bluegenes

#! /usr/bin/env python
import os
import sys
import argparse
import screed

def make_outdir(output_dirname):
    if not os.path.exists(output_dirname):
        try:
            os.makedirs(output_dirname)

bluegenes

import os
import sys
import argparse
import glob
from shutil import copyfile


# requires python >= 3.6
# run: python copy_samplefiles.py haptophyta.txt --source ../../pep/ --destination ../../haptophyta_pep

bluegenes

#Author: Tessa Pierce

import argparse
import screed
import re

def extract_contigs(in_fasta, pattern, outF):
    if not outF:
        outF = in_fasta.split('.fa')[0] + '_' + pattern + '.fa'
    with screed.open(in_fasta) as seqF:

bluegenes

import os

from snakemake.remote import FTP
FTP = FTP.RemoteProvider()

data_dir='data_subset'

targets = []
with open('SRA_accessions.txt', 'r') as f:
    for line in f:

bluegenes

for f in *fq.gz; do
   echo 'starting on file' $f
   cp "$f" "$f~" &&
   gzip -cd "$f~" | sed 's/^@ERR\S*\s/@/' | gzip > "$f"
   rm "$f~"
done

bluegenes

###################################################################
"""Function: Take in a dammit gff3, dammit fasta, dammit namemap.
Output gff3 and fasta with trinity names.
by Dr. Tessa Pierce
"""
###################################################################

import sys
import os
import argparse

bluegenes

import os
import argparse
import screed

def generate_geneTransMap(fasta, geneTransMap, transGeneMap):
    if transGeneMap:
        outT = open(transGeneMap, "w")
    with open(geneTransMap, "w") as outG:
        with screed.open(fasta) as seqs:
            for read in seqs:

bluegenes

###################################################################
"""Function: Take in a list of trinity gene names, a dammit namemap,
and a dammit fasta file. Output fasta of matching dammit contigs.
"""
###################################################################

import sys
import os
import argparse
import screed