vdb-dump extended help

(1) dumping a vdb-table:

    the only mandatory option to vdb-dump is the name of the object to dump:

    vdb-dump OBJECT

    the OBJECT can be:

        a) absolute or relative path to a vdb-table (a directory)

            on linux:   vdb-dump /panfs/traces/sra0/SRR/000000/SRR000001


            on windows: vdb-dump \\panfs\traces\sra0\SRR\000000\SRR000001
                        vdb-dump Y:\sra0\SRR\000000\SRR000001
                        ( if "\\panfs\traces" is mapped to the driveletter Y on your windows-pc )

        b) absolute or relative path to a file containing a vdb-table

            on linux/windows:   vdb-dump SRR044989.sra

        c) an accession

            on linux/windows:   vdb-dump SRR000001
            
            outside NCBI you need internet access to reach accessions stored at NCBI and you need
            remote access enabled in your configuration

       If you specify only the object, vdb-dump will dump all columns for all rows to the standard-output.


The --table / -T option:
========================
vdb-dump is designed to operate on a vdb-database. A vdb-database can contain more then one table.
If you do not specify the table-name, vdb-dump will first try to interpret the given object as a vdb-database
( and try to dump the table "SEQUENCE", if that table does not exist: the first table it finds in this database ).
If this try (silently) fails, because the given object is not a database, vdb-dump will try to interpret
the given object as a table. If the object is not a vdb-database or vdb-table, the tool will fail.


The --rows / -R option:
=======================
With this option you can restrict which rows will be dumped.
vdb-dump file.sra -R 5      ... will dump only row number 5
vdb-dump file.sra -R 5-20   ... will dump rows number 5 to number 20 (15 rows)
The ranges can be mixed:
vdb-dump file.sra -R 5,7-20,200-201,300,305  ... will dump these rows/ranges
If you omit the range, vdb-dump will output all rows.


The --columns -C option:
========================
With this option you can restrict which columns per row will be dumped.
vdb-dump file.sra -C NAME,READ ... will dump only the columns NAME and READ per row


the --exclude -x option:
========================
If you want to dump all columns, except some specific ones.
vdb-dump file.sra -x READ,RD_FILTER ... will dump all columns but the READ-column
and the RD_FILTER-column.


The --row_id_on -I option:
==========================
vdb-dump does not output the row-id per default, it has to be switched on with this option:

vdb-dump SRR000001 -R1 -CNAME,SPOT_LEN
    NAME: EM7LVYS01C1LWG
SPOT_LEN: 255

vdb-dump SRR000001 -R1 -CNAME,SPOT_LEN -I
ROW-ID = 1
    NAME: EM7LVYS01C1LWG
SPOT_LEN: 255


The --line_feed -l option:
==========================
vdb-dump separates the rows by one empty line (line-feed) per default:

vdb-dump SRR000001 -R1-3 -CNAME,SPOT_LEN   
    NAME: EM7LVYS01C1LWG
SPOT_LEN: 255

    NAME: EM7LVYS01B2EMP
SPOT_LEN: 248

    NAME: EM7LVYS01C2YO0
SPOT_LEN: 307

with this option you can change that:

vdb-dump SRR000001 -R1-3 -CNAME,SPOT_LEN -l2
    NAME: EM7LVYS01C1LWG
SPOT_LEN: 255


    NAME: EM7LVYS01B2EMP
SPOT_LEN: 248


    NAME: EM7LVYS01C2YO0
SPOT_LEN: 307


The --colname_off -N option:
============================
vdb-dump prints the name of every column in front of the it's data:

vdb-dump SRR000001 -R1-2 -CNAME,SPOT_LEN
    NAME: EM7LVYS01C1LWG
SPOT_LEN: 255

    NAME: EM7LVYS01B2EMP
SPOT_LEN: 248

With this option it prints only the data:

vdb-dump SRR000001 -R1-2 -CNAME,SPOT_LEN -N 
EM7LVYS01C1LWG
255

EM7LVYS01B2EMP
248


The --in_hex -X option:
=======================
With this option all numeric outputs are printed as hexadecimal numbers:

$vdb-dump SRR000001 -R1-2 -CNAME,SPOT_LEN -X
    NAME: EM7LVYS01C1LWG
SPOT_LEN: 0xFF

    NAME: EM7LVYS01B2EMP
SPOT_LEN: 0xF8


The --dna_baese -D option:
==========================
With this option you can force columns into printed as DNA-base "ACGT",
but only if the column has a datatype with more than one dimension.
If a column has a datatype with a dimension of 2, each dimension 1 bit,
it is automatically printed as DNA-base.


