Changes from JWS3 is merged

[jabaws.git] / conf / temp / blastdbcmd.txt

diff --git a/conf/temp/blastdbcmd.txt b/conf/temp/blastdbcmd.txt
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+Analog of fastacmd for blast+\r
+\r
+-bash-3.2$ /local/opt/bin/blastdbcmd -help\r
+USAGE\r
+  blastdbcmd [-h] [-help] [-db dbname] [-dbtype molecule_type]\r
+    [-entry sequence_identifier] [-entry_batch input_file] [-pig PIG] [-info]\r
+    [-range numbers] [-strand strand] [-mask_sequence_with numbers]\r
+    [-out output_file] [-outfmt format] [-target_only] [-get_dups]\r
+    [-line_length number] [-ctrl_a] [-version]\r
+\r
+DESCRIPTION\r
+   BLAST database client, version 2.2.23+\r
+\r
+OPTIONAL ARGUMENTS\r
+ -h\r
+   Print USAGE and DESCRIPTION;  ignore other arguments\r
+ -help\r
+   Print USAGE, DESCRIPTION and ARGUMENTS description;  ignore other arguments\r
+ -version\r
+   Print version number;  ignore other arguments\r
+\r
+ *** BLAST database options\r
+ -db <String>\r
+   BLAST database name\r
+   Default = `nr'\r
+ -dbtype <String, `guess', `nucl', `prot'>\r
+   Molecule type stored in BLAST database\r
+   Default = `guess'\r
+\r
+ *** Retrieval options\r
+ -entry <String>\r
+   Comma-delimited search string(s) of sequence identifiers:\r
+        e.g.: 555, AC147927, 'gnl|dbname|tag', or 'all' to select all\r
+        sequences in the database\r
+    * Incompatible with:  entry_batch, pig, info\r
+ -entry_batch <File_In>\r
+   Input file for batch processing (Format: one entry per line)\r
+    * Incompatible with:  entry, pig, info\r
+ -pig <Integer, >=0>\r
+   PIG to retrieve\r
+    * Incompatible with:  entry, entry_batch, target_only, info\r
+ -info\r
+   Print BLAST database information\r
+    * Incompatible with:  entry, entry_batch, outfmt, strand, target_only,\r
+   ctrl_a, get_dups, pig, range\r
+\r
+ *** Sequence retrieval configuration options\r
+ -range <String>\r
+   Range of sequence to extract (Format: start-stop)\r
+    * Incompatible with:  info\r
+ -strand <String, `minus', `plus'>\r
+   Strand of nucleotide sequence to extract\r
+   Default = `plus'\r
+    * Incompatible with:  info\r
+ -mask_sequence_with <String>\r
+   Produce lower-case masked FASTA using the algorithm IDs specified (Format:\r
+   N,M,...)\r
+\r
+ *** Output configuration options\r
+ -out <File_Out>\r
+   Output file name\r
+   Default = `-'\r
+ -outfmt <String>\r
+   Output format, where the available format specifiers are:\r
+                %f means sequence in FASTA format\r
+                %s means sequence data (without defline)\r
+                %a means accession\r
+                %g means gi\r
+                %o means ordinal id (OID)\r
+                %t means sequence title\r
+                %l means sequence length\r
+                %T means taxid\r
+                %L means common taxonomic name\r
+                %S means scientific name\r
+                %P means PIG\r
+                %mX means sequence masking data, where X is an optional comma-\r
+                separted list of integers to specify the algorithm ID(s) to\r
+                diaplay (or all masks if absent or invalid specification).\r
+                Masking data will be displayed as a series of 'N-M' values\r
+                separated by ';' or the word 'none' if none are available.\r
+        For every format except '%f', each line of output will correspond to\r
+        a sequence.\r
+   Default = `%f'\r
+    * Incompatible with:  info\r
+ -target_only\r
+   Definition line should contain target GI only\r
+    * Incompatible with:  pig, info, get_dups\r
+ -get_dups\r
+   Retrieve duplicate accessions\r
+    * Incompatible with:  info, target_only\r
+\r
+ *** Output configuration options for FASTA format\r
+ -line_length <Integer, >=1>\r
+   Line length for output\r
+   Default = `80'\r
+ -ctrl_a\r
+   Use Ctrl-A as the non-redundant defline separator\r
+    * Incompatible with:  info\r