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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 DEBIAN

fastx_clipper

FASTX_CLIPPER(1)						   User Commands						  FASTX_CLIPPER(1)

NAME

       fastx_clipper - FASTA/Q Clipper

DESCRIPTION

       usage:  fastx_clipper  [-h]  [-a  ADAPTER]  [-D] [-l N] [-n] [-d N] [-c] [-C] [-o] [-v] [-z] [-i INFILE] [-o OUTFILE] Part of FASTX Toolkit
       0.0.13.2 by A. Gordon (gordon@cshl.edu)

       [-h]   = This helpful help screen.

	      [-a ADAPTER] = ADAPTER string. default is CCTTAAGG (dummy adapter).  [-l N]	= discard sequences shorter  than  N  nucleotides.
	      default is 5.  [-d N]	  = Keep the adapter and N bases after it.

	      (using '-d 0' is the same as not using '-d' at all. which is the default).

       [-c]   = Discard non-clipped sequences (i.e. - keep only sequences which contained the adapter).

       [-C]   = Discard clipped sequences (i.e. - keep only sequences which did not contained the adapter).

       [-k]   = Report Adapter-Only sequences.

       [-n]   = keep sequences with unknown (N) nucleotides. default is to discard such sequences.

       [-v]   = Verbose - report number of sequences.

       If [-o] is specified,
	      report will be printed to STDOUT.

	      If [-o] is not specified (and output goes to STDOUT), report will be printed to STDERR.

       [-z]   = Compress output with GZIP.

       [-D]   = DEBUG output.

       [-M N] = require minimum adapter alignment length of N.

       If less than N nucleotides aligned with the adapter - don't clip it.
	      [-i INFILE]  = FASTA/Q input file. default is STDIN.

	      [-o OUTFILE] = FASTA/Q output file. default is STDOUT.

SEE ALSO

       The quality of this automatically generated manpage might be insufficient.  It is suggested to visit

	      http://hannonlab.cshl.edu/fastx_toolkit/commandline.html

       to get a better layout as well as an overview about connected FASTX tools.

fastx_clipper 0.0.13.2						     May 2012							  FASTX_CLIPPER(1)
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