--- name: "mcxdeblast" section: "1" platform: "linux" package: "mcl" version: "1:14-137+ds-9+b1" release: "Debian 11 (Bullseye)" platforms: ["linux"] url: "https://new.carta.tech/mcxdeblast" --- # mcxdeblast(1) mcxdeblast - parse BLAST files and stream output directly into mcl or write mcxassemble input. **mcxdeblast** file-name **mcxdeblast** **\[--score=**\ (*bit scores\|e-values\|normalize bit score*)**\]** **\[--m9** (*expect BLAST column format*)**\]** **\[--out** \ (*output file*)**\]** **\[--line-mode** abc (*write ID1 ID2 score format*)**\]** **\[--sort=**\ (*alphabetic\|occurrence sorting*)**\]** **\[--xi-dat=**\ (*strip \ from file-name*)**\]** **\[--xo-dat=**\ (*add \ to base name*)**\]** **\[--bcut=**\ (*bit score cutoff*)**\]** **\[--ecut=**\ (*E-value cutoff*)**\]** **\[--rcut=**\ (*raw value cutoff*)**\]** **\[--tab=**\ (*tab file*)**\]** \ **mcxdeblast** parses BLAST files. In *stream mode* mcxdeblast output can be directly streamed to mcl by using the mcxdeblast **--line-mode**=*abc* option and equipping mcl with either **--abc** or **--expect-abc**. 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 *assemble mode*, 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 **mclblastline**. Enter stream mode by specifying **--line-mode**=*abc*. Use **--m9** if the input is in columnar output. Pipe the result to a file or directly to mcl. Example invocations can be found in **the mcl manual**. If the input file is named `iput`, mcxdeblast will by default create files `iput.hdr`, `iput.raw`, `iput.tab`, `iput.map`, and `iput.err`. The `hdr` file contains information about the number of nodes found. It will be read by **mcxassemble**. The `raw` 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 `tab` 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 **mcxassemble** for the syntax of a tab file. The `err` file contains a list of any errors encountered. If the **--tab**=**fname** option is used mcxdeblast changes its behaviour. It will read the file **fname**, and use the bindings found therein. It will no longer output any of the `hdr`, `map`, or `tab` files. The `hdr` file should be provided by the same application that generated the specified tab file, and the `map` file should no longer be necessary (it might be convenient though and perhaps the future will bring a new **--map** option). The **--tab**=**fname** 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 `raw` file. The respective `raw` files can simply be concatenated and fed to mcxassemble using its **-raw** option. Additionally, a `hdr` file has to be specified for mcxassemble using its **-hdr** option. The syntax of `hdr` files is described in the **mcxassemble** manual. Currently there is usually only one variable in the `hdr` 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. **--tab**=\ (*tab file*)\ Specify a tab file to use, rather than automatically generating one. **--out** \ (*output file*)\ Specify the name for the output file. **--score**=\ (*bit scores\|e-values\|norm bit score*)\ Specify whether to use bit scores, E-values, or bit scores normalized by length of the HSP. **--sort**=\ (*alphabetic\|occurrence sorting*)\ Specify how to sort labels. **--m9** (*expect BLAST column format*)\ Use this option to parse BLAST output formatted with the -m 9 option. **--line-mode**=abc (*write ID1 ID2 SCORE format*)\ Use this to stream output directly into mcl. Here `abc` is a literal; **--line-mode** may acquire other line output modes. **--xi-dat**=\ (*strip \ from \*)\ 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. **--xo-dat**=\ (*add \ to base name*)\ Attaches the suffix to the base name. Use this to distinguish between different parses. One might for example use **--score**=*b* **--bcut**=*5* **--xo-dat**=*b*. **--bcut**=\ (*bit score cutoff*)\ Bit scores below the cutoff value are ignored. This triggers the output of bit scores and ignores all other values. **--ecut**=\ (*E-value cutoff*)\ E-values below the cutoff value are ignored. This triggers the output of E-values and ignores all other values. **--rcut**=\ (*raw value cutoff*)\ Raw values below the cutoff value are ignored. This triggers the output of raw values and ignores all other values. Stijn van Dongen. Jason Stajich implemented the **--m9** option. Abel Ureta-Vidal and Dinakarpandian Deendayal contributed helpful comments and fixes. **mclblastline**, **mcxassemble**, **mcl**, **clmformat**.