view utils.py @ 5:e7c80e9b70ae draft

planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit f18ea51d27ec7addfa6413716391cfefebc8acbc-dirty

#!/usr/bin/env python

'''
This file include common used functions for converting file format to gff3
'''
from collections import OrderedDict
import json
import subprocess
import os
import tempfile


def write_features(field, attribute, gff3):
    '''
    The function write the features to gff3 format (defined in https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md)
    field, attribute are ordered dictionary 
    gff3 is the file handler
    '''
    attr = []
    for v in field.values():
        gff3.write(str(v) + '\t')
    for k, v in attribute.items():
        s = str(k) + '=' + str(v)
        attr.append(s)
    gff3.write(';'.join(attr))
    gff3.write('\n')

def getChromSizes(reference, tool_dir):
    #TODO: find a better way instead of shipping the two exec files with the tool
    faToTwoBit = os.path.join(tool_dir, 'faToTwoBit')
    twoBitInfo = os.path.join(tool_dir, 'twoBitInfo')
    try:
        twoBitFile = tempfile.NamedTemporaryFile(bufsize=0)
        chrom_sizes = tempfile.NamedTemporaryFile(bufsize=0, suffix='.chrom.sizes', delete=False)
    except IOError as err:
        print "Cannot create tempfile err({0}): {1}".format(err.errno, err.strerror)
    try:
        p = subprocess.Popen(['faToTwoBit', reference, twoBitFile.name])
        p.communicate()
    except OSError as err:
        print "Cannot generate twoBitFile from faToTwoBit err({0}): {1}".format(err.errno, err.strerror)
    try:
        p = subprocess.Popen(['twoBitInfo', twoBitFile.name, chrom_sizes.name])
        p.communicate()
    except OSError as err:
        print "Cannot generate chrom_sizes from twoBitInfo err({0}): {1}".format(err.errno, err.strerror)
    return chrom_sizes

def sequence_region(chrom_sizes):
    '''
    This function read from a chromatin size file generated by twoBitInfo and write the information to dict
    return a dict
    '''
    f = open(chrom_sizes, 'r')
    sizes = f.readlines()
    sizes_dict = {}
    for line in sizes:
        chrom_info = line.rstrip().split('\t')
        sizes_dict[chrom_info[0]] = chrom_info[1]
    return sizes_dict

def child_blocks(parent_field, parent_attr, gff3):
    num = 0
    blockcount = int(parent_attr['blockcount'])
    chromstart = parent_attr['chromstarts'].split(',')
    blocksize = parent_attr['blocksizes'].split(',')
    while num < blockcount:
        child_attr = OrderedDict()
        child_field = parent_field
        child_field['type'] = 'exon_junction'
        child_field['start'] = int(chromstart[num]) + int(parent_field['start'])
        child_field['end'] = int(child_field['start']) + int(blocksize[num]) - 1
        child_attr['ID'] = parent_attr['ID'] + '_exon_' + str(num+1)
        child_attr['Parent'] = parent_attr['ID']
        write_features(child_field, child_attr, gff3)
        num = num + 1

def add_tracks_to_json(trackList_json, new_tracks, modify_type):
    '''
    Add to track configuration (trackList.json)
    # modify_type =  'add_tracks': add a new track like bam or bigwig, new_track = dict()
    # modify_type = 'add_attr': add configuration to the existing track, new_track = dict(track_name: dict())
    '''
    with open(trackList_json, 'r+') as f:
        data = json.load(f)
        if modify_type == 'add_tracks':
            data['tracks'].append(new_tracks)
        elif modify_type == 'add_attr':
            for k in new_tracks:
                for track in data['tracks']:
                    if k.lower() in track['urlTemplate'].lower():
                        attr = new_tracks[k]
                        for k, v in attr.items():
                            track[k] = v
        f.seek(0, 0)
        f.write(json.dumps(data, separators=(',' , ':'), indent=4))
        f.truncate()
        f.close()

def gtfToGff3(gtf_file, gff3_file, chrom_sizes):
    '''
    Covert gtf file output from StringTie to gff3 format
    '''
    gff3 = open(gff3_file, 'w')
    gff3.write("##gff-version 3\n")
    sizes_dict = sequence_region(chrom_sizes)
    seq_regions = dict()
    parents = dict()
    with open(gtf_file, 'r') as gtf:
        for line in gtf:
            if line.startswith('#'):
                continue
            field = OrderedDict()
            attribute = OrderedDict()
            li = line.rstrip().split("\t")
            #print li
            field['seqid'] = li[0]
            #print field['seqid']
            if field['seqid'] not in seq_regions:
                end_region = sizes_dict[field['seqid']]
                gff3.write("##sequence-region " + field['seqid'] + ' 1 ' + str(end_region) + '\n')
                seq_regions[field['seqid']] = end_region
            field['source'] = li[1]
            field['type'] = li[2]
                # The first base in a chromosome is numbered 0 in BED format
            field['start'] = li[3]
            field['end'] = li[4]
            field['score'] = li[5]
            field['strand'] = li[6]
            field['phase'] = li[7]
            attr_li = li[8].split(';')
            gene_id = attr_li[0].split()[1].strip('"')
            attribute['ID'] = gene_id + '_' + field['type'] + '_' + str(field['start']) + '_' + str(field['end'])
            if field['type'] == 'transcript':
                parents[gene_id] = attribute['ID']
                attribute['transcript_id'] = attr_li[1].split()[1].strip('"')
                attribute['coverage'] = attr_li[2].split()[1].strip('"')
                attribute['fpkm'] = attr_li[3].split()[1].strip('"')
                attribute['tpm'] = attr_li[4].split()[1].strip('"')
            elif field['type'] == 'exon':
                attribute['Parent'] = parents[gene_id]
                attribute['transcript_id'] = attr_li[1].split()[1].strip('"')
                attribute['coverage'] = attr_li[3].split()[1].strip('"')
            write_features(field, attribute, gff3)
    gff3.close()

def sanitize_name_path(input_path):
    '''
    Galaxy will name all the files and dirs as *.dat, 
    the function is simply replacing '.' to '_' for the dirs
    '''
    return input_path.replace('.', '_')