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splign  

2010-03-29 02:24:22|  分类: 生物信息编程 |  标签: |举报 |字号 订阅

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usage
  d:\program files\blast\bin\splign.exe [-h] [-help] [-xmlhelp] [-hits hits]
    [-comps comps] [-mklds mklds] [-ldsdir ldsdir] [-query query] [-subj subj]
    [-disc] [-w mbwordsize] [-compartment_penalty compartment_penalty]
    [-min_compartment_idty min_compartment_identity]
    [-min_singleton_idty min_singleton_identity]
    [-min_singleton_idty_bps min_singleton_identity_bps]
    [-min_exon_idty identity] [-max_intron max_intron] [-max_space max_space]
    [-direction direction] [-log log] [-asn asn] [-aln aln]
    [-logfile file_name] [-conffile file_name] [-version] [-version-full]
    [-dryrun]

description
   splign: 1.39.8
   (gpipe)

optional arguments
 -h
   print usage and description;  ignore other arguments
 -help
   print usage, description and arguments description;  ignore other arguments
 -xmlhelp
   print usage, description and arguments description in xml format;  ignore
   other arguments
 -hits <file_in>
   [batch mode] externally computed local alignments (such as blast hits), in
   blast tabular format. the file must be collated by subject and query (e.g.
   sort -k 2,2 -k 1,1).
 -comps <file_in>
   [batch mode] compartments computed with compart utility.
 -mklds <string>
   [batch mode] make lds db under the specified directory with cdna and
   genomic fasta files or symlinks.
 -ldsdir <string>
   [batch mode] directory holding lds subdirectory.
 -query <file_in>
   [pairwise mode] fasta file with the spliced sequence.
 -subj <file_in>
   [pairwise mode] fasta file with the genomic sequence.
 -disc
   [pairwise mode] use discontiguous megablast to facilitate alignment of more
   divergent sequences such as those from different organisms (cross-species
   alignment).
 -w <integer>
   [pairwise mode] megablast word size
   default = '28'
 -compartment_penalty <real, 0..1>
   penalty to open a new compartment (compartment identification parameter).
   multiple compartments will only be identified if they have at least this
   level of coverage.
   default = '0.55'
 -min_compartment_idty <real, 0..1>
   minimal compartment identity to align.
   default = '0.7'
 -min_singleton_idty <real>
   minimal singleton compartment identity to use per subject and strand,
   expressed as a fraction of the query's length.
 -min_singleton_idty_bps <integer>
   minimal singleton compartment identity to use per subject and strand, in
   base pairs. the actual value passed to the compartmentization procedure is
   the least of (min_singleton_idty * query_length) and
   min_singleton_identity_bps.
   default = '9999999'
 -min_exon_idty <real, 0..1>
   minimal exon identity. segments with lower identity will be marked as gaps.
   default = '0.75'
 -max_intron <integer, 7..2000000>
   the upper bound on intron length, in base pairs.
   default = '1200000'
 -max_space <real, 500..4096>
   the max space to allocate for a splice, in mb. specify lower values to
   spend less time stitching over large genomic intervals.
   default = '4096'
 -direction <string, 'antisense', 'auto', 'both', 'sense'>
   query sequence orientation. auto orientation begins with the longest orf
   direction (d1) and proceeds with the opposite direction (d2) if found a
   non-consensus splice in d1 or poly-a tail in d2.
   default = 'sense'
 -log <file_out>
   splign log file
   default = 'splign.log'
 -asn <file_out>
   asn.1 output file name
 -aln <file_out>
   pairwise alignment output file name
 -logfile <file_out>
   file to which the program log should be redirected
 -conffile <file_in>
   program's configuration (registry) data file
 -version
   print version number;  ignore other arguments
 -version-full
   print extended version data;  ignore other arguments
 -dryrun
   dry run the application: do nothing, only test all preconditions

 

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