.\" Copyright (c) 2014 Stijn van Dongen .TH "mcxdeblast" 1 "16 May 2014" "mcxdeblast 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 mcxdeblast \- parse BLAST files and stream output directly into mcl or write mcxassemble input\&. .SH SYNOPSIS \fBmcxdeblast\fP file-name \fBmcxdeblast\fP \fB[--score=\fP (\fIbit scores|e-values|normalize bit score\fP)\fB]\fP \fB[--m9\fP (\fIexpect BLAST column format\fP)\fB]\fP \fB[--out\fP (\fIoutput file\fP)\fB]\fP \fB[--line-mode\fP abc (\fIwrite ID1 ID2 score format\fP)\fB]\fP \fB[--sort=\fP (\fIalphabetic|occurrence sorting\fP)\fB]\fP \fB[--xi-dat=\fP (\fIstrip from file-name\fP)\fB]\fP \fB[--xo-dat=\fP (\fIadd to base name\fP)\fB]\fP \fB[--bcut=\fP (\fIbit score cutoff\fP)\fB]\fP \fB[--ecut=\fP (\fIE-value cutoff\fP)\fB]\fP \fB[--rcut=\fP (\fIraw value cutoff\fP)\fB]\fP \fB[--tab=\fP (\fItab file\fP)\fB]\fP .SH DESCRIPTION \fBmcxdeblast\fP parses BLAST files\&. In \fIstream mode\fP mcxdeblast output can be directly streamed to mcl by using the mcxdeblast \fB--line-mode\fP=\fIabc\fP option and equipping mcl with either \fB--abc\fP or \fB--expect-abc\fP\&. This can be considered the easy, lightweight and fast track\&. This functionality was recently acquired by mcl\&. In the classic and slightly more heavy-handed \fIassemble mode\fP, mcxdeblast creates output files suitable for use by mcxassemble\&. The latter can in turn create input suitable for mcl\&. This is the mode in which mcxdeblast is employed by \fBmclblastline\fP\&. .SH STREAM MODE Enter stream mode by specifying \fB--line-mode\fP=\fIabc\fP\&. Use \fB--m9\fP if the input is in columnar output\&. Pipe the result to a file or directly to mcl\&. Example invocations can be found in \fBthe mcl manual\fP\&. .SH ASSEMBLE MODE If the input file is named \fCiput\fP, mcxdeblast will by default create files \fCiput\&.hdr\fP, \fCiput\&.raw\fP, \fCiput\&.tab\fP, \fCiput\&.map\fP, and \fCiput\&.err\fP\&. The \fChdr\fP file contains information about the number of nodes found\&. It will be read by \fBmcxassemble\fP\&. The \fCraw\fP file contains the co-occurrence scores between different nodes (peptides), also to be read by mcxassemble\&. The co-occurrence scores are in terms of mcl indentiers, which are subjected to rearranging by mcxassemble in order to correctly align them with the tab file\&. The \fCtab\fP file contains bindings between mcl identifiers (after rearranging as specified in the map file) and the BLAST labels (peptide identifiers)\&. Refer to the manual of \fBmcxassemble\fP for the syntax of a tab file\&. The \fCerr\fP file contains a list of any errors encountered\&. If the \fB--tab\fP=\fBfname\fP option is used mcxdeblast changes its behaviour\&. It will read the file \fBfname\fP, and use the bindings found therein\&. It will no longer output any of the \fChdr\fP, \fCmap\fP, or \fCtab\fP files\&. The \fChdr\fP file should be provided by the same application that generated the specified tab file, and the \fCmap\fP file should no longer be necessary (it might be convenient though and perhaps the future will bring a new \fB--map\fP option)\&. The \fB--tab\fP=\fBfname\fP option can be convenient e\&.g\&. if you split a BLAST job over multiple machines and want to apply mcxdeblast to each of the subresults\&. You do this by generating a single central tab file in advance\&. Then provide each instance of mcxdeblast with this tab file\&. Each instance will generate a \fCraw\fP file\&. The respective \fCraw\fP files can simply be concatenated and fed to mcxassemble using its \fB-raw\fP option\&. Additionally, a \fChdr\fP file has to be specified for mcxassemble using its \fB-hdr\fP option\&. The syntax of \fChdr\fP files is described in the \fBmcxassemble\fP manual\&. Currently there is usually only one variable in the \fChdr\fP file, which is the number of bindings listed in the tab file\&. This number, in turn, should equal the total number of different peptides encountered in the BLAST input\&. .SH OPTIONS .ZI 2m "\fB--tab\fP= (\fItab file\fP)" \& .br Specify a tab file to use, rather than automatically generating one\&. .in -2m .ZI 2m "\fB--out\fP (\fIoutput file\fP)" \& .br Specify the name for the output file\&. .in -2m .ZI 2m "\fB--score\fP= (\fIbit scores|e-values|norm bit score\fP)" \& .br Specify whether to use bit scores, E-values, or bit scores normalized by length of the HSP\&. .in -2m .ZI 2m "\fB--sort\fP= (\fIalphabetic|occurrence sorting\fP)" \& .br Specify how to sort labels\&. .in -2m .ZI 2m "\fB--m9\fP (\fIexpect BLAST column format\fP)" \& .br Use this option to parse BLAST output formatted with the -m 9 option\&. .in -2m .ZI 2m "\fB--line-mode\fP=abc (\fIwrite ID1 ID2 SCORE format\fP)" \& .br Use this to stream output directly into mcl\&. Here \fCabc\fP is a literal; \fB--line-mode\fP may acquire other line output modes\&. .in -2m .ZI 2m "\fB--xi-dat\fP= (\fIstrip from \fP)" \& .br If set, the suffix is stripped from file-name in order to obtain the base name for output\&. If does not end with suffix, it is assumed to be the base name, and is added in order to obtain the (real) file-name\&. .in -2m .ZI 2m "\fB--xo-dat\fP= (\fIadd to base name\fP)" \& .br Attaches the suffix to the base name\&. Use this to distinguish between different parses\&. One might for example use \fB--score\fP=\fIb\fP \fB--bcut\fP=\fI5\fP \fB--xo-dat\fP=\fIb\fP\&. .in -2m .ZI 2m "\fB--bcut\fP= (\fIbit score cutoff\fP)" \& .br Bit scores below the cutoff value are ignored\&. This triggers the output of bit scores and ignores all other values\&. .in -2m .ZI 2m "\fB--ecut\fP= (\fIE-value cutoff\fP)" \& .br E-values below the cutoff value are ignored\&. This triggers the output of E-values and ignores all other values\&. .in -2m .ZI 2m "\fB--rcut\fP= (\fIraw value cutoff\fP)" \& .br Raw values below the cutoff value are ignored\&. This triggers the output of raw values and ignores all other values\&. .in -2m .SH AUTHOR Stijn van Dongen\&. Jason Stajich implemented the \fB--m9\fP option\&. Abel Ureta-Vidal and Dinakarpandian Deendayal contributed helpful comments and fixes\&. .SH SEE ALSO \fBmclblastline\fP, \fBmcxassemble\fP, \fBmcl\fP, \fBclmformat\fP\&.