showdb.usage

emboss的linux版本的源代码

<b>Here is a sample session with showdb</b>
<p>
Display information on the currently available databases: 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>showdb </b>
Displays information on the currently available databases

# Name           Type  ID  Qry All Comment
# ============== ==== ==  === === =======
qapblast         P    OK  OK  OK  BLAST swissnew
qapblastall      P    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit    P    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc P    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc P    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta         P    OK  OK  OK  FASTA file swissnew entries
qapflat          P    OK  OK  OK  Swissnew flatfiles
qapflatall       P    OK  OK  OK  Swissnew flatfiles, all fields indexed
qapflatexc       P    OK  OK  OK  Swissnew flatfiles, no updated sequence file
qapflatinc       P    OK  OK  OK  Swissnew flatfiles, only updated sequence file
qapir            P    OK  OK  OK  PIR
qapirall         P    OK  OK  OK  PIR
qapirinc         P    OK  OK  OK  PIR
qapxfasta        P    OK  OK  OK  FASTA file swissnew entries
qapxflat         P    OK  OK  OK  Swissnew flatfiles
qapxflatexc      P    OK  OK  OK  Swissnew flatfiles, no updated sequence file
qapxflatinc      P    OK  OK  OK  Swissnew flatfiles, only updated sequence file
qaxpir           P    OK  OK  OK  PIR
qaxpirall        P    OK  OK  OK  PIR
qaxpirinc        P    OK  OK  OK  PIR
tpir             P    OK  OK  OK  PIR using NBRF access for 4 files
tsw              P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
tswnew           P    OK  OK  OK  Swissnew as 3 files in native format with EMBL CD-ROM index
twp              P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM index
genbanksrs       N    OK  -   -   Genbank IDs
qanfasta         N    OK  OK  OK  FASTA file EMBL rodents
qanfastaall      N    OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanflat          N    OK  OK  OK  EMBL flatfiles
qangcg           N    OK  OK  OK  GCG format EMBL
qangcgall        N    OK  OK  OK  GCG format EMBL
qangcgexc        N    OK  OK  OK  GCG format EMBL without prokaryotes
qangcginc        N    OK  OK  OK  GCG format EMBL only prokaryotes
qanxfasta        N    OK  OK  OK  FASTA file EMBL rodents
qanxfastaall     N    OK  OK  OK  FASTA file EMBL rodents, all fields indexed
qanxflat         N    OK  OK  OK  EMBL flatfiles
qanxflatall      N    OK  OK  OK  EMBL flatfiles, all fields indexed
qanxgcg          N    OK  OK  OK  GCG format EMBL
qanxgcgall       N    OK  OK  OK  GCG format EMBL
qanxgcgexc       N    OK  OK  OK  GCG format EMBL without prokaryotes
qanxgcginc       N    OK  OK  OK  GCG format EMBL only prokaryotes
qapirexc         N    OK  OK  OK  PIR
qasrswww         N    OK  -   -   Remote SRS web server
qawfasta         N    OK  OK  OK  FASTA file wormpep entries
qawxfasta        N    OK  OK  OK  FASTA file wormpep entries
qaxpirexc        N    OK  OK  OK  PIR
tembl            N    OK  OK  OK  EMBL in native format with EMBL CD-ROM index
temblall         N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblrest        N    -   -   OK  EMBL in native format with EMBL CD-ROM index
temblvrt         N    -   -   OK  EMBL in native format with EMBL CD-ROM index
tgb              N    OK  -   -   Genbank IDs
tgenbank         N    OK  OK  OK  GenBank in native format with EMBL CD-ROM index

</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 2</b>
<p>
Write the results to a file: 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>showdb -outfile showdb.out </b>
Displays information on the currently available databases

</pre></td></tr></table><p>
<p>
<a href="#output.2">Go to the output files for this example</a><p><p>
<p>
<b>Example 3</b>
<p>
Display information on one explicit database: 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>showdb -database tsw </b>
Displays information on the currently available databases

# Name         Type  ID  Qry All Comment
# ============ ==== ==  === === =======
tsw            P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index

