Shell Programming and Scripting

Reading sequence file 10.codon
Found 8 sequences of length 3081
Alignment looks like a valid DNA alignment.
Estimated diversity is (pairwise deletion - ignoring missing/ambig):  6.1%
Found 51 informative sites.
Writing alignment of informative sites to: Phi.inf.sites
Writing list of informative sites to:      Phi.inf.list
Calculating all pairwise incompatibilities...
Done:   0.0%^H^H^H^H^H^H100.0%

Distribution of scaled incompatibility scores:
Score (%):
 0   (84.9): ooooooooooooooooooooooooooooooooooooooooooo
 1   (15.1): oooooooo

Using a window size of 100 with k as 2

Calculating analytical mean and variance

Doing permutation test for PHI

Doing permutation test for NSS

The Neighbour Similarity score is 8.0000e-01

Doing Permutation test for MAXCHI

Number of umabiguous polymorphic sites is 678
Writing  alignment of polymorphic unambig sites to: Phi.poly.sites
Window size is 452 polymorphic sites

Best breakpoint for Max Chi found with sequences CtBTz and CtSwe. r and s are 24 and 26
Value of maximum breakpoint is:    19.8

Coordinates of breakpoint with only polymorphic sites (start,breakpoint,end) = (0, 226, 452)
Coordinates of breakpoint with all sites (start,breakpoint,end)=(98, 1260, 2265)

                      PHI Values
                      ----------
              Analytical    (1000) Permutations

Mean:          1.51e-01          1.51e-01
Variance:      7.16e-04          7.21e-04
Observed:      1.11e-01          1.11e-01


     **p-Value(s)**
       ----------

NSS:                 4.16e-01  (1000 permutations)
Max Chi^2:           0.00e+00  (1000 permutations)
PHI (Permutation):   9.50e-02  (1000 permutations)
PHI (Normal):        6.63e-02

Reading sequence file 100.codon
....
.....
.....
.....

     **p-Value(s)**
       ----------

NSS:                 1.00e+00  (1000 permutations)
Max Chi^2:           9.93e-01  (1000 permutations)
PHI (Permutation):   1.00e+00  (1000 permutations)
PHI (Normal):        1.00e+00

Reading sequence file 102.codon
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.....
....
....
....
     **p-Value(s)**
       ----------

NSS:                 1.26e-01  (1000 permutations)
Max Chi^2:           4.38e-01  (1000 permutations)
PHI (Permutation):   3.82e-01  (1000 permutations)
PHI (Normal):        3.82e-01

10 4.16e-01 0.00e+00 9.50e-02 6.63e-02 (tab delimited)
100 1.00e+00  9.93e-01 1.00e+00 1.00e+00
102 1.26e-01 4.38e-01 3.82e-01 3.82e-01

awk '
/^Reading sequence file/ {r1=$4;gsub(/\..*/,"",r1)}
/^NSS:/ {r2=$2} /^Max Chi/ {r3=$3}
/^PHI \(Permutation\)/ {r4=$3}
/^PHI \(Normal\)/ {r5=$3;print r1,r2,r3,r4,r5}' file