SJShaw

#!/bin/bash
#
# Requires JQ, on debian/ubuntu derivatives, this can be installed with "apt install jq"
#
# Either provide an antiSMASH JSON results file as the argument or pipe it in
jq -r '.records[].areas[] | [.start, .end, (.products | join(","))] | flatten | @tsv' "$@"

SJShaw

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

from Bio.SeqFeature import FeatureLocation, CompoundLocation
from Bio.Seq import Seq
from helperlibs.bio import seqio


def split_location_on_cut(location, cut_point):

SJShaw

#!/usr/bin/env python

import json
import os
import sys

from mibig_html.common.secmet import Record


def check(json_file, gbk_dir):

SJShaw

#!/bin/bash
for line in `git diff --cached --name-only --diff-filter=ACM | grep -v retired | grep -e json`; do
  if [[ "$line" != *.json ]] ; then
    continue
  fi
  test `tail -c 1 $line`
  if [ "$?" == "1" ] ; then
    truncate -s -1 $line
    echo "Aborting commit due to trailing newline; add changes and recommit"
    exit 1

SJShaw

#!/usr/bin/env python

"""
Removes specific module(s) results from antiSMASH results JSON 

Modules are expected to be named as per a python `__name__` result,
e.g. "antismash.modules.clusterblast"
"""

SJShaw

#!/usr/bin/env python

import argparse


class Item:
    def __init__(self, name, depth):
        self.name = name
        self.depth = depth
        self.children = []

SJShaw

#!/usr/bin/env python3

import argparse
import os
import sys
from typing import IO


def _main(accession: str, source: IO, destination: IO) -> int:
    if not accession:

SJShaw

#!/usr/bin/env python3

import json
import sys


def merge(inputs):
    """ Merges the data in the given input handles and returns the result """
    assert len(inputs) > 1
    record_ids = set()

SJShaw

#!/usr/bin/env python

from __future__ import print_function, division

import sys

from helperlibs.bio import seqio

def strip_record(seq_record):
    new_features = []

SJShaw

#!/bin/bash

echo "Checking for blockers..."
for line in `git diff --cached --name-only --diff-filter=ACM | grep [.]py$`; do
  grep -i "do not commit" $line > /dev/null 2>&1
  if [ "$?" == "0" ] ; then
    echo "Aborting commit due to 'do not commit' entry in file $line"
    exit 1
  fi
done