Sponsored Content
Full Discussion: Recode alphabet into numbers
Top Forums Shell Programming and Scripting Recode alphabet into numbers Post 302684313 by alister on Thursday 9th of August 2012 11:51:41 AM
Old 08-09-2012
If there are N rows in genotype.bim, there are 2N+2 columns in each row of genotype.ped?

Also, how large are these files? If they are humongous, it would help to know in advance, lest time is wasted on an unsuitable approach. If the files are very large, it would help to know something about the hardware (available ram, free storage, etc).

Regards,
Alister
 

9 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

What can i do to check that the input is all alphabet.. ?

What can i do to check that the input is all alphabet.. ? (4 Replies)
Discussion started by: XXXXXXXXXX
4 Replies

2. Shell Programming and Scripting

To check if the first character is a alphabet or number

Hi, I need to find whether the first character in a line is a alphabet or a number. If its a number i should sort it numerically. If its a alphabet i should sort it based on the ASCII value.And if it is something other than alphabet or number then sort it based on ASCII value. The code i used... (2 Replies)
Discussion started by: ragavhere
2 Replies

3. SuSE

need help with recode command for CR/LF

Not sure if this is a Linux issue or specific to SuSE Linux, but, in the infinite wisdom of the developers they decided to do away with the dos2unix and unix2dos commands which were very handy in handling the CR/LF issue between unix and dos/windows files. More to the point I've created a tr... (1 Reply)
Discussion started by: 2reperry
1 Replies

4. Shell Programming and Scripting

Writing an algorithm to recode data points

I have a file that has been partially recoded so that data points that were formerly letter combinations are now -1, 0, or 1. I need to finish recoding the GG and CC data points. The file looks like this: ID 1 2 3 4 5 6 7 8 83845676 0 0 0 0 CC -1 CC CC 838469. -1 -1 1 GG CC 0 CC 1 83847041... (10 Replies)
Discussion started by: doobedoo
10 Replies

5. Shell Programming and Scripting

Recode A/T/G/C to 0/1 using a reference column

Hello, I have a large file that contains 114 total columns with over 6,000 rows and a header; the final 27 columns are coded in A/T/G/C. There is also a reference column coded A/T/C/G. e.g. OLD_file col1 col2 3 ref ... 27 28 29 30 ... 1 r 22 A ... G A G A ... 2 f 22 C ... T T C T ...... (2 Replies)
Discussion started by: peanuts48
2 Replies

6. Shell Programming and Scripting

Alphabet counting

I have a text file in the following format CCCCCGCCCCCCCCCCcCCCCCCCCCCCCCCC AAAATAAAAAAAAAAAaAAAAAAAAAAAAAAA TGTTTTTTTTTTTTGGtTTTTTTTTTTTTTTT TTTT-TTTTTTTTTCTtTTTTTTTTTTTTTTT Each row/line will have 32 letters and each line will only have multiple occurrences of 2 letters out of a pool... (1 Reply)
Discussion started by: Lucky Ali
1 Replies

7. Shell Programming and Scripting

last character is digit or alphabet!

Hello, I have to find out whether the last character is digit or alphabet. I manage to strip the last character but would need some help if there is one liner available to test the above. set x = WM echo $x | sed 's/.*\(.$\)/\1/' O/P M I would like a one liner code to test whether the... (1 Reply)
Discussion started by: dixits
1 Replies

8. Shell Programming and Scripting

Conditional for every letter in alphabet

I wanted to know if there was a more efficient to do this. I was to setup a conditional for every letter of the alphabet, like so (I am parsing an array): for i in "${arr}"; do if ]; then echo "$i starts with A" else echo "$i does not start with A" fi done I want to do this A-Z, is there... (6 Replies)
Discussion started by: sudo
6 Replies

9. UNIX for Beginners Questions & Answers

Shell Script - Alphabet in code

Hi e Hi everyone, I can't make this script work, #! /bin/bash declare -A crypt=( ="A" ="a" ="B" ="b" ="C" ="c" =' ' ='!' ) encode () { local word=$1 for ((i=0; i<${#word}; ++i)) ; do local char=${word:$i:1} printf %s' ' ${crypt} done ... (5 Replies)
Discussion started by: Pinguino
5 Replies
funtablerowget(3)						SAORD Documentation						 funtablerowget(3)

NAME
FunTableRowGet - get Funtools rows SYNOPSIS
#include <funtools.h> void *FunTableRowGet(Fun fun, void *rows, int maxrow, char *plist, int *nrow) DESCRIPTION
The FunTableRowGet() routine retrieves rows from a Funtools binary table or raw event file, and places the values of columns selected by FunColumnSelect() into an array of user structs. Selected column values are automatically converted to the specified user data type (and to native data format) as necessary. The first argument is the Fun handle associated with this row data. The second rows argument is the array of user structs into which the selected columns will be stored. If NULL is passed, the routine will automatically allocate space for this array. (This includes proper allocation of pointers within each struct, if the "@" pointer type is used in the selection of columns. Note that if you pass NULL in the second argument, you should free this space using the standard free() system call when you are finished with the array of rows.) The third maxrow argument specifies the maximum number of rows to be returned. Thus, if rows is allocated by the user, it should be at least of size maxrow*sizeof(evstruct). The fourth plist argument is a param list string. Currently, the keyword/value pair "mask=transparent" is supported in the plist argument. If this string is passed in the call's plist argument, then all rows are passed back to the user (instead of just rows passing the filter). This is only useful when FunColumnSelect() also is used to specify "$region" as a column to return for each row. In such a case, rows found within a region have a returned region value greater than 0 (corresponding to the region id of the region in which they are located), rows passing the filter but not in a region have region value of -1, and rows not passing any filter have region value of 0. Thus, using "mask=transparent" and the returned region value, a program can process all rows and decide on an action based on whether a given row passed the filter or not. The final argument is a pointer to an int variable that will return the actual number of rows returned. The routine returns a pointer to the array of stored rows, or NULL if there was an error. (This pointer will be the same as the second argument, if the latter is non-NULL). /* get rows -- let routine allocate the row array */ while( (buf = (Ev)FunTableRowGet(fun, NULL, MAXROW, NULL, &got)) ){ /* process all rows */ for(i=0; i<got; i++){ /* point to the i'th row */ ev = buf+i; /* rearrange some values. etc. */ ev->energy = (ev->pi+ev->pha)/2.0; ev->pha = -ev->pha; ev->pi = -ev->pi; } /* write out this batch of rows */ FunTableRowPut(fun2, buf, got, 0, NULL); /* free row data */ if( buf ) free(buf); } As shown above, successive calls to FunTableRowGet() will return the next set of rows from the input file until all rows have been read, i.e., the routine behaves like sequential Unix I/O calls such as fread(). See evmerge example code for a more complete example. Note that FunTableRowGet() also can be called as FunEventsGet(), for backward compatibility. SEE ALSO
See funtools(7) for a list of Funtools help pages version 1.4.2 January 2, 2008 funtablerowget(3)
All times are GMT -4. The time now is 03:11 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy