ASN2ASN(1) NCBI Tools User's Manual ASN2ASN(1)NAME
asn2asn - convert NCBI data between text and binary ASN.1
SYNOPSIS
asn2asn [-] [-b] [-e] [-i filename] [-l filename] [-o filename] [-s] [-x]
DESCRIPTION
asn2asn converts data in NCBI's ASN.1 format between binary and text subformats, or to isomorphic XML.
OPTIONS
A summary of options is included below.
- Print usage message
-b Input asnfile in binary mode
-e Input is a Seq-entry
-i filename
Read input from filename rather than stdin
-l filename
Log errors to filename
-o filename
Write output to filename rather than stdout
-s Output asnfile in binary mode
-x Output XML instead of ASN.1
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO asn2ff(1), asn2gb(1), asn2xml(1), asndhuff(1)NCBI 2002-08-30 ASN2ASN(1)
Check Out this Related Man Page
ASN2FSA(1) NCBI Tools User's Manual ASN2FSA(1)NAME
asn2fsa - convert biological sequence data from ASN.1 to FASTA
SYNOPSIS
asn2fsa [-] [-A acc] [-D] [-E] [-H] [-L filename] [-T] [-a type] [-b] [-c] [-d path] [-e N] [-f path] [-g] [-h filename] [-i filename] [-k]
[-l] [-m] [-o filename] [-p path] [-q filename] [-r] [-s] [-u] [-v filename] [-x str] [-z]
DESCRIPTION
asn2fsa converts biological sequence data from ASN.1 to FASTA.
OPTIONS
A summary of options is included below.
- Print usage message
-A acc Accession to fetch
-D Use Dash for Gap
-E Extended Seq-ids
-H HTML spans
-L filename
Log file
-T Use Threads
-a type
Input ASN.1 type:
a Automatic (default)
z Any
e Seq-entry
b Bioseq
s Bioseq-set
m Seq-submit
t batch processing (suitable for official releases; autodetects specific type)
-b Bioseq-set is Binary
-c Bioseq-set is Compressed
-d path
Path to ReadDB Database
-e N Line length (70 by default; may range from 10 to 120)
-f path
Path to indexed FASTA data
-g Expand delta gaps into Ns
-h filename
Far component cache output file name
-i filename
Single input file (standard input by default)
-k Local fetching
-l Lock components in advance
-m Master style for near segmented sequences
-o filename
Nucleotide Output file name
-p path
Path to ASN.1 Files
-q filename
Quality score output file name
-r Remote fetching from NCBI
-s Far genomic contig for quality scores
-u Recurse
-v filename
Protein output file name
-x str File selection substring (.ent by default) [String]
-z Print quality score gap as -1
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO asn2all(1), asn2asn(1), asn2ff(1), asn2gb(1), asn2xml(1), asndhuff(1).
NCBI 2011-09-02 ASN2FSA(1)
permission of a filename.sh is -rwxr-xr-x
./filename.sh -> command not found
sh filename.sh -> then success...
why is that so?
i suspect is the -rwxr-xr-x (5 Replies)
Greetings to all,
I would like to read input from a file and make duplications from it with Linux shell.
For e.g.
Input file
-----------
ABC
ABB
ABA
-------------------------------
Output file
------------
ABC
ABC
ABC
ABB
ABB (6 Replies)
I have a script which includes an FTP. The filename is too long for my target area. The filename is HD012_ABCD_EFGH_061004_F_300_40. I need to the filename to be HD012_ABCD_EFGH_061004_F_. Any ideas. (5 Replies)
Hi all,
I have a print control file (dflt) for Oracle which is in binary. As I am going to develope an application in Window environment, I would like to reference the dflt file. But it is in binary format and I cannot access it. Anyone can suggest me how to convert the file into text or... (5 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)
Hi all,
I am trying to write a script that will delete a certain amount of text from the end of a filename.
For example.
Input:
name of file (more text).pdf
Output:
name of file.pdf
So is it possible to write a script the deletes, in this example twelve (12) digits from the end... (6 Replies)
Hi
Suppose I have a variable called filename and it it contains the name of a file. I then would like to append an extension to that filename. The filename currently has no extensions.
How do I do this?
Thanks (11 Replies)
Hi I am using the following to get the filename
ls -lrt filename* | tail -1 | awk {'print$9'}
o/p : filename-20101117
want to extract 20101117 from the filename ..
Pls advise (8 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)
I am trying to parse a file but the filehas binary data inline mixed with text fields.
I tried the binutils strings function , it get the binary data out but put the char following the binary data in a new line .
input file
app_id:1936 pgm_num:0 branch:TBNY ord_num:0500012(–QMK) deal_num:0... (12 Replies)
Kindly help i need to write a code for Decode/Compile the ASN.1 which is found in javascript or C language if any got a final working Code:D (16 Replies)
I have a binary file with all content is text, i want convert this binary to a regular file because i want to parse it.
Thx.
---------- Post updated at 05:01 AM ---------- Previous update was at 04:34 AM ----------
I have found the solution
cat file | tr -d '\0' (8 Replies)