This works like a charm, except that it takes a tab-delimited file and returns a space-delimited file. My fault for not mentioning it in the original post.
Hi :)
I have some problems with "FOR"...
I have a text file in this format:
name1
www.link1/random_number
name2
www.link2/random_number
name3
www.link3/random_number
...
(Names and info changes)
Now, I need: (4 Replies)
Hi this is my first time posting ever. I'm relatively new in using AWK/SED, I've been trying many a solution. I'm trying to replace the 59th column in a file where if I encounter '' then I would like to replace it with the word NULL.
example
0 , '' , '' , 0 , 195.538462
change it to
0... (5 Replies)
hi,
i have file say email.temp looks like
Bell_BB 17
Bell_MONTHLY 888
SOLO_UNBEATABLE 721
and another file r3
Bell BB,Bell_BB
Bell,Bell_MONTHLY
SOLO,SOLO_UNBEATABLE
i want email.temp files $1 say Bell_BB should be replaced by r3 Bell BB and Bell_MONTHLY by... (2 Replies)
How would I do this? How could i use <> symbols for numbers in the find/replace code below?
perl -pi -e 's/test/tst/'
OR is there a better way?
100 5000 2 432 4 2 33 4 5 6 65 300 301
needs to be:
100 300 2 300 4 2 33 4 5 6 65 300 300
also it might not always need spaces... i... (12 Replies)
Dear board,
(I am trying to post this the 3rd time, seems there's some conflicts with my firefox with this forum, now use IE)
------
yes, I have searched the forum, but seems my ? is too complicated.
------------origianl file ---------------
\storage\qweq\ertert\ertert\3452\&234\test.rec... (4 Replies)
I have looked around and there are several examples of how to use sed, but I don't think any of them help me very much with what I am trying to do.
I have a text file like this....
1! SRCNAM = 00001 !
1! X = 50.0000, 0.0000,... (10 Replies)
Hello all. I am a beginner UNIX user who is using UNIX to work on a bioinformatics project for my university.
I have a bit of a complicated issue in trying to use sed (or awk) to "find and replace" bases (letters) in a genetics data spreadsheet (converted to a text file, can be either... (3 Replies)
All,
I have thousands of lines in a file with following format
DATA=_ONE_XXX_YYY_CCC_HHHG_
DATA1=_GGG_JJJJ_HHH_UUU_JJJJ_HHHH_LLL_
DATA3=_MMM_GG_NN_QQQQ_FFF_III_
I want to replace _ with . by ignoring the first (=_) and last (_)
So that out put should looks like... (4 Replies)
i Have a file as following
view pz19a0c0/1000T_J_3MoDw9DSLh1ZsCubdua-LKOQmbtiVgkIsiMbSiwF467?sessionId=15451401994597121249
view pz19a0c0/100086X67pR0MwzWnhhSO6sAEoxeFMyhh-IIbUCCdxicaQM4FC9?sessionId=154514019945971212494898
view/cart ... (5 Replies)
Discussion started by: Raghuram717
5 Replies
LEARN ABOUT DEBIAN
asnval
ASNVAL(1) NCBI Tools User's Manual ASNVAL(1)NAME
asnval - validate ASN.1 biological sequence records
SYNOPSIS
asnval [-] [-A] [-B] [-C N] [-D] [-E str] [-F] [-G] [-J] [-K] [-L filename] [-M] [-N flags] [-P N] [-Q N] [-R N] [-S N] [-T] [-U] [-X] [-Y]
[-Z] [-a type] [-b] [-c] [-d path] [-e] [-f str] [-i filename] [-k] [-l] [-o filename] [-p path] [-q] [-r] [-u] [-v N] [-x str]
DESCRIPTION
asnval is a command-line tool to validate ASN.1-format biological sequence records.
OPTIONS
A summary of options is included below.
- Print usage message
-A Validate Alignments
-B Validate Barcodes
-C N Max count
-D Disable message suppression
-E str Only Error Code to Show
-F Test network access
-G GI lookup from accession
-J Require ISO-JTA?
-K Summary to error file
-L filename
Log File
-M Match locus_tag against General ID
-N flags
Latitude-longitude / country flags
0 none
1 test state/province
2 ignore water exception
3 both of the above
-P N Highest severity for error to show:
0 none
1 informational
2 warning
3 error (default for -Q)
4 grounds for rejection (default for -P, -R)
-Q N Lowest severity for error to show, per P
-R N Severity for error in return code, per P
-S N Skip count
-T Use Threads
-U Genome center submission
-X Exon splice check
-Y Check against old IDs
-Z Remote CDS product fetch
-a type
Input ASN.1 type:
a Automatic (default)
c Catenated
z Any
e seq-Entry
b Bioseq
s bioseq-Set
m seq-subMit
t baTch bioseq-set
u batch seq-sUbmit
-b Batch file is Binary
-c Batch file is Compressed
-d path
Path to Indexed Binary ASN.1 Data
-e Ignore transcription/translation Exceptions
-x str Substring filter
-i filename
Single input file (standard input by default)
-k Local fetching
-l Lock components in advance
-o filename
Single output file
-p path
Path to ASN.1 Files
-q Taxonomy lookup
-r Remote Fetching from ID
-u Recurse
-v N Verbosity:
1 Standard report (default)
2 Accession / severity / code (space delimited)
3 Accession / severity / code (tab delimited)
4 XML report
5 Accession / GI / severity / code (tab delimited)
-x str File selection substring (.ent by default)
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO asndisc(1), cleanasn(1), sequin(1).
NCBI 2012-06-24 ASNVAL(1)