Command line interface

Simple pretty-printing of sequences on the command line is done with the monoseq command. It reads one or more sequences from a file or from standard input and pretty-prints them to standard output. The input can be a raw sequence, or any number of sequences in FASTA format.

Example:

martijn@hue:~$ S=MIMANQPLWLDSEVEMNHYQQSHIKSKSPYFPEDKHICWIKIFKAFGT
martijn@hue:~$ echo $S$S$S$S | monoseq
  1  MIMANQPLWL DSEVEMNHYQ QSHIKSKSPY FPEDKHICWI KIFKAFGTMI MANQPLWLDS
 61  EVEMNHYQQS HIKSKSPYFP EDKHICWIKI FKAFGTMIMA NQPLWLDSEV EMNHYQQSHI
121  KSKSPYFPED KHICWIKIFK AFGTMIMANQ PLWLDSEVEM NHYQQSHIKS KSPYFPEDKH
181  ICWIKIFKAF GT

Formatting options

The number of letters per block can be specified with the -b argument and the -l argument sets the number of blocks per line.

Annotations

Subsequences can be specified for annotation with the -a argument followed by the first and the last position of the subsequence, both one-based. For example, to annotate the first 10 bases and the 17th base, you would add -a 1 10 -a 17 17.

In addition, annotation is read from the BED track specified with the -e argument. If the input is a raw sequence, only the first chromosome is used from the BED track. If the input is a FASTA file, chromosomes are matched with record names.

More information

Use the --help argument for more information.