DB Live shell
Launch a new DatabaseBuddy live shell session. Within the live shell, use the 'help' keyword on its own to get a list of available keywords, and then 'help <keyword>' to display detailed documentation on the given keyword.
Tab completion is implemented in the shell, as is history using the up and down keys. Hopefully this won't happen, but if the shell crashes your work will be saved to a file starting with 'DbSessionDump_tmp'. You can reload the data in this session with the 'load' command once you relaunch the shell.
$: db -ls
####################### Welcome to the DatabaseBuddy live shell #######################
Type 'help' for a list of available commands or 'help <command>' for further details.
To end the session, use the 'quit' command.
Your session is currently unpopulated. Use 'search' to retrieve records.
DbBuddy> help
----------------------------- DatabaseBuddy Help -----------------------------
A general workflow: 1) search databases with search terms or accession numbers
2) show summary information (no sequence has been downloaded yet)
3) Create filtered set of results with keep and remove
4) restore some records from the trash bin to the filtered set
5) fetch full sequence records for the filtered set
6) Switch to a format that includes sequences, like fasta or genbank
7) write sequences to a file or save the live session
Further details about each command can be accessed by typing 'help <command>'
Available commands:
============================================================================
bash delete fetch help load remove save show status undo
database failures format keep quit restore search sort trash write
DbBuddy> database uniprot
Database search list updated to ['uniprot']
DbBuddy> search perk1
Retrieving summary data for 64 records from UniProt
Querying UniProt with the search term 'perk1'...
DbBuddy> show 10
ACCN DB entry_name length organism-id organism protein_names comments record
P78543 uniprot BTG2_HUMAN 158 9606 Homo sapiens (Human) Protein BTG2 (BTG family member 2) (NGF-inducib... Function (1); Post-translational modification (... summary
P28482 uniprot MK01_HUMAN 360 9606 Homo sapiens (Human) Mitogen-activated protein kinase 1 (MAP kinase ... Alternative products (1); Catalytic activity (1... summary
P27361 uniprot MK03_HUMAN 379 9606 Homo sapiens (Human) Mitogen-activated protein kinase 3 (MAP kinase ... Alternative products (1); Catalytic activity (1... summary
Q9C660 uniprot PEK10_ARATH 762 3702 Arabidopsis thaliana (Mouse-ear cress) Proline-rich receptor-like protein kinase PERK1... Catalytic activity (1); Sequence similarities (... summary
Q9SGY7 uniprot PEK11_ARATH 718 3702 Arabidopsis thaliana (Mouse-ear cress) Putative proline-rich receptor-like protein kin... Catalytic activity (1); Sequence similarities (... summary
Q9ZUE0 uniprot PEK12_ARATH 720 3702 Arabidopsis thaliana (Mouse-ear cress) Proline-rich receptor-like protein kinase PERK1... Catalytic activity (1); Function (1); Induction... summary
O65530 uniprot PEK14_ARATH 731 3702 Arabidopsis thaliana (Mouse-ear cress) Proline-rich receptor-like protein kinase PERK1... Catalytic activity (1); Sequence similarities (... summary
Q9CAL8 uniprot PEK13_ARATH 710 3702 Arabidopsis thaliana (Mouse-ear cress) Proline-rich receptor-like protein kinase PERK1... Catalytic activity (1); Disruption phenotype (1... summary
Q9LV48 uniprot PERK1_ARATH 652 3702 Arabidopsis thaliana (Mouse-ear cress) Proline-rich receptor-like protein kinase PERK1... Alternative products (1); Catalytic activity (1... summary
Q9LK03 uniprot PERK2_ARATH 717 3702 Arabidopsis thaliana (Mouse-ear cress) Proline-rich receptor-like protein kinase PERK2... Catalytic activity (1); Sequence similarities (... summary
DbBuddy> keep (length>250)
Filter # Recs removed
(length>250) 5
59 records remain.
DbBuddy> keep (?i)proline
Filter # Recs removed
(?i)proline 30
29 records remain.
