comparison util/subtools.py @ 38:d17f629f5486 draft

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit e4c1d387db160a3bf4a1e8abc288bdffbbbe2818-dirty

37:43909f065bee

import json
import subprocess
import os
import sys
import tempfile
import string
import logging

class PopenError(Exception):
    def __init__(self, cmd, error, return_code):
        self.cmd = cmd

    filename = bamfile + '.bai'
    if os.path.exists(filename):
        return filename
    else:
        raise ValueError('Did not find bai file')

def flatfile_to_json(inputFile, dataType, trackType, trackLabel, outputFolder, options=None, compress=True):
    if "bed" in dataType:
        fileType = "--bed"
    elif "gff" in dataType:

38:d17f629f5486

import json
import subprocess
import os
import sys
import tempfile
import shutil
import logging

class PopenError(Exception):
    def __init__(self, cmd, error, return_code):
        self.cmd = cmd

    filename = bamfile + '.bai'
    if os.path.exists(filename):
        return filename
    else:
        raise ValueError('Did not find bai file')

def createFastaIndex(fastaFile):
    subprocess.call(['samtools', 'faidx', fastaFile])
    filename = fastaFile + '.fai'
    if os.path.exists(filename):
        return filename
    else:
        raise ValueError('Did not find fai file')

def gff3sort(inputFile, outputFile, precise=False):
    array_call = ['gff3sort.pl', inputFile, '>', outputFile]
    if precise:
        array_call.append('--precise')
    p = _handleExceptionAndCheckCall(array_call)
    return p

def bedSort(inputFile, outputFile):
    array_call = ['sort', '-k1,1', '-k2,2n', '-k6,6', inputFile, '>', outputFile]
    p = _handleExceptionAndCheckCall(array_call)
    return p

def bgzip(inputFile):
    subprocess.call(['bgzip', inputFile])
    filename = inputFile + '.gz'
    if os.path.exists(filename):
        return filename
    else:
        raise ValueError('Did not find gz file')

def createTabix(inputFile, dataType):
    subprocess.call(['tabix', '-p', dataType, inputFile])
    filename = inputFile + '.tbi'
    if os.path.exists(filename):
        return filename
    else:
        raise ValueError('Did not find tbi file')

def generate_tabix_indexed_track(inputFile, dataType, outputFolder):
    if "bed" in dataType:
        fileType = 'bed'
        sortedFile = tempfile.NamedTemporaryFile(bufsize=0)
        bedSort(inputFile, sortedFile.name)
    elif "gff" in dataType:
        fileType = 'gff'
        sortedFile = tempfile.NamedTemporaryFile(bufsize=0)
        gff3sort(inputFile, sortedFile.name)
    compressedFile = bgzip(sortedFile)
    tabixFile = createTabix(compressedFile, fileType)
    trackPath = os.path.join(outputFolder, inputFile)
    trackIndexPath = os.path.join(outputFolder, inputFile+'.tbi')
    shutil.copy(compressedFile, trackPath)
    shutil.copy(tabixFile, trackIndexPath)

def flatfile_to_json(inputFile, dataType, trackType, trackLabel, outputFolder, options=None, compress=True):
    if "bed" in dataType:
        fileType = "--bed"
    elif "gff" in dataType: