dpryan79

#include "htslib/sam.h"
#include "htslib/bgzf.h"
#include <stdlib.h>
#include <stdio.h>
#include <inttypes.h>
#include <string.h>

void process_alignment(bam1_t *b, bam_hdr_t *hdr, FILE *of, int length) {
    int32_t pos = b->core.pos, apos = 0;
    int i, j, op, op_len;

dpryan79

@HD	VN:1.0
@SQ	SN:1	LN:195471971
39V34V1:69:D265MACXX:3:1213:20484:44810	133	1	11042802	0	35M15S	=	11042802	0	CTCCCCCCTCCCCCCCCCCCCACCTCTTTGCCCTGGGGTCCCCCCTTTGT	<'7BBB############################################	XC:i:35

dpryan79

#!/usr/bin/env python
# This is just a quick hack and hasn't been tested, but it'll likely work
import pysam
import argparse
import gzip

def writeAlignment(of, al):
    name = al.query_name
    seq = al.query_sequence
    qual = al.query_qualities

dpryan79

#!/usr/bin/env python
e2g = []
e2u = []
g2e = []
g2u = []
u2e = []
u2g = []
ifile = open("GCA_000001405.22_GRCh38.p7_assembly_report.txt", "r")
for line in ifile:
    if line.startswith("#"):

dpryan79

#!/usr/bin/env python3
import urllib.request
import json
from subprocess import Popen
from time import sleep


def checkUp(path, timeout):
    p = Popen(['ls', path])
    try:

dpryan79

#!/usr/bin/env python
import deeptools.utilities
from deeptools import bamHandler
from deeptools import mapReduce
from deeptools import writeBedGraph
from deeptools import utilities
from deeptools.utilities import getCommonChrNames, toBytes

import sys
import shutil

dpryan79

#!/usr/bin/env python
import argparse
import numpy as np
import sys

from deeptools import parserCommon, bamHandler, utilities
from deeptools.mapReduce import mapReduce
from deeptools._version import __version__
import deeptools.config as cfg

dpryan79

#!/usr/bin/env python
import argparse
import pyBigWig

parser = argparse.ArgumentParser(description="Convert the chromosome names of a bigWig file.")
parser.add_argument("conv", metavar="conversion.txt", help="Text file with two columns, the first a chromosome name and the second the converted chromosome name.")
parser.add_argument("input", metavar="input.bigWig", help="Input bigWig file")
parser.add_argument("output", metavar="output.bigWig", help="Output bigWig file name")
args = parser.parse_args()

dpryan79

This demonstrates the issue discussed in https://bitbucket.org/snakemake/snakemake/issues/916/integrated-r-scripts-and-directory

To reproduce that and test any fixes, simply clone this github respository and chmod -R a-w it. Then go to a different directory and snakemake -s path/to/the/snakefile/here. With an unpatched copy of snakemake you'll get a permissions error. Note that the Snakefile has examples using R and Rmd files, so you'll need to ensure that R is in your PATH.

dpryan79

#!/usr/bin/env python
# This can take up to ~20 minutes and use up to ~2GB RAM for mammals
import argparse
import py2bit
from deeptoolsintervals import GTF, tree
from deeptoolsintervals.parse import openPossiblyCompressed, parseExonBounds, findRandomLabel

parser = argparse.ArgumentParser(description="Generate a blacklist file of polyX stretches of a given minimum length not within a specified distance of a TES")
parser.add_argument("--output", "-o", help="Output file", required=True)
parser.add_argument("--tb", help="2bit file", required=True)