</pre></td></tr></table><p>
<p>
<a href="#input.3">Go to the input files for this example</a><br><p>
<p>
<b>Example 4</b>
<p>
Display information on the databases formatted in HTML: 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>showdb -html </b>
Displays information on the currently available databases

<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Name</th><th>Type</th><th>ID</th><th>Qry</th><th>All</th><th>Comment</th></tr>
<tr><td>qapblast</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>BLAST swissnew</td></tr>
<tr><td>qapblastall</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>BLAST swissnew, all fields indexed</td></tr>
<tr><td>qapblastsplit</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>BLAST swissnew split in 5 files</td></tr>
<tr><td>qapblastsplitexc</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>BLAST swissnew split in 5 files, not file 02</td></tr>
<tr><td>qapblastsplitinc</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>BLAST swissnew split in 5 files, only file 02</td></tr>
<tr><td>qapfasta</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>FASTA file swissnew entries</td></tr>
<tr><td>qapflat</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>Swissnew flatfiles</td></tr>
<tr><td>qapflatall</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>Swissnew flatfiles, all fields indexed</td></tr>
<tr><td>qapflatexc</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>Swissnew flatfiles, no updated sequence file</td></tr>
<tr><td>qapflatinc</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>Swissnew flatfiles, only updated sequence file</td></tr>
<tr><td>qapir</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>PIR</td></tr>
<tr><td>qapirall</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>PIR</td></tr>
<tr><td>qapirinc</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>PIR</td></tr>
<tr><td>qapxfasta</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>FASTA file swissnew entries</td></tr>
<tr><td>qapxflat</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>Swissnew flatfiles</td></tr>
<tr><td>qapxflatexc</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>Swissnew flatfiles, no updated sequence file</td></tr>
<tr><td>qapxflatinc</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>Swissnew flatfiles, only updated sequence file</td></tr>
<tr><td>qaxpir</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>PIR</td></tr>
<tr><td>qaxpirall</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>PIR</td></tr>
<tr><td>qaxpirinc</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>PIR</td></tr>
<tr><td>tpir</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>PIR using NBRF access for 4 files</td></tr>
<tr><td>tsw</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>Swissprot native format with EMBL CD-ROM index</td></tr>
<tr><td>tswnew</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>Swissnew as 3 files in native format with EMBL CD-ROM index</td></tr>
<tr><td>twp</td><td>P</td><td>OK  </td><td>OK  </td><td>OK  </td><td>EMBL new in native format with EMBL CD-ROM index</td></tr>
<tr><td>genbanksrs</td><td>N</td><td>OK  </td><td>-   </td><td>-   </td><td>Genbank IDs</td></tr>
<tr><td>qanfasta</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>FASTA file EMBL rodents</td></tr>
<tr><td>qanfastaall</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>FASTA file EMBL rodents, all fields indexed</td></tr>
<tr><td>qanflat</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>EMBL flatfiles</td></tr>
<tr><td>qangcg</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>GCG format EMBL</td></tr>
<tr><td>qangcgall</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>GCG format EMBL</td></tr>
<tr><td>qangcgexc</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>GCG format EMBL without prokaryotes</td></tr>
<tr><td>qangcginc</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>GCG format EMBL only prokaryotes</td></tr>
<tr><td>qanxfasta</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>FASTA file EMBL rodents</td></tr>
<tr><td>qanxfastaall</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>FASTA file EMBL rodents, all fields indexed</td></tr>
<tr><td>qanxflat</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>EMBL flatfiles</td></tr>
<tr><td>qanxflatall</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>EMBL flatfiles, all fields indexed</td></tr>
<tr><td>qanxgcg</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>GCG format EMBL</td></tr>
<tr><td>qanxgcgall</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>GCG format EMBL</td></tr>
<tr><td>qanxgcgexc</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>GCG format EMBL without prokaryotes</td></tr>
<tr><td>qanxgcginc</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>GCG format EMBL only prokaryotes</td></tr>
<tr><td>qapirexc</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>PIR</td></tr>
<tr><td>qasrswww</td><td>N</td><td>OK  </td><td>-   </td><td>-   </td><td>Remote SRS web server</td></tr>
<tr><td>qawfasta</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>FASTA file wormpep entries</td></tr>
<tr><td>qawxfasta</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>FASTA file wormpep entries</td></tr>
<tr><td>qaxpirexc</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>PIR</td></tr>
<tr><td>tembl</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>EMBL in native format with EMBL CD-ROM index</td></tr>
<tr><td>temblall</td><td>N</td><td>-   </td><td>-   </td><td>OK  </td><td>EMBL in native format with EMBL CD-ROM index</td></tr>
<tr><td>temblrest</td><td>N</td><td>-   </td><td>-   </td><td>OK  </td><td>EMBL in native format with EMBL CD-ROM index</td></tr>
<tr><td>temblvrt</td><td>N</td><td>-   </td><td>-   </td><td>OK  </td><td>EMBL in native format with EMBL CD-ROM index</td></tr>
<tr><td>tgb</td><td>N</td><td>OK  </td><td>-   </td><td>-   </td><td>Genbank IDs</td></tr>
<tr><td>tgenbank</td><td>N</td><td>OK  </td><td>OK  </td><td>OK  </td><td>GenBank in native format with EMBL CD-ROM index</td></tr>
</table>

