UNIX for Dummies Questions & Answers

#!/usr/bin/perl
open I, "$ARGV[0]";
local $/;
$_=<I>;
s/^(>.*)\n//;
print "$1\n";
s/\n//g;
$a=1;
while (/N+|[ACGT]+/g){
  $s=$&;
  $l=length $s;
  @F=split //, $s;
  for $i (@F){
    $h{$i}++
  }
  print "$a-" . ($a+$l-1) . "\t$l\t";
  for $i (keys %h){
    print "$i=$h{$i} ";
  }
  print "\n";
  %h=();
  $a+=$l;
}

# cat text
>S8_SK1.chr01
DDDDDDDDDTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNCAGCATGCAATAAGGTGACATAGATATACCCACACACCACACCCTAACACTAACCCTAATCTAACCCTGGCCAACCTGTTTVVVVVVVVVVVVV
TGTATACTGATTTTACGTACNNNNNNNNNNNNNNRRRRRRRRRRRRRRRRRRRRRRRRRTTTTTTTTTTTTTTTTTTTTTTTTMMMMMIIIIIIIIIIIIAAA
>S8_SK1.chr02
VVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVDDDDDDDDDDDDDDDDDDDDDDDDDDDDDASSSAAAAAACCCCCCCCCCCCCCCAAAAAA
YYYYYYYYYYYYYYYYYYYYYYYZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAADDDDD
ASAOIJRJFFFFFFTTTTTPPPPPAAAAKKKKKKKKKKKKKKKKKKKKKKKKKKKKMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMNAAAAA
>S8_SK1.chr03
WWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDFFFFFFFFFFFFFFF
JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
AAASADEAAAABACNNNNNNNNNNNNNNNNNNNNNXXXXXXXXXXXXXXXXXXXZZZZZZZZZZZZZZZZAWQERERRRR

# ./justdoit text
>S8_SK1.chr01
     1-100       100    D=9 N=71 T=20
   101-214       113    A=28 C=28 G=9 N=19 T=16 V=13
   215-318       103    A=8 C=3 G=3 I=12 M=5 N=14 R=25 T=33
>S8_SK1.chr02
     1-106       106    A=13 C=15 D=29 S=3 V=46
   107-212       105    A=37 D=5 Y=23 Z=40
   213-318       105    A=11 F=6 I=1 J=2 K=28 M=43 N=1 O=1 P=5 R=1 S=1 T=5
>S8_SK1.chr03
      1-88        88    D=36 F=15 W=37
    89-184        95    H=35 J=60
   185-265        80    A=10 B=1 C=1 D=1 E=3 N=21 Q=1 R=5 S=1 W=1 X=19 Z=16

#!/bin/bash
##justdoit

while read -r line
do
 if [ $(echo $line|grep "^>") ] ; then
    firstc=1 ; l=0 ; xgr=()
    firstline="$line" ;  echo "$firstline"
 else
    xgr=()
    ((l++))
    for i in {A..Z}
     do
      count=${#line}
      if [ $(echo $line | grep $i) ]; then
       st=$(echo $line | grep -o $i |wc -l)
       xgr=(${xgr[@]} $i=$st )
      fi
     done
      if [ $l -eq 1 ] ; then
       firstc=1 ; lastc=$count
      else
       (( firstc = $lastc + 1 ))
       (( lastc = $firstc + $count ))
      fi
    gr="${xgr[@]}"
    printf "%10s %3c %5d %3c %s\n" "$firstc-$lastc" " " "$count" "" "$gr"
 fi
done<$1

# cat charlist
0 P ! 1 A Q a q '"' 2 B R b r \# 3 C S c s \$ 4 D T d t % 5 E U e u \& 6 F V f v 'â' G W g w '(' 8 H X h x ')' 9 I Y i y '*' J Z j + \; K \[ k '{' , '<' L '\' l '|' - = M ] m '}' \. '>' N '\^' n \~ '/' '?' O _ o D E L 2 F P Z d n x 3 = G e o y 4 H R f p z 5 I S g q 6 @ J T h r 7 A K U _ i s 8 B L V t 9 C M W a k u D E L 0 \: D N X b l v E O Y c m w

