Seq-view

Visualizing your Sequences on the Terminal with color

Attention: biopython is prerequisite before you run this script

1. Quick Start

2. Aligned fasta

3. Fastq

Quick start

Normal view:

Python3.7 Seq-view1.3 -i Example1.fa

Update

This script can automatically distinguish the fasta and fastq file by simply using the command above. And when all sequences in a fasta file share equal number of length, it can add '-a' automatically.

Aligned fasta:

Python3.7 Seq-view1.3 -i Example2.fa

It will show like:

If you still want the colorful output, you can add a -c C like that:

Seq-view1.3 -i Example3.fq  -f fastq -r 1,2000  -a 200 -c C

Extra:

you can also print the Seq from 45 to 50:

Python3.7 Seq-view1.3 -i Example2.fa -r 45,50
#or
Python3.7 Seq-view1.3 -i Example2.fa  -r 4,5

You can also change the base number per line during the print when you print "aligned Seq":

Python3.7 Seq-view1.3 -i Example2.fa -a 200 -r 4,5

For fastq visulization

There have 3 functions for the fastq view:

1: print the fastq with Seq and scores (normal view):

Seq-view1.2 -i Example3.fq  -f fastq -r 1,2000

2: Print the aligned the sequences only, so that it is easy to show the adapter on the head or tail of the Seq:

Seq-view1.2 -i Example3.fq  -f fastq -r 1,2000  -a 200

3: Print the score of the Sequence only (So, you can view the score of the whole seq directly. and the score of the base which lower than 22 will be marked with the red background):

Seq-view1.2 -i Example3.fq  -f fastq -r 1,2000  -fq s