Merge branch 'JABAWS_Release_2_0'

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

diff --git a/conf/temp/blastdbcmd.txt b/conf/temp/blastdbcmd.txt
deleted file mode 100644 (file)
index 368428d..0000000
--- a/conf/temp/blastdbcmd.txt
+++ /dev/null
@@ -1,98 +0,0 @@
-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