHLVFDNIAQGFGFPSIKHEEKTR
GRVQRLTDAILEASLNIRTPEPSLAFRYSPKINEKTRHLVFDNIAQGFGFPSIKHEEKNT

instead of
Code:
>H8V34IS02HC5PK_rframe3
GRVQRSDRRHTRGILEYQDAGAVSCIQILAQNQRKTRHLVFDNIAQGF
GFPSIKHEEKTRR***TISIFHRTRPPTGRLFFAWRRA*INAGEPRQERKGRGVALQNPWNLLWETVFDYS
LTNIQMGPKQATLRSSKTSRTYGTHCGTGQIGNSLHFRNQGCMP*GQ
>H8V34IS02FU9GO_rframe1
SDACNALTDAILEASLNIRTPEPSLSFRYSPKINEKTRHLVFDNIAQGFGFPSIKHEEKNTKMLIDYFHIPPDEAAHWALVLCMAPGVNKRRGTQKSRTEGGGALCVAKPIELAMSDGF
DYSLTNAQMGLKTGDPTQFKDFEDVWNAFVEQLKFGVALHFRNRDVCRRAEIR
>H8V34IS02FTRDI_rframe3
GRVQRSDRRHTRSILEYQNAGAVPFIQVLTQDQRKTRHLVFDNIAQGFGFPSIKHDEKNT
KMMIDYFNIPPDEAAHWALVLCMAPGVNKRRGTQKSRTEGGGGFCVGKPMELAMGDGFD
YSLTNTQIGPKTGDPTQFNSFEDVWNAFEEQVKFAAALHFRNRDVCRRAEIKY*

ideally, I get a fasta file containing the selected sequences.
Cheers, Marion.




Quote:
Originally Posted by MadeInGermany
Have you tried
Code:
grep "FDCIR" file

?
Multiple matches:
Code:
grep -e "FDCIR" -e "ALSNG" file

or
Code:
grep "\
FDCIR
ALSNG" file

or
Code:
egrep "FDCIR|ALSNG" file


Moderator's Comments:
Mod Comment Please use code tags next time for your code and data. Thanks


---------- Post updated at 04:19 AM ---------- Previous update was at 03:47 AM ----------

Hi
Thank you for the quick reply.
I did not work, the new file is empty.

Any other suggestions?
Cheers, Marion.


Quote:
Originally Posted by jim mcnamara
Code:
#  Try awk (or nawk on Solaris)
awk ' />/ {arr[$0]=""; i=$0; next}
        {arr[i]=arr[i] $0}
        END {for( p in arr) { if ( index(arr[p], "FCDIR")>0 ) {print p, arr[p] }}}
       '   fasta_file > newfile

# 6  
Old 09-25-2014
This one, if matches, returns the whole string from > to the next >
Code:
awk -v search="FDCIR|ALSNG" '$1~/^>/ {buf=sep=""; found=0} found==1 {print; next} {buf=buf sep $0; sep=RS} $0~search {print buf; found=1}' file

# 7  
Old 09-25-2014
Perfect, exactly what I needed: Dankeschön!
Cheers, Marion.



Quote:
Originally Posted by MadeInGermany
This one, if matches, returns the whole string from > to the next >
Code:
awk -v search="FDCIR|ALSNG" '$1~/^>/ {buf=sep=""; found=0} found==1 {print; next} {buf=buf sep $0; sep=RS} $0~search {print buf; found=1}' file

 
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