</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 5</b>
<p>
Display protein databases only: 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>showdb -nonucleic </b>
Displays information on the currently available databases

# Name           Type  ID  Qry All Comment
# ============== ==== ==  === === =======
qapblast         P    OK  OK  OK  BLAST swissnew
qapblastall      P    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit    P    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc P    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc P    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta         P    OK  OK  OK  FASTA file swissnew entries
qapflat          P    OK  OK  OK  Swissnew flatfiles
qapflatall       P    OK  OK  OK  Swissnew flatfiles, all fields indexed
qapflatexc       P    OK  OK  OK  Swissnew flatfiles, no updated sequence file
qapflatinc       P    OK  OK  OK  Swissnew flatfiles, only updated sequence file
qapir            P    OK  OK  OK  PIR
qapirall         P    OK  OK  OK  PIR
qapirinc         P    OK  OK  OK  PIR
qapxfasta        P    OK  OK  OK  FASTA file swissnew entries
qapxflat         P    OK  OK  OK  Swissnew flatfiles
qapxflatexc      P    OK  OK  OK  Swissnew flatfiles, no updated sequence file
qapxflatinc      P    OK  OK  OK  Swissnew flatfiles, only updated sequence file
qaxpir           P    OK  OK  OK  PIR
qaxpirall        P    OK  OK  OK  PIR
qaxpirinc        P    OK  OK  OK  PIR
tpir             P    OK  OK  OK  PIR using NBRF access for 4 files
tsw              P    OK  OK  OK  Swissprot native format with EMBL CD-ROM index
tswnew           P    OK  OK  OK  Swissnew as 3 files in native format with EMBL CD-ROM index
twp              P    OK  OK  OK  EMBL new in native format with EMBL CD-ROM index

</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 6</b>
<p>
Display the information with no headings: 
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>showdb -noheading </b>
Displays information on the currently available databases

qapblast         P    OK  OK  OK  BLAST swissnew
qapblastall      P    OK  OK  OK  BLAST swissnew, all fields indexed
qapblastsplit    P    OK  OK  OK  BLAST swissnew split in 5 files
qapblastsplitexc P    OK  OK  OK  BLAST swissnew split in 5 files, not file 02
qapblastsplitinc P    OK  OK  OK  BLAST swissnew split in 5 files, only file 02
qapfasta         P    OK  OK  OK  FASTA file swissnew entries
qapflat          P    OK  OK  OK  Swissnew flatfiles
qapflatall       P    OK  OK  OK  Swissnew flatfiles, all fields indexed
qapflatexc       P    OK  OK  OK  Swissnew flatfiles, no updated sequence file
qapflatinc       P    OK  OK  OK  Swissnew flatfiles, only updated sequence file
qapir            P    OK  OK  OK  PIR
qapirall         P    OK  OK  OK  PIR
qapirinc         P    OK  OK  OK  PIR
qapxfasta        P    OK  OK  OK  FASTA file swissnew entries
qapxflat         P    OK  OK  OK  Swissnew flatfiles
qapxflatexc      P    OK  OK  OK  Swissnew flatfiles, no updated sequence file