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Full Discussion: Checking missing data's sequence (shell script | UNIX command)
Top Forums UNIX for Advanced & Expert Users Checking missing data's sequence (shell script | UNIX command) Post 302731837 by Yoda on Thursday 15th of November 2012 11:34:17 PM
Old 11-16-2012
Code:
#!/bin/bash

find . -type f | sed 's/\.\///g' | sort > file_list.dat

awk ' { print substr($1,1,4) } ' file_list.dat | uniq | while read name
do
        str_seq=$( sort file_list.dat | grep $name | head -1 | cut -c 5-8 )
        end_seq=$( sort file_list.dat | grep $name | tail -1 | cut -c 5-8 )

        if echo $str_seq | egrep -q '^[0-9]'
        then
                for sq in $( seq $str_seq $end_seq )
                do
                        if [ ! -f "${name}${sq}" ]
                        then
                                echo "${name}${sq} missing."
                        fi
                done
        fi
done

This User Gave Thanks to Yoda For This Post:
septian.tri
 

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LEARN ABOUT DEBIAN

unknown

UNKNOWN(1)						      General Commands Manual							UNKNOWN(1)

NAME

       unknown - identify possible genotypes for unknowns

SYNOPSIS

       A program to rapidly identify which genotypes are possible for individuals typed as unknowns in the input pedigree.

       unknown [ -cl ]

DESCRIPTION

       unknown infers possible genotypes and mating combinations for parents with unknown genotypes for ilink(1), mlink(1) and linkmap(1).

OPTIONS

       -c     Use conditional allele frequencies.

       -l     Choose a good set of loop breakers automatically.

RETURN VALUE

       0     Successful completion

ERRORS

       10    File not found
       255   Failure

EXAMPLES

       Normally, unknown(1) is run immediately prior to its sister programs, ilink(1), mlink(1) and linkmap(1), like this:

       unknown
       mlink

FILES

       unknown(1) reads the two files pedfile.dat and datafile.dat as its own input and produces various temporary files that are used as input to
       the next program. These temporary files are ipedfile.dat, upedfile.dat, speedfile.dat and newspeedfile.dat.

NOTES

       unknown(1) is part of the FASTLINK package, which is a re-implementation of the LINKAGE suite  of  computer  tools  that  help  investigate
       genetic linkage as first proposed G.M. Lathrop, J.M. Lalouel, C. Julier, and J. Ott.

AUTHORS

       Dylan Cooper, Alejandro Schaffer, and Tony Schurtz based on work originally by Jurg Ott, Ph.D, et. al.

       This manual page was written by Elizabeth Barham <lizzy@soggytrousers.net> for the Debian GNU/Linux system (but may be used by others).

WORD-WIDE-WEB
       http://www.ncbi.nlm.nih.gov/CBBResearch/Schaffer/fastlink.html

SEE ALSO

       ilink(1), linkmap(1), lodscore(1), mlink(1).

								  April 15, 2003							UNKNOWN(1)
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