---
name: "mclblastline"
section: "1"
platform: "linux"
package: "mcl"
version: "1:14-137+ds-9+b1"
release: "Debian 11 (Bullseye)"
platforms: ["linux"]
url: "https://new.carta.tech/mclblastline"
---

# mclblastline(1)

mclblastline - a pipeline for clustering from BLAST files. **mclblastline** file-name

**mclblastline** \[deblast options\] \[pipeline options\] file-name

**NOTE**\
 **mcl** has acquired the ability to proceed from label input as produced by **mcxdeblast**. This enables a very lightweight mechanism of generating clusterings from BLAST files. You might want to use this mechanism, documented in the **mcl manual**.

**NOTE**\
 mclblastline used to require (given default parameters) the presence of the **zoem** 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 *will* be invoked when the --fmt-fancy option is supplied. In that case, zoem obviously has to be installed. **mclblastline** wraps around **mclpipeline**. It supplies the **--parser**=*app* and **--parser-tag**=*str* options, setting them respectively to *mcxdeblast* and *blast*. This tells **mclpipeline** to use **mcxdeblast** as the parse script in its pipeline. The significance of the *blast* 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 **--score**=*x* option. When using mclblastline, you specify it as **--blast-score**=*x*. There are two exceptions to this rule, namely the **--xi-dat**=*str* and **--xo-dat**=*str* options. Refer to the **mclpipeline** manual for more information.

Additionally, all mclpipeline options are acceptable to **mcxdeblast** as well. The **--whatif** is useful for getting a feel for the pipeline. The **--mcl-I**=*f* inflation option and **--mcl-scheme**=*i* scheme index options are your basic means for respectively manipulating cluster granularity and allocating resources. Read the **mcl** manual entries for a description of the corresponding **-I** and **-scheme** mcl options.

The best advice is to glance over the **mcxdeblast** and **mclpipeline** options in order to get a feeling for which of those may come in handy for you. Then start experimenting. Use the **--whatif** option, it will tell you what would happen without actually doing it. All **mcxdeblast** and **mclpipeline** options. mcxdeblast options must be passed using the mechanism described above.

```
   mclblastline --blast-score=b
      --blast-sort=a --blast-bcut=5 --mcl-I=2.5 myblastfile
```

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 `myblastfile.I25s2` (I25 identifying the inflation value and s2 identifying the resource scheme) and the formatted output will be in the file `myblastfile.I25s2.fmt`.

```
   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 ..
```

The first run prepares an input matrix to be read by **mcl**. In this case its file will be named `myblastfile.sym`. The subsequent runs use this matrix. **CAVEAT** there are some options that you need to repeat when executing such a resumed run. They are clearly marked in the **mclpipeline** manual - namely those options that affect names of (intermediate) files. Most importantly, this concerns the mclpipeline options that have prefix **--xo** or **--xi**. For example,

```
   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 ..
```

In this case, the matrix file will be named `myblastfile.b.sym`, and the **--xo-dat** options must be repeated in all runs so that the pipeline reconstructs the correct file name(s).

Stijn van Dongen

**mcxdeblast**, **mclpipeline**, **mcxassemble**.