ASN2XML(1) NCBI Tools User's Manual ASN2XML(1)NAME
asn2xml - translate biological data from ASN.1 to XML
SYNOPSIS
asn2xml [-] [-b F] [-e] [-i filename] [-l filename] [-o filename] [-s]
DESCRIPTION
asn2xml converts an NCBI Seq-entry or Bioseq-set from ASN.1 format to an isomorphic XML representation. It differs from asn2asn -x in that
it converts packed sequence data back into human-readable ASCII text.
OPTIONS
A summary of options is included below.
- Print usage message
-b F Input asnfile in text mode
-e Input is a Seq-entry
-i filename
Read ASN.1 from filename (default is stdin)
-l filename
Log errors to filename (default is stderr)
-o filename
Write XML to filename (default is stdout)
-s Input is a Seq-submit
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO asn2all(1), asn2asn(1), asn2ff(1), asn2fsa(1), asn2gb(1), asndhuff(1), gene2xml(1), /usr/share/doc/ncbi-tools-bin/README.asn2xml,
/usr/share/doc/libncbi6/ncbixml.txt.gz
NCBI 2005-05-16 ASN2XML(1)
:confused:
Bad if test:
if
returns an error
I have changed filename to
"filename"s su
"$filename"
'filename''
'$filename''
"./filename"
"./$filename"
error is usually
why cant I test the filename?
Thanks (4 Replies)
Hi,
I have a requirement that i need to store only the filename without its extension. Can anyone please help me to do this.
For Example, i have stored the filename in a varialble called fname. I need to extract all the charecters before the first occurence of the dot.
If fname has value... (3 Replies)
I have the following output which I need to obtain the values for "Next Seq is xxx" and "Last Seq is xxx" and "Pending count is xxx". You will notice that the number of words prior to that value can be variable hence the reason for asking this question.
LINECMD> Line /xxx///ABC9_SND is UP.... (3 Replies)
Hi All,
I'm trying to run a simple shell program to change all the files named *.cvs to *.txt. I am trying to use WHILE and this is what I have so far:
This changes the first file from *.cvs to *.txt, but it is not cycling through the other files.
My suspicion is that I don't have the... (5 Replies)
If I have a filename as
filename.txt.20090807
and I use
for FILE in `find . -name "filename*" -type f`
do
my_time=${FILE#./filename.txt.}
I get my output as 20090807
However if my filename is
filename.Y20090807.txt
Is there a way I can use metacharacters in my... (3 Replies)
Hi all,
Can any one explain me what the below 'if' statement checking for?
if ; then
do something
fi
Iam aware of the remaining options like -z, -r, -w, -x etc., with 'if' statement, but I dont know about '-s' :confused:.
Thanks in advance,
Mysore 101 Ganapati. (4 Replies)
I don't really know much about UNIX commands, so if someone could help me understand how to do this, I'd really appreciate it.
I have a text file with data that looks like this (filename: numbers.txt):
1 1 1 1 1 1 1 1 1 2 1 1_2 2_1
1 1 1 1 1 1 1 1 2 1 2 1_2 2_1
1 1 1 1 1 1 1 1 2 1 2 1_2 2_1... (12 Replies)
Hi,
I've got a large to task to do, which I've broken into three section. I'm just stuck on one of the sections.
I have to change the end of a filename from .txt to .doc in a directory. So if I have a directory called "folder1" and two files contained in it called "file1.txt" and "file2.txt",... (7 Replies)
Well I have read several threads on the subject ... but being a newbie like me makes it hard to understand ...
What I need is the following:
Input data:
------- snip ---------
<FavouriteLocations> <FavouriteLocations class="FavouriteList"><Item... (6 Replies)
Is there an easy way to strip off a filename's extension?
For example, here's a filename:
blahblahblah.thisisok.thisisnotok
I want to get rid of .thisisnotok from the filename, so that what's left is
blahblahblah.thisisok
Thanks. I have a directory full of filenames that need to be... (5 Replies)
Hello Friends,
I know you all are busy and inteligent too...
I am stuck with one small issue if you can help me then it will be really great.
My problem is I am having some files i.e.
Input.txt1
Input.txt2
Input.txt3
Now my task is I need to check the total number of rows in... (4 Replies)