The --max_length -M option:
===========================
With this options you can truncate the output of columns longer than this limit.

vdb-dump SRR000001 -R1-2 -CREAD
READ: TCAGGGGGGAGCTTAAATTTGAAACTAGAAAAATTTTGAACAAAATAATCATAATTGTTAGCTGATGAAAAACTAGAAAAGATTTTCTGAGTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGGTTCCAACGGTATCCCGTAGTGTGCATTCATCCCTGCTCTGGATACAGTCAGCTCCCAAATTCCATAAACAACTCCTTTGTAAGTAACCTCCTTTTGACAGGGGGTACTGAGCGGGCTGGCAAGGCN

READ: TCAGGGGGGGGTTACACGTGCAGATTTGTTACACGGGTGTACTGTGAGGTTTGGGGTACGAATGATCCCGTTACCTAGATAGTGAGCATGGAACCCGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGGTTCCAACAATGTGCAGGGCTCAGGTCAGCATTAGGGTCAGGTTCTTAGGAAAAGAAAGAGCAAAAACAATGAAACACAATACAAAGTAAAGAACACTGAGCGGGCTGGCAAGGCN

vdb-dump SRR000001 -R1-2 -CREAD -M40
READ: TCAGGGGGGAGCTTAAATTTGAAACTAGAA ...

READ: TCAGGGGGGGGTTACACGTGCAGATTTGTT ...


The --indent_with -i option:
============================
With this option you can limit the length of the output-line and force a left-edge
indenting.

vdb-dump $vdb-dump SRR000001 -R1-2 -CREAD -i80
READ: TCAGGGGGGAGCTTAAATTTGAAACTAGAAAAATTTTGAACAAAATAATCATAATTGTTAGCTGATGAAAAACT
      AGAAAAGATTTTCTGAGTGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGGTTCCAACGGTATCCCGTAG
      TGTGCATTCATCCCTGCTCTGGATACAGTCAGCTCCCAAATTCCATAAACAACTCCTTTGTAAGTAACCTCCTT
      TTGACAGGGGGTACTGAGCGGGCTGGCAAGGCN

READ: TCAGGGGGGGGTTACACGTGCAGATTTGTTACACGGGTGTACTGTGAGGTTTGGGGTACGAATGATCCCGTTAC
      CTAGATAGTGAGCATGGAACCCGTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGGTTCCAACAATGTGCA
      GGGCTCAGGTCAGCATTAGGGTCAGGTTCTTAGGAAAAGAAAGAGCAAAAACAATGAAACACAATACAAAGTAA
      AGAACACTGAGCGGGCTGGCAAGGCN


The --format -f option:
=======================
This selects other than the default-output formating:

csv = comma-separated on one line
---------------------------------
vdb-dump SRR000001 -R1-2 -CNAME,SPOT_LEN -fcsv
EM7LVYS01C1LWG,255
EM7LVYS01B2EMP,248

xml = xml-section
-----------------
vdb-dump $vdb-dump SRR000001 -R1-2 -CNAME,SPOT_LEN -fxml
<row_1>
 <NAME>
EM7LVYS01C1LWG
 </NAME>
 <SPOT_LEN>
255
 </SPOT_LEN>
</row_1>

<row_2>
 <NAME>
EM7LVYS01B2EMP
 </NAME>
 <SPOT_LEN>
248
 </SPOT_LEN>
</row_2>

json = json format
------------------
vdb-dump $vdb-dump SRR000001 -R1-2 -CNAME,SPOT_LEN -fjson
{
"row_id": 1,
"NAME":"EM7LVYS01C1LWG",
"SPOT_LEN":255
},

{
"row_id": 2,
"NAME":"EM7LVYS01B2EMP",
"SPOT_LEN":248
},

piped = format friendly to beeing piped into other processes
------------------------------------------------------------
vdb-dump $vdb-dump SRR000001 -R1-2 -CNAME,SPOT_LEN -fpiped
1, NAME: "EM7LVYS02FOYNU"
1, SPOT_LEN: 284

2, NAME: "EM7LVYS02GCAPL"
2, SPOT_LEN: 262

sra-dump = simulates the output of a deprecated tool
------------------------------------------------------------
vdb-dump $vdb-dump SRR000001 -R1-2 -CNAME,SPOT_LEN -fsra-dump
1, NAME: EM7LVYS02FOYNU
1, SPOT_LEN: 284

