finswimmer

from BCBio import GFF

in_file = "test.gff"
out_file = "test.parse.gff3"
limit_info = {
        'gff_id': ["1"], # chromosome 1
        'gff_type': ["ncRNA"] # get non coding RNA
    }

with open(out_file, "w") as out_handle, open(in_file) as in_handle:

finswimmer

import gzip

reads = 0
bases = 0

with gzip.open('your.fastq.gz', 'rb') as read:
    for id in read:
        seq = next(read)
        reads += 1
        bases += len(seq.strip())

finswimmer

import requests
import sys
import argparse


def set_args():
    parser = argparse.ArgumentParser()
    group = parser.add_mutually_exclusive_group()
    group.add_argument("-t", "--transcript", help="ensembl's transcript id")
    group.add_argument("-l", "--list", help="file which contains list of transcript id's")

finswimmer

import sys
from pysam import VariantFile

vcf_in = VariantFile(sys.argv[1])

print(str(vcf_in.header).strip())

for rec in vcf_in:
    for key, value in rec.info.items():
        if vcf_in.header.info[key].number not in ("A", "R", "G", ".", "0"):

finswimmer

import sys


def replace(text, replacement):
    new = ''

    for c in text:
        try:
            new += replacement[c]
        except KeyError:

finswimmer

import glob
import sys
import pandas


def read_filenames(names):
    for arg in names:
        if "*" in arg:
            for file in glob.glob(arg):
                yield file

finswimmer

import sys

with open(sys.argv[1], "r") as gtf:
    header = next(gtf)
    last_gene = {
        "gene": None,
        "chr": None,
        "end": None,
    }

finswimmer

import sys
from Bio import SeqIO


def mismatch(seq1, seq2):
    index = []

    for i, (s1, s2) in enumerate(zip(seq1, seq2)):
        if s1 != s2:
            index.append(i)

finswimmer

import sys
from Bio import SeqIO


def mismatch(seq1, seq2):
    index = []

    for i, (s1, s2) in enumerate(zip(seq1, seq2)):
        if s1 != s2:
            index.append(i)

finswimmer

ENSPFO	Poecilia formosa (Amazon molly)
ENSJJA	Jaculus jaculus (Lesser Egyptian jerboa)
ENSPCO	Propithecus coquereli (Coquerel's sifaka)
ENSNGA	Nannospalax galili (Upper Galilee mountains blind mole rat)
ENSMFA	Macaca fascicularis (Crab-eating macaque)
ENSMIC	Microcebus murinus (Mouse Lemur)
MGP_CAROLIEiJ_	Mus caroli (Ryukyu mouse)
ENSFAL	Ficedula albicollis (Flycatcher)
ENSCLA	Chinchilla lanigera (Long-tailed chinchilla)
ENSPEM	Peromyscus maniculatus bairdii (Northern American deer mouse)