Extract sequences from a FASTA file based on another file Post: 302881703

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Top Forums Shell Programming and Scripting Extract sequences from a FASTA file based on another file Post 302881703 by kurumi on Tuesday 31st of December 2013 10:31:58 AM

12-31-2013

Registered User

if you have Ruby

Code:

f2 = File.open("file2").readlines.map(&:strip)      # read file2 , store in array
File.open("file1").read.split(">").each do |record|  
  if not record.eql?("") and 
    f2.include?( record[0..3] + record[5] )         # if array contains first 4 chars and the 6th char, print
     puts ">#{record}"   
  end
end

result

Code:

# ruby test.rb
>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 PHP

dbase_add_record

DBASE_ADD_RECORD(3)							 1						       DBASE_ADD_RECORD(3)

dbase_add_record - Adds a record to a database

SYNOPSIS

       bool dbase_add_record (int  $dbase_identifier, array  $record)

DESCRIPTION

	Adds the given data to the database.

PARAMETERS

	      o $dbase_identifier
		- The database link identifier, returned by dbase_open(3) or dbase_create(3).

	      o $record
		-  An  indexed	array  of  data.  The  number  of  items  must	be  equal  to  the  number  of	fields	in the database, otherwise
		dbase_add_record(3) will fail.

	      Note

		      If you're using dbase_get_record(3) return value for this parameter, remember to reset the key named deleted.

RETURN VALUES

	Returns TRUE on success or FALSE on failure.

EXAMPLES

       Example #1

	      Inserting a record in a dBase database

	      <?php

	      // open in read-write mode
	      $db = dbase_open('/tmp/test.dbf', 2);

	      if ($db) {
		dbase_add_record($db, array(
		    date('Ymd'),
		    'Maxim Topolov',
		    '23',
		    'max@example.com',
		    'T'));
		dbase_close($db);
	      }

	      ?>

SEE ALSO

       dbase_delete_record(3), dbase_replace_record(3).

PHP Documentation Group 												       DBASE_ADD_RECORD(3)

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