is ensuring, or is supposed to, match $4 in file1 with the array split from file2. So using the first value RPS19 as an example, only those lines in file2 with RPS19 are used. Thank you .
Hi Guru's,
I am trying to grep a range of line numbers (based on match) and then look for another match which starts with a special character '$' and print the line number. I have the below code but it is actually printing the line number counting starting from the first line of the range i am... (15 Replies)
In the files attached, I am trying to:
if Files.txt $1 is in the range of Exons.txt $1, then in Files.txt $4 the value from Exons.txt $3 is copied else if no match is found Exons.txt $3 = "Intron"
For example, the first value in File.txt $1 is chr1:14895-14944 and is not found in any range... (4 Replies)
Hi All,
Seeking for your assistance to print all the specific field when the condition met.
Ex:
file1.txt
1|203|3|31243|5341|6452|623|22|00|01
3|45345|123214|6534|3423|6565|643|343|232|10
if field 1 = 1 and field 3 = 3 and field 5 = 5341 and field 6 = 6452
it will print from $1 to $10.... (2 Replies)
I am trying to use awk to print the unique entries in $2
So in the example below there are 3 lines but 2 of the lines match in $2 so only one is used in the output.
File.txt
chr17:29667512-29667673 NF1:exon.1;NF1:exon.2;NF1:exon.38;NF1:exon.4;NF1:exon.46;NF1:exon.47 703.807... (5 Replies)
Trying to print the unique values in $2 before the -, currently the count is displayed. Hopefully, the below is close. Thank you :).
file
chr2:46603668-46603902 EPAS1-902|gc=54.3 253.1
chr2:211471445-211471675 CPS1-1205|gc=48.3 264.7
chr19:15291762-15291983 NOTCH3-1003|gc=68.8 195.8... (3 Replies)
In file1 field $18 is removed.... column header is "Otherinfo", then each line in file1 is used to search file2 for a match. When a match is found the last four strings in file2 are copied to file1.
Maybe:
cut -f1-17 file1 and then match each line to file2
file1
Chr Start End ... (6 Replies)
I am trying to use awk to find all the $2 values in file2 which is ~30MB and tab-delimited, that are between $2 and $3 in file1 which is ~2GB and tab-delimited.
I have just found out that I need to use $1 and $2 and $3 from file1 and $1 and $2of file2 must match $1 of file1 and be in the range... (6 Replies)
I have a file.txt containing the following:
Query= HWI-ST863:386:C5Y8UACXX:3:2302:16454:89688 1:N:0:ACACGAAT
Length=100
Score E
Sequences producing significant alignments: (Bits) Value
... (2 Replies)
In the awk below I am trying to print the entire line, along with the header row, if $2 is SNV or MNV or INDEL. If that condition is met or is true, and $3 is less than or equal to 0.05, then in $7 the sub pattern :GMAF= is found and the value after the = sign is checked. If that value is less than... (0 Replies)
Discussion started by: cmccabe
0 Replies
LEARN ABOUT DEBIAN
plan9-join
JOIN(1) General Commands Manual JOIN(1)NAME
join - relational database operator
SYNOPSIS
join [ options ] file1 file2
DESCRIPTION
Join forms, on the standard output, a join of the two relations specified by the lines of file1 and file2. If one of the file names is the
standard input is used.
File1 and file2 must be sorted in increasing ASCII collating sequence on the fields on which they are to be joined, normally the first in
each line.
There is one line in the output for each pair of lines in file1 and file2 that have identical join fields. The output line normally con-
sists of the common field, then the rest of the line from file1, then the rest of the line from file2.
Input fields are normally separated spaces or tabs; output fields by space. In this case, multiple separators count as one, and leading
separators are discarded.
The following options are recognized, with POSIX syntax.
-a n In addition to the normal output, produce a line for each unpairable line in file n, where n is 1 or 2.
-v n Like -a, omitting output for paired lines.
-e s Replace empty output fields by string s.
-1 m
-2 m Join on the mth field of file1 or file2.
-jn m Archaic equivalent for -n m.
-ofields
Each output line comprises the designated fields. The comma-separated field designators are either 0, meaning the join field, or
have the form n.m, where n is a file number and m is a field number. Archaic usage allows separate arguments for field designators.
-tc Use character c as the only separator (tab character) on input and output. Every appearance of c in a line is significant.
EXAMPLES
sort /etc/passwd | join -t: -1 1 -a 1 -e "" - bdays
Add birthdays to the /etc/passwd file, leaving unknown birthdays empty. The layout of /adm/users is given in passwd(5); bdays con-
tains sorted lines like
tr : ' ' </etc/passwd | sort -k 3 3 >temp
join -1 3 -2 3 -o 1.1,2.1 temp temp | awk '$1 < $2'
Print all pairs of users with identical userids.
SOURCE
/src/cmd/join.c
SEE ALSO sort(1), comm(1), awk(1)BUGS
With default field separation, the collating sequence is that of sort -b -ky,y; with -t, the sequence is that of sort -tx -ky,y.
One of the files must be randomly accessible.
JOIN(1)