comparison cherry_pick_fasta.py @ 6:d8fa616a228a draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cherry_pick_fasta commit 8384f1bb5378232bbe78319e06a3522674c7c1fe"

5:144b856e926c

#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Chery pick of fasta sequences satisfying a query string in their header/name
import argparse

from Bio import SeqIO


def Parser():
    the_parser = argparse.ArgumentParser(
        description='Cherry pick fasta sequences')

        querylist.append(line.rstrip())
    return querylist


def buid_fasta_dict(fasta):
    seq_dict = {rec.id: rec.seq for rec in SeqIO.parse(fasta, "fasta")}
    return seq_dict


def write_fasta_result(fasta_dict, file):
    line_length = 60

6:d8fa616a228a

import argparse


def Parser():
    the_parser = argparse.ArgumentParser(
        description='Cherry pick fasta sequences')

        querylist.append(line.rstrip())
    return querylist


def buid_fasta_dict(fasta):
    seq_dict = dict()
    f = open(fasta, 'r')
    content = f.read()
    segmented_content = content.split('>')
    segmented_content = segmented_content[1:]
    for seq in segmented_content:
        sliced_seq = seq.split('\n')
        header = sliced_seq[0]
        sliced_seq = sliced_seq[1:]
        sequence = ''.join(sliced_seq)
        seq_dict[header] = sequence
    return seq_dict


def write_fasta_result(fasta_dict, file):
    line_length = 60