Fast Fasta TUI viewer

fasview.py

#!/usr/bin/env python3
import os
import statistics
import sys

from Bio import SeqIO

term_width = os.get_terminal_size().columns
term_height = os.get_terminal_size().lines
id_width = 15
default_color = "\033[0m"
bold_color = "\033[1m"
underline_color = "\033[4m"
orange_color = "\033[33m"
sep = " ... "


def gc(x):
    """Compute GC content."""
    val = sum([x.seq.count(k) for k in ["g", "c"]]) / len(x.seq) * 100
    return val


def process(file):
    records = list(SeqIO.parse(file, "fasta"))
    nr = len(records)
    avg_len = round(statistics.mean([len(r.seq) for r in records]), 1)
    avg_gc = round(statistics.mean([gc(r) for r in records]), 1)
    trunc = False

    if nr > term_height - 2:
        records = (
            records[: int((term_height - 1) / 2)]
            + records[-(int((term_height - 1) / 2)) :]
        )
        trunc = True
        nr_trunc = len(records)

    opt = "(" + str(nr_trunc) + " displayed) " if trunc else ""
    header = (
        underline_color
        + str(nr)
        + " seq. "
        + opt
        + "avg length: "
        + str(avg_len)
        + " GC: "
        + str(avg_gc)
        + "%"
        + default_color
    )
    print(header)
    for r in records:
        if len(str(r.id)) < id_width:
            id = str(r.id).ljust(id_width)
        else:
            id = str(r.id)[: id_width - 1].ljust(id_width)
        seq = str(r.seq).lower()
        seq_width = int((term_width - id_width - len(sep)) / 2)
        lineout = (
            bold_color + id + default_color + seq[:seq_width] + sep + seq[-seq_width:]
        )
        print(lineout)


if __name__ == "__main__":
    process(sys.argv[1])

Homemade previewer for Fasta files (require Biopython). There are better alternatives.

Preview:

~ % fasview tmp/aa.fasta                                                                                                                                                                                   
7 seq. avg length: 514.7 GC: 0.0%
S_Podospora_an agggatcattaaagagttgcaagactcccacaaaccatcgcgaaccgaacccctgagcagttgcttcggcgggccggccccccaccgcggggcg ... tcacctcgctgcggagtggcgcgggcgcctgccgtgaaacccccgacccccaaaggttgacctcggatcaggtaggaatacccgctgaacttaa
CBS112042_Podo agggatcattaaagagttgcaagactcccacaaaccatcgcgaaccgaacccctgagcagttgcttcggcgggccggccccccaccgcggggcg ... tcacctcgctgcggagtggcgcgggcgcctgccgtgaaacccccgacccccaaaggttgacctcggatcaggtaggaatacccgctgaacttaa
T_Podospora_co agggatcattaaagagttgcaaaactcccacaaaccatcgcgaaccaaacccctgagcagttgcttcggcgggccggccccccaccgcggggcg ... acctcgctgcggagtggcgcgggcgcctgccgtgaaacccccgacccccccaaaggttgacctcggatcaggtaggaatacccgctgaacttaa
CBS411.78_Podo agggatcattaaagagttgcaagactcccacaaaccatcgcgaaccgaacccctgagcagttgcttcggcgggccggccccccaccgcggggcg ... tcacctcgctgcggagtggcgcgggcgcctgccgtgaaacccccgaccaccaaaggttgacctcggatcaggtaggaatacccgctgaacttaa
CBS237-71_Podo agggatcattaaagagttgcaagactcccacaaaccatcgcgaaccgaacccctgagcagttgcttcggcgggccggccccccaccgcggggcg ... tcacctcgctgcggagtggcgcgggcgcctgccgtgaaacccccgacccccaaaggttgacctcggatcaggtaggaatacccgctgaacttaa
CBS253.71_Podo agggatcattaaagagttgcaagactcccacaaaccatcgcgaaccgaacccctgagcagttgcttcggcgggccggccccccaccgcggggcg ... tcacctcgctgcggagtggcgcgggcgcctgccgtgaaacccccgaccaccaaaggttgacctcggatcaggtaggaatacccgctgaacttaa
CBS415.72_Podo agggatcattaaagagttgcaagactcccacaaaccatcgcgaaccgaacccctgagcagttgcttcggcgggccggccccccaccgcggggcg ... cacctcgctgcggagtggcgcgggcgcctgccgtgaaacccccgaccccccaaaggttgacctcggatcaggtaggaatacccgctgaacttaa
~

(Bold syntax and underline rendered in terminal only.)