DbBuddy> remove Arabidopsis
Filter # Recs removed
Arabido 14
15 records remain.
DbBuddy> restore Fopius
Filter # Recs recovered
Fopius 2
47 records remain in the trash bin.
DbBuddy> sort organism
DbBuddy> show
ACCN DB entry_name length organism-id organism protein_names comments record
A0A0C9QIX7 uniprot A0A0C9QIX7_9HYME 616 64838 Fopius arisanus PERK1_1 protein summary
A0A0C9QMF9 uniprot A0A0C9QMF9_9HYME 243 64838 Fopius arisanus PERK1_0 protein (Fragment) summary
A0A0B2SMF4 uniprot A0A0B2SMF4_GLYSO 443 3848 Glycine soja (Wild soybean) Proline-rich receptor-like protein kinase PERK1... summary
A0A0B2QGN5 uniprot A0A0B2QGN5_GLYSO 475 3848 Glycine soja (Wild soybean) Proline-rich receptor-like protein kinase PERK1... summary
A0A0B2S263 uniprot A0A0B2S263_GLYSO 552 3848 Glycine soja (Wild soybean) Proline-rich receptor-like protein kinase PERK1... summary
A0A0B2PWC3 uniprot A0A0B2PWC3_GLYSO 536 3848 Glycine soja (Wild soybean) Proline-rich receptor-like protein kinase PERK1 summary
A0A0B2QDW8 uniprot A0A0B2QDW8_GLYSO 521 3848 Glycine soja (Wild soybean) Proline-rich receptor-like protein kinase PERK1... summary
A0A0B0PF39 uniprot A0A0B0PF39_GOSAR 395 29729 Gossypium arboreum (Tree cotton) (Gossypium nan... Proline-rich receptor-like protein kinase PERK1 summary
A0A0B0NAE1 uniprot A0A0B0NAE1_GOSAR 664 29729 Gossypium arboreum (Tree cotton) (Gossypium nan... Proline-rich receptor-like protein kinase PERK1 summary
A0A0B0MM60 uniprot A0A0B0MM60_GOSAR 610 29729 Gossypium arboreum (Tree cotton) (Gossypium nan... Proline-rich receptor-like protein kinase PERK1 Caution (1) summary
A0A0B0P0U9 uniprot A0A0B0P0U9_GOSAR 649 29729 Gossypium arboreum (Tree cotton) (Gossypium nan... Proline-rich receptor-like protein kinase PERK1 summary
W9RKU6 uniprot W9RKU6_9ROSA 571 981085 Morus notabilis Proline-rich receptor-like protein kinase PERK1 summary
W9RJX7 uniprot W9RJX7_9ROSA 479 981085 Morus notabilis Proline-rich receptor-like protein kinase PERK1 Sequence similarities (1) summary
W9QCU0 uniprot W9QCU0_9ROSA 718 981085 Morus notabilis Proline-rich receptor-like protein kinase PERK1 Sequence similarities (1) summary
W9R6G7 uniprot W9R6G7_9ROSA 418 981085 Morus notabilis Proline-rich receptor-like protein kinase PERK1 Sequence similarities (1) summary
M7ZHJ2 uniprot M7ZHJ2_TRIUA 445 4572 Triticum urartu (Red wild einkorn) (Crithodium ... Proline-rich receptor-like protein kinase PERK1... Sequence similarities (1) summary
M7ZEM3 uniprot M7ZEM3_TRIUA 584 4572 Triticum urartu (Red wild einkorn) (Crithodium ... Proline-rich receptor-like protein kinase PERK1... Sequence similarities (1) summary
DbBuddy> fetch
Retrieving 17 full records from UniProt...
Retrieved 8.92 K residues of sequence data
DbBuddy> format fasta
Output format changed to fasta
DbBuddy> write perk1.fasta
17 fasta records written to /home/sequences/perk1.fasta.
Records written to file
DbBuddy> quit
Goodbye
