04-06-2009
Merge lines in Flat file based on first 5 characters
Hi
I have the fixed width flat file having the following data
12345aaaaaaaaaabbbbbbbbbb
12365sssssssssscccccccccc
12365sssss
12367ddddddddddvvvvvvvvvv
12367 vvvvv
Here the first column is length 5 second is length 10 third is length 10
if the second or third column exceeds length it is repeated in next line with the first column repeated
Now I need the file to be modified in such a way that there is only one row for the data like
12345aaaaaaaaaa bbbbbbbbbb
12365sssssssssssssss cccccccccc
12367dddddddddd vvvvvvvvvvvvvvv
changing the lenght of the second and third column to 20 instead of 10.
I am trying to write this in perl or shell.
Kindly help me..
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LEARN ABOUT DEBIAN
bp_bioflat_index
BP_BIOFLAT_INDEX(1p) User Contributed Perl Documentation BP_BIOFLAT_INDEX(1p)
NAME
bioflat_index.pl - index sequence files using Bio::DB::Flat
DESCRIPTION
Create or update a biological sequence database indexed with the
Bio::DB::Flat indexing scheme. The arguments are a list of flat files
containing the sequence information to be indexed.
USAGE
bioflat_index.pl <options> file1 file2 file3...
Options:
--create Create or reinitialize the index. If not specified,
the index must already exist.
--format <format> The format of the sequence files. Must be one
of "genbank", "swissprot", "embl" or "fasta".
--location <path> Path to the directory in which the index files
are stored.
--dbname <name> The symbolic name of the database to be created.
--indextype <type> Type of index to create. Either "bdb" or "flat".
"binarysearch" is the same as "flat".
Options can be abbreviated. For example, use -i for --indextype.
The following environment variables will be used as defaults if the corresponding options are not provided:
OBDA_FORMAT format of sequence file
OBDA_LOCATION path to directory in which index files are stored
OBDA_DBNAME name of database
OBDA_INDEX type of index to create
perl v5.14.2 2012-03-02 BP_BIOFLAT_INDEX(1p)