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Full Discussion: bash script to parse sequence...
Top Forums UNIX for Dummies Questions & Answers bash script to parse sequence... Post 302476661 by Fahmida on Thursday 2nd of December 2010 07:50:00 AM
Old 12-02-2010
bash script to parse sequence...
Hi,

I have 4000 list files and 4000 sequence data files. Each list file contains a number of 'headers' and data file contains 'header and data'. I would like to extract data from the data file using the list file and write into a new file. As each of the files are quite large, an efficient piece of script(preferably bash) will be much appreciated. Example below:

Example list file:
HTML Code:
contig00002 length=653   numreads=34
contig00005 length=636   numreads=21
contig00015 length=662   numreads=51
contig00033 length=584   numreads=24
contig00045 length=539   numreads=19
contig00073 length=454   numreads=67
contig00046 length=660   numreads=27
contig00014 length=746   numreads=18
contig00089 length=298   numreads=19
.....
.....
Example data file:
HTML Code:
>contig00001 length=477   numreads=22
GGGGCTGACGTGGCCGCTAATACGACTCACTATAGGGAGAGTAAGTGAAT
GTCACATCGTTTGGATCAAGACCCATTTGCAGCACAAGCCCTGTTTTGTT
>contig00002 length=530   numreads=27
GGGCTGACGTGGCCGCTAATACGACTCACTATAGGGAGAGGAGGATAGGG
AGCTGAGCAGCCAGTGACAGGATCCAGCTCCAGGGGGTGAATGGGGATGG
>contig00004 length=670   numreads=22
GGGGCTGACGTGGCCGCTAATACGACTCACTATAGGGAGAGATTGTTGAA
GTGGAAAGCCATTTTGACTATTACCGCCCGGTGGCAGAAACCAAACCTGG
.....
....
Example output file:
HTML Code:
>contig00002 length=653   numreads=34
GGGCAGCTGCGGCCGCTAATACGACTCACTATAGGGAGAGGCTTGCTCAA
ATCCGCGTTCAAGGATTTCCAGATTGGTAAGAACTTCAGATTCCTTGACG
>contig00005 length=636   numreads=21
GGGCAGCTGCGGCCGCTAATACGACTCACTATAGGGAGAGATCGTGGCGA
TCGCCAATCACCCAGGTGCCGTTAGCCAGAGCTGGTTTGATGACCGTTTC
>contig00015 length=662   numreads=51
GGGCAGCTGCGGCCGCTAATACGACTCACTATAGGGAGAGAGCTCCAGCA
GAATGGACACGCCTCCTGAGCTGTGATAGGGAGAGCATAAACACGCCTCC
.....
.....
Thanks in advance.
 

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LEARN ABOUT CENTOS

umad_recv

UMAD_RECV(3)						    OpenIB Programmer's Manual						      UMAD_RECV(3)

NAME

       umad_recv - receive umad

SYNOPSIS

       #include <infiniband/umad.h>

       int umad_recv(int portid, void *umad, int *length, int timeout_ms);

DESCRIPTION

       umad_recv() waits up to timeout_ms milliseconds for a packet to be received from the port specified by portid.  The packet is copied to the
       umad buffer if there is sufficient room and the received length is indicated.  If the buffer is not large enough, the size of the umad buf-
       fer  needed  is	returned  in length.  A negative timeout_ms makes the function block until a packet is received. A timeout_ms parameter of
       zero indicates a non blocking read.

       Note length is a pointer to the length of the data portion of the umad buffer.  This means that umad  must  point  to  a  buffer  at  least
       umad_size() + *length bytes long.

       Note also that *length must be >= 256 bytes.

RETURN VALUE

       umad_recv() returns non negative receiving agentid on success, and a negative value on error as follows:
	-EINVAL      invalid port handle or agentid or *length is less than the minimum supported
	-EIO	     receive operation failed
	-EWOULDBLOCK non blocking read can't be fulfilled

SEE ALSO

       umad_poll(3)

AUTHOR

       Hal Rosenstock <halr@voltaire.com>

OpenIB								   May 11, 2007 						      UMAD_RECV(3)
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