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Full Discussion: Joining files in a complex way
Top Forums Shell Programming and Scripting Joining files in a complex way Post 302403403 by stateperl on Friday 12th of March 2010 10:49:11 AM
Old 03-12-2010
smallchanges
hEY small alteration at defining hashes
Code:
# define hashes - %chartonum, %numtochar and %mainhash
my %chartonum = qw(A/A 1 A/G 2 G/G 3);
my %numtochar = qw(1 A/A 2 A/G 3 G/G);

Change like this
1st set = AA or CC or GG or TT
2nd set=AC, AG, AT, CG, CT, GT etc

2nd set MUST be 2
1stset MUST be 1 OR 3 - if it has T/T and G/G take one as 1 and another as 3
but output should have where (A/A or others ) 1 or 2 or 3 came from
For example

Code:
# define hashes - %chartonum, %numtochar and %mainhash
my %chartonum = qw(A/A 1 T/T 3 G/G 1 C/C 3 A/T 2 A/G 2 A/C 2 T/A 2 T/G 2 T/C 2 G/A 2 G/C 2 C/A 2 C/T 2 C/G 2);

tHIS ONE IS WROKING BUT NOT GIVING WHERE THE VALUES CAME [A/A OR G/G OR OTHERS FROM like this
the second bold is shouldn't be T/T
input1
Code:
"aphab"    "S1"    "S2"    "S3"
"a"    "T/T"    "A/A"    "A/A"
"b"    "A/G"    "A/G"    "A/A"
"c"    "T/T"    "G/G"    "A/A"
"d"    "G/G"    "A/G"    "A/G"
"e"    "A/G"    "G/G"    "A/G"
"f"     "T/T"    "G/G"    "A/G"
"g"    "T/T"    "G/G"    "G/G"
"h"    "T/T"    "G/G"    "G/G"
"I"     "T/T"    "G/G"    "G/G"

input2

Code:
"ID"    "Label"    "log"
"S1"    "xxx"    2.8
"S1"    "xxx"    3
"S1"    "xxx"    4
"S2"    "yyy"    6.8
"S2"    "yyy"    7
"S2"    "yyy"    7.4
"S2"    "yyy"    8
"S3"    "zzz"    12
"S3"    "zzz"    14
"S3"    "zzz"    16
"S3"    "zzz"    18
"S3"    "zzz"    20

Code:
$ perl combine.pl
"ID"        "Label"     "StYPE"     "Ntype"     "Stype_No"  "log"
"S1"        "xxx"       "T/T"       1           6           2.8
"S1"        "xxx"       "A/G"       2           2           3
"S1"        "xxx"       "G/G"       3           1           4
"S2"        "yyy"       "A/A"       1           1           6.8
"S2"        "yyy"       "A/G"       2           2           7
"S2"        "yyy"       "G/G"       3           6           7.4
"S2"        "yyy"       "NULL"      "null"      "null"      8
"S3"        "zzz"       "A/A"       1           3           12
"S3"        "zzz"       "A/G"       2           3           14
"S3"        "zzz"       "G/G"       3           3           16
"S3"        "zzz"       "NULL"      "null"      "null"      18
"S3"        "zzz"       "NULL"      "null"      "null"      20

 

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