Hello,
How can I take a file in XML format and convert it to a comma separated format? Is there any scripts or programs that can
do this for Unix? I tried surfing the net for such an application, but everything seems to be for Windows OS. Any help or suggestions are greatly appreciated.
... (2 Replies)
Hi,
Request To guide me in writing a shell program for the following requirement:
Example:if the Input File contains the follwing data
Input File Data:
80723240029,12,323,443,88,98,7,98,67,87
80723240030,12,56,6,,,3,12,56,6,7,2,3,12,56,6,7,2,3,88,98,7,98,67,87... (5 Replies)
Hi All,
I am new to this forum, could any one help me out in resolving the below issue.
Input of the flat file contains several lines of text for example find below:
5022090,2,4,7154,88,,,,,4/1/2011 0:00,Z,L,2
5022090,3,1,6648,88,,,,,4/1/2011 0:00,Z,,1... (0 Replies)
I have a requirement to read the xml file and split the files into two diffrent files in Unix shell script. Could anyone please help me out with this requirement.
Sample file
---------------
0,<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<Information... (3 Replies)
Hi Friends,
I want to convert a XML file to flat file.
Sample I/p:
<?xml version='1.0' encoding='UTF-8' ?>
<DataFile xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance' contactCount='4999' date='2012-04-14' time='22:00:14' xsi:noNamespaceSchemaLocation='gen
.xsd'>
<Contact... (3 Replies)
dear all,
i need your advice, i have xml file like this
input.xml
<?xml version="1.0" encoding="UTF-8"?>
<session xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance'>
<capture>
<atribut name="tmp_Filename" value="INTest.rbs"/>
<atribut name="size_Filename" value="INTest.rbs"/>... (2 Replies)
Hi All,
I am writing a shell script to extract oracle table into a pipe dilemited flat file. Below is my code and I have attached two files that I have abled to generate so far.
1. Table.txt ==> database extract file
2. flat.txt ==> pipe delimited after some manipulation of the original db... (5 Replies)
Hi All,
I have a csv file which is comma seperated. I need to convert to flat file with preferred column length
country,id
Australia,1234
Africa,12399999
Expected output
country id
Australia 1234
Africa 12399999
the flat file should predefined length on respective... (8 Replies)
Discussion started by: rohit_shinez
8 Replies
LEARN ABOUT DEBIAN
asn2gb
ASN2GB(1) NCBI Tools User's Manual ASN2GB(1)NAME
asn2gb - convert ASN.1 biological data to a GenBank-style flat format
SYNOPSIS
asn2gb [-] [-A accession] [-F] [-a asn-type] [-b] [-c] [-d] [-f format] [-g N] [-h N] [-i filename] [-j N] [-k N] [-l filename] [-m mode]
[-n filename] [-o filename] [-p] [-q filename] [-r] [-s style] [-t N] [-u N] [-y N]
DESCRIPTION
asn2gb converts descriptions of biological sequences from NCBI's ASN.1 format to one of several flat-file formats, and is the successor to
asn2ff(1).
OPTIONS
A summary of options is included below.
- Print usage message
-A accession
Accession to fetch; may take the form accession,complexity,flags where complexity should normally be 0 and a flags value of -1
enables fetching of external features (as with the legacy -F option)
-F Fetch remote annotations (equivalent to specifying -A accession,0,-1)
-a asn-type
ASN.1 Type:
[Single record]
a Any (autodetected; default)
e seq-Entry
b Bioseq
s bioseq-Set
m seq-subMit
q Catenated
[Release file; components individually processed and freed]
t baTch bioseq-set
u batch seq-sUbmit
-b Input file is binary
-c Batch file is compressed
-d Seq-loc minus strand
-f format
Format:
b GenBank (default)
bp or pb
GenBank and GenPept
e EMBL
p GenPept
q nucleotide GBSet (XML)
r protein GBSet (XML)
t Feature table only
x nucleotide INSDSet (XML)
y tiny seq (XML)
Y FASTA
z protein INSDSet (XML)
-g N Bit flags (all default to off):
1 HTML
2 XML
4 ContigFeats
8 ContigSrcs
16 FarTransl
-h N Lock/Lookup Flags (all default to off):
8 LockProd
16 LookupComp
64 LookupProd
-i filename
Input file name (default = stdin)
-j N Start location (default is 0, beginning of sequence)
-k N End location (default is 0, end of sequence)
-l filename
Log file
-m mode
Mode:
r Release
e Entrez
s Sequin (default)
d Dump
-n filename
Asn2Flat Executable (default = asn2flat)
-o filename
Output file name (default = stdout)
-p Propagate top descriptors
-q filename
Ffdiff Executable (default = /netopt/genbank/subtool/bin/ffdiff)
-r Enable remote fetching
-s style
Style:
n Normal (default)
s Segment
m Master
c Contig
-t N Batch:
1 Report
2 Sequin/Release
3 asn2gb SSEC/nocleanup
4 asn2flat BSEC/nocleanup
5 asn2gb/asn2flat
6 asn2gb NEW dbxref/OLD dbxref
7 oldasn2gb/newasn2gb
-u N Custom flags (all default to off):
4 Hide features
1792 Hide references
8192 Hide sources
262144 Hide translations
-y N Feature itemID
AUTHOR
The National Center for Biotechnology Information.
SEE ALSO asn2all(1), asn2asn(1), asn2ff(1), asn2fsa(1), asn2xml(1), asndhuff(1), insdseqget(1), /usr/share/doc/libncbi6-dev/asn2gb.txt.gz.
NCBI 2011-09-02 ASN2GB(1)