Shell Programming and Scripting

# Output of GENE for sequence file 100.fasta
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# Maximum BLAST-like scores:
# Inner      Max         Sim     S.D.s above     S.D. of
#  frags    Score      P-value    sim. mean        sims
# SCORE     4.145      0.6043        -0.01       0.0274
# OuterSeq
#  frags    0.125      1.0000         0.00       0.0000
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#Output of GENE for sequence file 101.fasta
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## Maximum BLAST-like scores:
# Inner      Max         Sim     S.D.s above     S.D. of
#  frags    Score      P-value    sim. mean        sims
# SCORE     2.665      0.8360         0.44       0.0439
# OuterSeq
#  frags  Not found      0.0000         0.00       0.0000
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#Output of GENE for sequence file 103.fasta
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## Maximum BLAST-like scores:
# Inner      Max         Sim     S.D.s above     S.D. of
#  frags    Score      P-value    sim. mean        sims
# SCORE     3.665      0.8705         1.44       0.0039
# OuterSeq
#  frags  Not found      1.0000         2.00       0.0000

100  0.6043
101 0.8360 
103 0.8705

$ ruby -ane 'num=$_.scan(/^.*\b(\d+)\.fasta/)[0] if  /Output/; print "#{num[0]} #{$F[3]}\n" if /SCORE/  ' file
100 0.6043
101 0.8360
103 0.8705

awk -f awk_parser.awk the_file

BEGIN {

        # this_num denotes which sequence file we're currently handling
        # it's used as an index into the associative array caled "pval"
        this_num = 0
}

/Output of GENE/ , /SCORE/ {

        # capture the fasta number
        if( $0 ~ /Output of GENE/ ) {

                where = match( $0, /[0-9]+\.fasta/ )
                fasta_str = substr( $0, where, RLENGTH )

                where = match( fasta_str, /^[0-9]+/ )
                num = substr( fasta_str, where, RLENGTH )

                # print "Located gene sequence file: " num
                this_num = num

        }
        else if( $0 ~ /SCORE/ ) {
                # print "\thandling Sim p-value for SCORE row"
                pval[this_num] = $4
        }
}

END {
        for( seq_file in pval ) {
                print seq_file, pval[seq_file]
        }
}

100 0.6043
101 0.8360
103 0.8705

awk '/fasta$/{split($NF,m,".");printf m[1]}/SCORE/{printf " %s\n",$3}'  file

$ awk '/fasta$/{split($NF,m,".");printf m[1]}/SCORE/{printf " %s\n",$3}'  the_file

100 4.145
101 2.665
103 3.665

awk '/fasta$/{split($NF,m,".");printf m[1]}/SCORE/{printf " %s\n",$4}'  file