2, NAME: EM7LVYS02GCAPL
2, SPOT_LEN: 262

fastq = produces fastq-output
( the table needs to have a READ- and a QUALITY column, no splitting supported )
-------------------------------------------------------
vdb-dump $vdb-dump SRR000001 -R1 -ffastq
@SRR000001.1 EM7LVYS02FOYNU length=284
TCAGATTCTCCTAGCCTACATCCGTACGAGTTAGCGTGGGATTACGAGGTGCACACCATTTCATTCCGTACGGGTAAATTTTTGTATTTTTAGCAGACGGCAGGGTTTCACCATGGTTGACCAACGTACTAATCTTGAACTCCTGACCTCAAGTGATTTGCCTGCCTTCAGCCTCCCAAAGTGACTGGGTATTACAGATGTGAGCGAGTTTGTGCCCAAGCCTTATAAGTAAATTTATAAATTTACATAATTTAAATGACTTATGCTTAGCGAAATAGGGTAAG
+SRR000001.1 EM7LVYS02FOYNU length=284
=<8<85)9=9/3-8?68<7=8<3657747==49==+;FB2;A;5:'*>69<:74)9.;C?+;<B<B;(<';FA/;C>*GC8/%9<=GC8.#=2:5:16D==<EA2EA.;5=44<;2C=5;@73&<<2;5;6+9<?776+:24'26:7,<9A;=:;0C>*6?7<<C=D=<52?:9CA2CA23<2<;3CA12:A<9414<7<<6;99<2/=9#<;9B@27.;=6>:77>:1<A>+CA138?<)C@2166:A<B?->:%<<9<;33<;6?9;<;4=:%<$CA1+1%1

fasta = produces fasta-output
( the table needs to have a READ column )
-------------------------------------------------------
vdb-dump SRR000001 -R1 -f fasta
>SRR000001.1 EM7LVYS02FOYNU length=284
TCAGATTCTCCTAGCCTACATCCGTACGAGTTAGCGTGGGATTACGAGGTGCACACCATTTCATTCCGTA
CGGGTAAATTTTTGTATTTTTAGCAGACGGCAGGGTTTCACCATGGTTGACCAACGTACTAATCTTGAAC
TCCTGACCTCAAGTGATTTGCCTGCCTTCAGCCTCCCAAAGTGACTGGGTATTACAGATGTGAGCGAGTT
TGTGCCCAAGCCTTATAAGTAAATTTATAAATTTACATAATTTAAATGACTTATGCTTAGCGAAATAGGG
TAAG


The --without_sra -n option:
============================
With this option you can switch off the special treatment (translation) of certain column-types

vdb-dump SRR000001 -R1 -C SPOT_DESC,PLATFORM
SPOT_DESC: spot_len=255, fixed_len=0, signal_len=400, clip_qual_right=235, num_reads=4
 PLATFORM: SRA_PLATFORM_454

vdb-dump SRR000001 -R1 -C SPOT_DESC,PLATFORM -n
SPOT_DESC: [255, 0, 0, 0, 144, 1, 235, 0, 4, 0, 0, 0, 0, 0, 0, 0]
 PLATFORM: 1


The --table_enum -E option:
===========================
If the object is a vdb-database, enumerate the tables it contains.


The --version -V option:
========================
Print the version of the vdb-manager used by vdb-dump.

vdb-dump -V
vdb-dump: 2.5.1


The column_enum_short -o option:
================================
Enumerates the columns and the default type of each column
vdb-dump SRR000001 -o

BASE_COUNT (U64)
BIO_BASE_COUNT (U64)
CLIP_ADAPTER_LEFT (INSDC:coord:one)
etc.


The column_enum -O option:
==========================
Enumerates the columns and all available type of each column

vdb-dump SRR000001 -O
SRR000001.01 : (032 bits [01],      Int)  CLIP_QUALITY_LEFT
      (INSDC:coord:one)
   CLIP_QUALITY_LEFT.type[0] = INSDC:coord:one (dflt)
   CLIP_QUALITY_LEFT.type[1] = U16
   CLIP_QUALITY_LEFT.type[2] = INSDC:coord:zero

SRR000001.02 : (032 bits [01],      Int)  CLIP_QUALITY_RIGHT
      (INSDC:coord:one)
  CLIP_QUALITY_RIGHT.type[0] = INSDC:coord:one (dflt)
  CLIP_QUALITY_RIGHT.type[1] = U16
  CLIP_QUALITY_RIGHT.type[2] = INSDC:coord:zero

SRR000001.03 : (008 bits [01],     Uint)  COLOR_MATRIX
      (U8)
        COLOR_MATRIX.type[0] = U8 (dflt)

etc.

The --id_range -r option:
=========================
Print the row-range that a table contains.

vdb-dump SRR000001 -r
id-range: first-row = 1, row-count = 470985


The --info option:
==================
prints a summary of meta-data about the accession

vdb-dump SRR000001 --info
acc    : SRR000001
path   : /somepath/SRR/000000/SRR000001
size   : 312,527,083
type   : Table
platf  : SRA_PLATFORM_454
SEQ    : 470,985
SCHEMA : NCBI:SRA:_454_:tbl:v2#1.0.7
TIME   : 0x0000000055248a41 (04/07/2015 21:54)
FMT    : SFF
FMTVER : 2.4.5
LDR    : sff-load.2.4.5
LDRVER : 2.4.5
LDRDATE: Feb 25 2015 (2/25/2015 0:0)
