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.
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
The number of letters per block can be specified with the
-b argument and
-l argument sets the number of blocks per line.
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
1 10 -a 17 17.
In addition, annotation is read from the BED track specified with the
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
--help argument for more information.