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comparison .bash_extras @ 1:fef95c7a391f

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author Henry S. Thompson <ht@inf.ed.ac.uk>
date Sat, 28 Feb 2026 15:51:58 +0000
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children 6c772ae7fce2
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0:a6c7f23cca94 1:fef95c7a391f
1 # Sourced by .bashrc and singularity runscript
2
3 cu ()
4 {
5 cvs update "$@" | egrep -v '^\?'
6 }
7
8 lss ()
9 {
10 ls -F --color=auto -lS "$@" | {
11 read one;
12 if [ -n "$one" -a "${one::5}" \!= "total" ]; then
13 echo "$one";
14 fi;
15 cat
16 }
17 }
18
19 ff ()
20 {
21 pat=$1;
22 shift;
23 find . -iname "*$pat*" $@
24 }
25
26 typecat ()
27 {
28 tt=$(type $1);
29 case $tt in
30 *\ is\ hashed\ *)
31 cat $(echo $tt | cut -f 4 -d ' ' | tr -d '()')
32 ;;
33 *\ is\ /*)
34 cat $(echo $tt | cut -f 3 -d ' ' | tr -d '()')
35 ;;
36 *)
37 type $1
38 ;;
39 esac
40 }
41
42 sus ()
43 {
44 sort "$@" | uniq -c | sort -k1nr,1
45 }
46
47 uz ()
48 {
49 igzip -dc "$@"
50 }
51
52 function tot ()
53 {
54 awk '{sum+=$1} END {printf "%u\n",sum}'
55 }
56
57 btot ()
58 {
59 python3 -c 'import sys
60 multiCol = dostats = sample = False
61 c = ""
62 p = 0
63 q = None
64 d = 2
65 ssq = 0
66 while len(sys.argv)>1:
67 if multiCol and sys.argv[1][0]!="-":
68 p=1
69 q=int(sys.argv.pop(1))
70 elif sys.argv[1]=="-c":
71 # add commas
72 c = ","
73 sys.argv.pop(1)
74 elif sys.argv[1]=="-a":
75 # do sum etc. for all columns [p]:q
76 multiCol = True
77 sys.argv.pop(1)
78 try:
79 q = int(sys.argv.pop(1))
80 except IndexError:
81 print("you must supply an N for multi-column")
82 exit(1)
83 elif sys.argv[1]=="-s":
84 # include mean and sample stdev
85 dostats = True
86 sample = True
87 sys.argv.pop(1)
88 elif sys.argv[1]=="-p":
89 # include mean and population stdev
90 dostats = True
91 sys.argv.pop(1)
92 elif sys.argv[1]=="-d":
93 sys.argv.pop(1)
94 d=int(sys.argv.pop(1))
95 else:
96 break
97 n=0
98 if multiCol:
99 w=q-p
100 import numpy as np
101 s=np.array([0]*w)
102 n=np.array([0]*w)
103 if dostats:
104 ssq=np.array([0]*w)
105 else:
106 s=0
107 if dostats:
108 ssq=0
109 import math
110 for l in sys.stdin: # ["1 11\n","2 22\n"]:
111 try:
112 if multiCol:
113 ll=l.split()[p:q]
114 ii=np.array([(0 if i.startswith("NaN") else int(i)) for i in ll])
115 s+=ii
116 ssq+=ii*ii
117 n+=np.array([(0 if i.startswith("NaN") else 1) for i in ll])
118 else:
119 if l[0]!="N":
120 i=int(l)
121 s+=i
122 if dostats:
123 ssq+=(i*i)
124 n+=1
125 except (NameError,ValueError) as e:
126 print(l,e,file=sys.stderr)
127 if dostats:
128 if multiCol:
129 m=s/n
130 var=(ssq/n)-pow(m,2)
131 if sample:
132 var=(n/(n-1))*var
133 sd=pow(var,0.5)
134 else:
135 m=float(s)/float(n)
136 var=(float(ssq)/float(n))-pow(float(m),2)
137 if sample:
138 var=(float(n)/float(n-1))*var
139 sd=math.sqrt(var)
140 if dostats:
141 if multiCol:
142 print("\t".join(f"{i:{c}.{d}f}" for i in s))
143 print("\t".join(f"{i:{c}.{d}f}" for i in m))
144 print("\t".join(f"{i:{c}.{d}f}" for i in sd))
145 else:
146 print(f"{s:}\t{m:}\t{sd:}")
147 else:
148 if multiCol:
149 print("\t".join(f"{i:}" for i in s))
150 else:
151 print(f"{s:}")
152
153 ' "$@"
154 }
155
156 headtail ()
157 {
158 case "$1" in -*)
159 n="$1"
160 shift
161 ;;
162 *) n="-10"
163 ;;
164 esac
165 cat "$@" | { sed -u ${n:1}q ; echo === ; tail $n ; }
166 }
167
168 export -f cu lss ff typecat sus uz tot btot headtail