1 Analog of fastacmd for blast+
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3 -bash-3.2$ /local/opt/bin/blastdbcmd -help
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5 blastdbcmd [-h] [-help] [-db dbname] [-dbtype molecule_type]
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6 [-entry sequence_identifier] [-entry_batch input_file] [-pig PIG] [-info]
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7 [-range numbers] [-strand strand] [-mask_sequence_with numbers]
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8 [-out output_file] [-outfmt format] [-target_only] [-get_dups]
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9 [-line_length number] [-ctrl_a] [-version]
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12 BLAST database client, version 2.2.23+
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16 Print USAGE and DESCRIPTION; ignore other arguments
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18 Print USAGE, DESCRIPTION and ARGUMENTS description; ignore other arguments
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20 Print version number; ignore other arguments
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22 *** BLAST database options
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26 -dbtype <String, `guess', `nucl', `prot'>
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27 Molecule type stored in BLAST database
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30 *** Retrieval options
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32 Comma-delimited search string(s) of sequence identifiers:
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33 e.g.: 555, AC147927, 'gnl|dbname|tag', or 'all' to select all
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34 sequences in the database
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35 * Incompatible with: entry_batch, pig, info
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36 -entry_batch <File_In>
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37 Input file for batch processing (Format: one entry per line)
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38 * Incompatible with: entry, pig, info
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41 * Incompatible with: entry, entry_batch, target_only, info
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43 Print BLAST database information
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44 * Incompatible with: entry, entry_batch, outfmt, strand, target_only,
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45 ctrl_a, get_dups, pig, range
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47 *** Sequence retrieval configuration options
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49 Range of sequence to extract (Format: start-stop)
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50 * Incompatible with: info
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51 -strand <String, `minus', `plus'>
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52 Strand of nucleotide sequence to extract
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54 * Incompatible with: info
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55 -mask_sequence_with <String>
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56 Produce lower-case masked FASTA using the algorithm IDs specified (Format:
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59 *** Output configuration options
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64 Output format, where the available format specifiers are:
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65 %f means sequence in FASTA format
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66 %s means sequence data (without defline)
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69 %o means ordinal id (OID)
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70 %t means sequence title
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71 %l means sequence length
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73 %L means common taxonomic name
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74 %S means scientific name
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76 %mX means sequence masking data, where X is an optional comma-
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77 separted list of integers to specify the algorithm ID(s) to
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78 diaplay (or all masks if absent or invalid specification).
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79 Masking data will be displayed as a series of 'N-M' values
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80 separated by ';' or the word 'none' if none are available.
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81 For every format except '%f', each line of output will correspond to
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84 * Incompatible with: info
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86 Definition line should contain target GI only
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87 * Incompatible with: pig, info, get_dups
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89 Retrieve duplicate accessions
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90 * Incompatible with: info, target_only
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92 *** Output configuration options for FASTA format
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93 -line_length <Integer, >=1>
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94 Line length for output
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97 Use Ctrl-A as the non-redundant defline separator
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98 * Incompatible with: info
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