Maybe because FS is set to '\t' and there appear to be no TABs in your second sample file, so the fields will not match. And you are setting the index to the entire record, save the first character. which is probably not what you want (you probably meant to use $1 here, but that would not be a sure way to do it either, because in the FASTA format the identifier is allowed to contain spaces). And the FASTA file is word wrapped, so you need to take out the newlines and not use getline to get only the second line ....
The best way to do that is is to use ">" as a record separator and use "\n" as the field separator. By setting OFS as the empty string, and assigning a value to one of the fields, all newlines will be replaced by empty strings, so this will effectively remove the word wrap. And the sequence will become one continuous string, which will make it suitable for substring selection.
Using your file order, we would get something like this.
If we read the files the other way around, then it becomes more memory efficient:
Last edited by Scrutinizer; 08-05-2015 at 04:52 AM..
I have this tar file which has files of (.ksh, .ini &.sql) and their hard and soft links.
Later when the original files and their directories are deleted (or rather lost as in a system crash), I have this tar file as the only source to restore all of them.
In such a case when I do,
tar... (4 Replies)
Hi all,
I have a data file from which i would like to extract only certain fields, which are not adjacent to each other. Following is the format of data file (data.txt) that i have, which has about 6 fields delimited by "|"
HARRIS|23|IT|PROGRAMMER|CHICAGO|EMP
JOHN|35|IT|JAVA|NY|CON... (2 Replies)
I need to extract the character before the last "|" in the following lines, which are 'N' and 'U'. The last "|" shouldn't be extracted. Also the no.s of "|" may vary in a line, but I need only the character before the last one.
... (5 Replies)
Hello,
I need your help to extract text from following:
./sherg_fyd_rur:blkabl="R23.21_BL2008_0122_1"
./serge_a75:rlwual="/main/r23.21=26-Mar-2008.05:00:20UTC@R11.31_BL2008_0325"
./serge_a75:blkabl="R23.21_BL2008_0325"
./sherg_proto_npiv:bkguals="R23.21_BL2008_0302 I80_11.31_LR"
I... (11 Replies)
Hi,
Can you help me on this two problems?
how can i get :
from input: /ect/exp/hom/bin ==> output: exp
and
from input: aex1234 =====>output: ex
thanks, (1 Reply)
Hi everyone,
I have a large text file containing DNA sequences in fasta format as follows:
>someseq
GAACTTGAGATCCGGGGAGCAGTGGATCTC
CACCAGCGGCCAGAACTGGTGCACCTCCAG
GCCAGCCTCGTCCTGCGTGTC
>another seq
GGCATTTTTGTGTAATTTTTGGCTGGATGAGGT
GACATTTTCATTACTACCATTTTGGAGTACA
>seq3450... (4 Replies)
Hi all,
I have a file like this
ID 3BP5L_HUMAN Reviewed; 393 AA.
AC Q7L8J4; Q96FI5; Q9BQH8; Q9C0E3;
DT 05-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 05-SEP-2012, entry version 71.
FT COILED 59 140 ... (1 Reply)
I am trying to extract a time from the below string in perl but not able to get the time properly
I just want to extract the time from the above line I am using the below syntax
x=~ /(.*) (\d+)\:(\d+)\:(\d+),(.*)\.com/
$time = $2 . ':' . $3 . ':' . $4;
print $time
Can... (1 Reply)
Hello, here I am posting my query again with modified data input files.
see my query is :
i have two input files file1 and file2.
file1 is smalldata.fasta
>gi|546671471|gb|AWWX01449637.1| Bubalus bubalis breed Mediterranean WGS:AWWX01:contig449636, whole genome shotgun sequence... (20 Replies)
Discussion started by: harpreetmanku04
20 Replies
LEARN ABOUT FREEBSD
join
JOIN(1) BSD General Commands Manual JOIN(1)NAME
join -- relational database operator
SYNOPSIS
join [-a file_number | -v file_number] [-e string] [-o list] [-t char] [-1 field] [-2 field] file1 file2
DESCRIPTION
The join utility performs an ``equality join'' on the specified files and writes the result to the standard output. The ``join field'' is
the field in each file by which the files are compared. The first field in each line is used by default. There is one line in the output
for each pair of lines in file1 and file2 which have identical join fields. Each output line consists of the join field, the remaining
fields from file1 and then the remaining fields from file2.
The default field separators are tab and space characters. In this case, multiple tabs and spaces count as a single field separator, and
leading tabs and spaces are ignored. The default output field separator is a single space character.
Many of the options use file and field numbers. Both file numbers and field numbers are 1 based, i.e., the first file on the command line is
file number 1 and the first field is field number 1. The following options are available:
-a file_number
In addition to the default output, produce a line for each unpairable line in file file_number.
-e string
Replace empty output fields with string.
-o list
The -o option specifies the fields that will be output from each file for each line with matching join fields. Each element of list
has either the form file_number.field, where file_number is a file number and field is a field number, or the form '0' (zero), repre-
senting the join field. The elements of list must be either comma (',') or whitespace separated. (The latter requires quoting to
protect it from the shell, or, a simpler approach is to use multiple -o options.)
-t char
Use character char as a field delimiter for both input and output. Every occurrence of char in a line is significant.
-v file_number
Do not display the default output, but display a line for each unpairable line in file file_number. The options -v 1 and -v 2 may be
specified at the same time.
-1 field
Join on the field'th field of file1.
-2 field
Join on the field'th field of file2.
When the default field delimiter characters are used, the files to be joined should be ordered in the collating sequence of sort(1), using
the -b option, on the fields on which they are to be joined, otherwise join may not report all field matches. When the field delimiter char-
acters are specified by the -t option, the collating sequence should be the same as sort(1) without the -b option.
If one of the arguments file1 or file2 is '-', the standard input is used.
EXIT STATUS
The join utility exits 0 on success, and >0 if an error occurs.
COMPATIBILITY
For compatibility with historic versions of join, the following options are available:
-a In addition to the default output, produce a line for each unpairable line in both file1 and file2.
-j1 field
Join on the field'th field of file1.
-j2 field
Join on the field'th field of file2.
-j field
Join on the field'th field of both file1 and file2.
-o list ...
Historical implementations of join permitted multiple arguments to the -o option. These arguments were of the form
file_number.field_number as described for the current -o option. This has obvious difficulties in the presence of files named 1.2.
These options are available only so historic shell scripts do not require modification and should not be used.
SEE ALSO awk(1), comm(1), paste(1), sort(1), uniq(1)STANDARDS
The join command conforms to IEEE Std 1003.1-2001 (``POSIX.1'').
BSD July 5, 2004 BSD