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Full Discussion: Extract sequences from a FASTA file based on another file
Top Forums Shell Programming and Scripting Extract sequences from a FASTA file based on another file Post 302881716 by Akshay Hegde on Tuesday 31st of December 2013 11:59:18 AM
Old 12-31-2013
One more awk :
Code:
$ cat file1
16VPA
1A04B
153LB

Code:
$ cat file2
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE
SRMPSPPMPVPPAALFNRLLDDLGFSAGPALCTMLDTWNEDLFSALPTNADLYRECKFLSTLPSDVVEWGDAYVPERTQI
DIRAHGDVAFPTLPATRDGLGLYYEALSRFFHAELRAREESYRTVLANFCSALYRYLRASVRQLHRQAHMRGRDRDLGEM
LRATIADRYYRETARLARVLFLHLYLFLTREILWAAYAEQMMRPDLFDCLCCDLESWRQLAGLFQPFMFVNGALTVRGVP
IEARRLRELNHIREHLNLPLVRSAATEEPGAPLTTPPTLHGNQARASGYFMVLIRAKLDSYSSFTTSPSEAVMREHAYSR
APTKNNYGSTIEGLLDLPDDDAPEEAGLAAPRLSFLPAGHTRRLST
>1A04:A|PDBID|CHAIN|SEQUENCE
SNQEPATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLSG
RIVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAAGEMVLSEALTPVLAASLRANRATTERDVNQLTPRER
DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQERIF
>1A04:B|PDBID|CHAIN|SEQUENCE
SNQEPATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLSG
RIVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAAGEMVLSEALTPVLAASLRANRATTERDVNQLTPRER
DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQERIF

Code:
$ awk -F"|" 'FNR==NR{A[">"$1];next;}{s = $1; if(!(f = /^>/ ? x : f) && gsub(":",x,s) && (s in A)) f = 1}f' file1 file2

Code:
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE
SRMPSPPMPVPPAALFNRLLDDLGFSAGPALCTMLDTWNEDLFSALPTNADLYRECKFLSTLPSDVVEWGDAYVPERTQI
DIRAHGDVAFPTLPATRDGLGLYYEALSRFFHAELRAREESYRTVLANFCSALYRYLRASVRQLHRQAHMRGRDRDLGEM
LRATIADRYYRETARLARVLFLHLYLFLTREILWAAYAEQMMRPDLFDCLCCDLESWRQLAGLFQPFMFVNGALTVRGVP
IEARRLRELNHIREHLNLPLVRSAATEEPGAPLTTPPTLHGNQARASGYFMVLIRAKLDSYSSFTTSPSEAVMREHAYSR
APTKNNYGSTIEGLLDLPDDDAPEEAGLAAPRLSFLPAGHTRRLST
>1A04:B|PDBID|CHAIN|SEQUENCE
SNQEPATILLIDDHPMLRTGVKQLISMAPDITVVGEASNGEQGIELAESLDPDLILLDLNMPGMNGLETLDKLREKSLSG
RIVVFSVSNHEEDVVTALKRGADGYLLKDMEPEDLLKALHQAAAGEMVLSEALTPVLAASLRANRATTERDVNQLTPRER
DILKLIAQGLPNKMIARRLDITESTVKVHVKHMLKKMKLKSRVEAAVWVHQERIF

 

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LEARN ABOUT SUSE

asn1_get_bit_der

asn1_get_bit_der(3)						     libtasn1						       asn1_get_bit_der(3)

NAME

       asn1_get_bit_der - API function

SYNOPSIS

       #include <libtasn1.h>

       int asn1_get_bit_der(const unsigned char * der, int der_len, int * ret_len, unsigned char * str, int str_size, int * bit_len);

ARGUMENTS

       const unsigned char * der
		   DER data to decode containing the BIT SEQUENCE.

       int der_len Length of DER data to decode.

       int * ret_len
		   Output variable containing the length of the DER data.

       unsigned char * str
		   Pre-allocated output buffer to put decoded BIT SEQUENCE in.

       int str_size
		   Length of pre-allocated output buffer.

       int * bit_len
		   Output variable containing the size of the BIT SEQUENCE.

DESCRIPTION

       Extract a BIT SEQUENCE from DER data.

RETURN VALUE

       Return ASN1_SUCCESS on success, or an error.

COPYRIGHT

       Copyright (C) 2006, 2007, 2008, 2009 Free Software Foundation, Inc..
       Copying	and  distribution  of  this file, with or without modification, are permitted in any medium without royalty provided the copyright
       notice and this notice are preserved.

SEE ALSO

       The full documentation for libtasn1 is maintained as a Texinfo manual.  If the info and libtasn1 programs are properly  installed  at  your
       site, the command

	      info libtasn1

       should give you access to the complete manual.

libtasn1								2.2						       asn1_get_bit_der(3)
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