# cat text
>S8_SK1.chr01
QQQQQQ@@@@@@@@zzzzzzz++z][.ZZWW!!!@!@!!#??(|||$$$%%&$&%$#&#$@#&$(&(&((P"{"}{|Z|||\\>>>>><<<<<<<||!@!@!@#!~@~!!@$#.....::::'';;
DDDDDDDDDTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNCAGCATGCAATAAGGTGACATAGATATACCCACACACCACACCCTAACACTAACCCTAATCTAACCCTGGCCAACCTGTTTVVVVVVVVVVVVV
TGTATACTGATTTTACGTACNNNNNNNNNNNNNNRRRRRRRRRRRRRRRRRRRRRRRRRTTTTTTTTTTTTTTTTTTTTTTTTMMMMMIIIIIIIIIIIIAAA
>S8_SK1.chr02
VVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVDDDDDDDDDDDDDDDDDDDDDDDDDDDDDASSSAAAAAACCCCCCCCCCCCCCCAAAAAA
YYYYYYYYYYYYYYYYYYYYYYYZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZZAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAADDDDD
ASAOIJRJFFFFFFTTTTTPPPPPAAAAKKKKKKKKKKKKKKKKKKKKKKKKKKKKMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMNAAAAA
>S8_SK1.chr03
WWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWWDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDFFFFFFFFFFFFFFF
JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
AAASADEAAAABACNNNNNNNNNNNNNNNNNNNNNXXXXXXXXXXXXXXXXXXXZZZZZZZZZZZZZZZZAWQERERRRR

# ./justdoit text
>S8_SK1.chr01
     1-126       126    'P'=1 '!'=12 'Q'=6 '#'=6 '$'=8 '%'=3 '&'=6 'W'=2 '*'=1 'Z'=3 '+'=2 ';'=2 '['=1 ']'=1 '.'=6 'P'=1 'Z'=3 'z'=8 '@'=16 'W'=2 ':'=4
   127-227       100    'D'=9 'T'=20 'N'=71 'D'=9 'T'=20 'D'=9 'D'=9 'N'=71
   228-341       113    'A'=28 'C'=28 'T'=16 'V'=13 'G'=9 'N'=19 'G'=9 'T'=16 'A'=28 'V'=13 'C'=28 'N'=19
   342-445       103    'A'=8 'R'=25 'C'=3 'T'=33 'G'=3 'I'=12 'M'=5 'N'=14 'G'=3 'R'=25 'I'=12 'T'=33 'A'=8 'C'=3 'M'=5 'N'=14
>S8_SK1.chr02
     1-106       106    'A'=13 'C'=15 'S'=3 'D'=29 'V'=46 'D'=29 'S'=3 'A'=13 'V'=46 'C'=15 'D'=29 'D'=29
   107-212       105    'A'=37 'D'=5 'Y'=23 'Z'=40 'D'=5 'Z'=40 'A'=37 'D'=5 'D'=5 'Y'=23
   213-318       105    'P'=5 'A'=11 'R'=1 'S'=1 'T'=5 'F'=6 'I'=1 'J'=2 'K'=28 'M'=43 'N'=1 'O'=1 'F'=6 'P'=5 'R'=1 'I'=1 'S'=1 'J'=2 'T'=5 'A'=11 'K'=28 'M'=43 'N'=1 'O'=1
>S8_SK1.chr03
      1-88        88    'D'=36 'F'=15 'W'=37 'D'=36 'F'=15 'W'=37 'D'=36 'D'=36
    89-184        95    'H'=35 'J'=60 'H'=35 'J'=60
   185-265        80    'A'=10 'Q'=1 'B'=1 'R'=5 'C'=1 'S'=1 'D'=1 'E'=3 'W'=1 'X'=19 'Z'=16 'N'=21 'D'=1 'E'=3 'Z'=16 'R'=5 'S'=1 'A'=10 'B'=1 'C'=1 'W'=1 'D'=1 'E'=3 'D'=1 'N'=21 'X'=19 'E'=3

# cat justdoit
#!/bin/bash
##justdoit
while read -r line
do
 if [ $(echo "$line"|grep "^>") ] ; then
    firstc=1 ; l=0 ; xgr=()
    firstline="$line" ;  echo "$firstline"
 else
    xgr=()
    ((l++))
    for i in `cat charlist`
     do
      count=${#line}
      if [ $(echo "$line" | grep $i) ]; then
       charcount=$(echo "$line" | grep -o "$i" |wc -l)
       val=$(eval echo "$i")
       xgr=(${xgr[@]} "'$val'=$charcount" )
      fi
     done
      if [ $l -eq 1 ] ; then
       firstc=1 ; lastc=$count
      else
       (( firstc = $lastc + 1 ))
       (( lastc = $firstc + $count ))
      fi
    gr="${xgr[@]}"
    printf "%10s %3c %5d %3c %s\n" "$firstc-$lastc" " " "$count" "" "$gr"
 fi
done<$1