And make sure that the output you show us includes the (exact) output you want produced for at least the following file2 input lines:
Note that the 1st line is this file2 is related to one entry from file1, the next 5 lines from this file2 are related to another entry from file1, and the last line from file2 is related to an entry that is not found in file1.
Is the output for the 5 lines related to the string gi|546669842|gb|AWWX01450698.1| supposed to generate 5 sets of output OR is the output for those 5 lines supposed to be combined into 1 set of output duplicating some of the output (due to overlapping ranges) OR is the output for those 5 lines supposed to be combined into 1 set of output containing the non-overlapping regions of thee requested ranges 1423 through 1760, 2384 through 2603, and 2620 through 2844 (where the start and stop points have been extended 100 characters in each direction and the five overlapping input regions in file2 have been combined into a three non-overlapping output regions)?
And, for the last entry in file2, there is no entry in your sample file1. Is anything supposed to appear in the output for this case? If so, what?
And, just for the record, the number of characters specified by the range 282 through 305 is 24 characters; not 23. (If you don't see why that is true, take the simpler example where the range 282 through 282 is 1 character; not 0.)
Last edited by Don Cragun; 08-06-2015 at 06:24 AM..
Reason: Fix typos in counts.
Hi,
I'm working hard on SQL and I came across a hurdle I'm hoping you can help me out with.
I have two tables
table1
headers: chrom start end name score strand
11 9720685 9720721 U0 0 +
21 9721043 9721079 U0 0 -
1 9721093 9721129 U0 0 +
20 ... (2 Replies)
Hi all,
I have difficulty to solve the followign problem.
mydata:
StartPoint EndPoint
22 55
2222 2230
33 66
44 58
222 240
11 25
22 60
33 45
The union of above... (2 Replies)
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, I have a file1 of many long sequences, each preceded by a unique header line. file2 is 3-columns list: headers name, start position, end position. I'd like to extract the sequence region of file1 specified in file2.
Based on a post elsewhere, I found the code:
awk... (2 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)
FILE_ID extraction from file name and save it in CSV file after looping through each folders
My files are located in UNIX Server, i want to extract file_id and file_name from each file .and save it in a CSV file. How do I do that?
I have folders in unix environment, directory structure is... (15 Replies)
Hi I have 2 files; usually the end position in the file1 is the start position in the file2 and the end position in file2 will be the start position in file1 (flanks)
file1
Id start end
aaa1 0 3000070
aaa1 3095270 3095341
aaa1 3100822 3100894
aaa1 ... (1 Reply)
Old skool UNIX and Linux geek here, but newbie to the world of DNS and bind. I've recently been tasked with replacing our DNS infrastructure, currently on Windows, with a RHEL based solution. And I assume that means using bind, which I've not used before. Here's my question:
Suppose our company... (3 Replies)
HI,
I have a Complete genome fasta file and I have list of sub sequence regions
in the format as :
4353..5633
6795..9354
1034..14456
I want a script which can mask these region in a single complete genome fasta file with the alphabet N
kindly help (2 Replies)
i want to extract specific region of interest from big file. i have only start position, end position and seq id, see my query is:
I have file1 is this
>GL3482.1
GAACTTGAGATCCGGGGA
GCAGTGGATCTCCACCAG
CGGCCAGAACTGGTGCAC
CTCCAGGCCAGCCTCGTC
CTGCGTGTC
>GL3550.1... (14 Replies)
Discussion started by: harpreetmanku04
14 Replies
LEARN ABOUT XFREE86
zcmp
ZDIFF(1) General Commands Manual ZDIFF(1)NAME
zcmp, zdiff - compare compressed files
SYNOPSIS
zcmp [ cmp_options ] file1 [ file2 ]
zdiff [ diff_options ] file1 [ file2 ]
DESCRIPTION
Zcmp and zdiff are used to invoke the cmp or the diff program on files compressed via gzip. All options specified are passed directly to
cmp or diff. If only file1 is specified, it is compared to the uncompressed contents of file1.gz. If two files are specified, their con-
tents (uncompressed if necessary) are fed to cmp or diff. The input files are not modified. The exit status from cmp or diff is pre-
served.
SEE ALSO cmp(1), diff(1), zmore(1), zgrep(1), znew(1), zforce(1), gzip(1), gzexe(1)BUGS
Messages from the cmp or diff programs may refer to file names such as "-" instead of to the file names specified.
ZDIFF(1)