.\" Copyright (c) 2014 Stijn van Dongen .TH "mclblastline" 1 "16 May 2014" "mclblastline 14-137" "USER COMMANDS " .po 2m .de ZI .\" Zoem Indent/Itemize macro I. .br 'in +\\$1 .nr xa 0 .nr xa -\\$1 .nr xb \\$1 .nr xb -\\w'\\$2' \h'|\\n(xau'\\$2\h'\\n(xbu'\\ .. .de ZJ .br .\" Zoem Indent/Itemize macro II. 'in +\\$1 'in +\\$2 .nr xa 0 .nr xa -\\$2 .nr xa -\\w'\\$3' .nr xb \\$2 \h'|\\n(xau'\\$3\h'\\n(xbu'\\ .. .if n .ll -2m .am SH .ie n .in 4m .el .in 8m .. .SH NAME mclblastline \- a pipeline for clustering from BLAST files\&. .SH SYNOPSIS \fBmclblastline\fP file-name \fBmclblastline\fP [deblast options] [pipeline options] file-name \fBNOTE\fP .br \fBmcl\fP has acquired the ability to proceed from label input as produced by \fBmcxdeblast\fP\&. This enables a very lightweight mechanism of generating clusterings from BLAST files\&. You might want to use this mechanism, documented in the \fBmcl manual\fP\&. \fBNOTE\fP .br mclblastline used to require (given default parameters) the presence of the \fBzoem\fP macro processor to produce detailed output\&. This is no longer the case\&. By default mclblastline now creates a line-based tab-separated dump file\&. Zoem \fIwill\fP be invoked when the --fmt-fancy option is supplied\&. In that case, zoem obviously has to be installed\&. .SH DESCRIPTION \fBmclblastline\fP wraps around \fBmclpipeline\fP\&. It supplies the \fB--parser\fP=\fIapp\fP and \fB--parser-tag\fP=\fIstr\fP options, setting them respectively to \fImcxdeblast\fP and \fIblast\fP\&. This tells \fBmclpipeline\fP to use \fBmcxdeblast\fP as the parse script in its pipeline\&. The significance of the \fIblast\fP tag is that any mcxdeblast option can be passed through mclblastline and mclpipeline by inserting this tag into the option\&. For example, mcxdeblast accepts the \fB--score\fP=\fIx\fP option\&. When using mclblastline, you specify it as \fB--blast-score\fP=\fIx\fP\&. There are two exceptions to this rule, namely the \fB--xi-dat\fP=\fIstr\fP and \fB--xo-dat\fP=\fIstr\fP options\&. Refer to the \fBmclpipeline\fP manual for more information\&. Additionally, all mclpipeline options are acceptable to \fBmcxdeblast\fP as well\&. The \fB--whatif\fP is useful for getting a feel for the pipeline\&. The \fB--mcl-I\fP=\fIf\fP inflation option and \fB--mcl-scheme\fP=\fIi\fP scheme index options are your basic means for respectively manipulating cluster granularity and allocating resources\&. Read the \fBmcl\fP manual entries for a description of the corresponding \fB-I\fP and \fB-scheme\fP mcl options\&. The best advice is to glance over the \fBmcxdeblast\fP and \fBmclpipeline\fP options in order to get a feeling for which of those may come in handy for you\&. Then start experimenting\&. Use the \fB--whatif\fP option, it will tell you what would happen without actually doing it\&. .SH OPTIONS All \fBmcxdeblast\fP and \fBmclpipeline\fP options\&. mcxdeblast options must be passed using the mechanism described above\&. .SH EXAMPLES .nf \fC mclblastline --blast-score=b --blast-sort=a --blast-bcut=5 --mcl-I=2\&.5 myblastfile .fi \fR This will use bit scores, sort cluster indices such that the corresponding labels are ordered alphabetically, ignore bit scores not exceeding 5, and use inflation value 2\&.5\&. In this case, the output clustering will be in the file named \fCmyblastfile\&.I25s2\fP (I25 identifying the inflation value and s2 identifying the resource scheme) and the formatted output will be in the file \fCmyblastfile\&.I25s2\&.fmt\fP\&. .nf \fC mclblastline --prepare-mcl myblastfile mclblastline --start-mcl --mcl-I=1\&.2 myblastfile mclblastline --start-mcl --mcl-I=1\&.6 myblastfile mclblastline --start-mcl --mcl-I=2\&.0 myblastfile mclblastline --start-mcl --mcl-I=2\&.4 myblastfile mclblastline --start-mcl --mcl-I=2\&.8 myblastfile etc \&.\&. .fi \fR The first run prepares an input matrix to be read by \fBmcl\fP\&. In this case its file will be named \fCmyblastfile\&.sym\fP\&. The subsequent runs use this matrix\&. \fBCAVEAT\fP there are some options that you need to repeat when executing such a resumed run\&. They are clearly marked in the \fBmclpipeline\fP manual - namely those options that affect names of (intermediate) files\&. Most importantly, this concerns the mclpipeline options that have prefix \fB--xo\fP or \fB--xi\fP\&. For example, .nf \fC mclblastline --prepare-mcl --blast-score=b --xo-dat=b myblastfile mclblastline --start-mcl --xo-dat=b --mcl-I=1\&.2 myblastfile mclblastline --start-mcl --xo-dat=b --mcl-I=1\&.6 myblastfile mclblastline --start-mcl --xo-dat=b --mcl-I=2\&.0 myblastfile mclblastline --start-mcl --xo-dat=b --mcl-I=2\&.4 myblastfile mclblastline --start-mcl --xo-dat=b --mcl-I=2\&.8 myblastfile etc \&.\&. .fi \fR In this case, the matrix file will be named \fCmyblastfile\&.b\&.sym\fP, and the \fB--xo-dat\fP options must be repeated in all runs so that the pipeline reconstructs the correct file name(s)\&. .SH AUTHOR Stijn van Dongen .SH SEE ALSO \fBmcxdeblast\fP, \fBmclpipeline\fP, \fBmcxassemble\fP\&.