JWS-67 configuration and manual file for jpred 3.0.1

[jabaws.git] / website / prog_docs / jpred.txt

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+Usage:
+    ./jpred.pl -in/-sequence <FILE1> [-out/-output <FILEPREFIX>] [-dbname
+    <DBNAME>] [-dbpath <PATH>] [-ncpu NNN] [-psi <psiblast output>]
+    [-pred-nohits] [-verbose] [-debug] [-help] [-man]
+
+Options:
+    -in/-sequence FILE
+         The path to the sequence file (in FASTA format) you want to
+         predict.
+
+    -out/-output FILEPREFIX
+         A prefix to the filenames created by Jpred, defaults to the value
+         set by -sequence/-in.
+
+    -dbpath PATH
+         Path to the uniref database used for PSI-BLAST querying.
+         Default: .
+
+    -dbname database
+         Database to use for PSI-BLAST querying. This only accepts databases
+         from a list which is pre-defined in the code.
+         Default: uniref90
+
+    -psi path
+         Path to a PSI-BLAST output file.
+
+    -ncpu NNN
+         Number of CPU used by jpred.pl. Maximum value is 8
+         Default: NNN = 1
+
+    -pred-nohits
+         Toggle allowing Jpred to make predictions even when there are no
+         PSI-BLAST hits.
+
+    -verbose
+         Verbose mode. Print more information while running jpred.
+
+    -debug
+         Debug mode. Print debugging information while running jpred.
+
+    -help
+         Gives help on the programs usage.
+
+    -man Displays this man page.
+