comparison util/subtools.py @ 7:5d5fdcb798da draft

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 12fb52d5b285935b2353d93a5aa291838df7893e

6:237707a6b74d

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:

    track_json = json.dumps(track_json)
    new_track = subprocess.Popen(['echo', track_json], stdout=subprocess.PIPE)
    p = subprocess.call(['add-track-json.pl', trackList], stdin=new_track.stdout)
    return p

def prepare_refseqs(fasta_file_name, outputFolder):
    array_call = ['prepare-refseqs.pl', '--fasta', fasta_file_name, '--out', outputFolder]
    p = _handleExceptionAndCheckCall(array_call)
    return p       

def generate_names(outputFolder):
    array_call = ['generate-names.pl', '-v', '--out', outputFolder]
    p = _handleExceptionAndCheckCall(array_call)
    return p  
   
def validateFiles(input_file, chrom_sizes_file_name, file_type, options=None):
    """

7:5d5fdcb798da

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 generate_indexed_refseq_track(fastaFile, referenceName, outputFolder):
    faiFile = createFastaIndex(fastaFile)
    refSeqFile = os.path.join(outputFolder, referenceName)
    refSeqIndexFile = os.path.join(outputFolder, referenceName+'.fai')
    shutil.copy(fastaFile, refSeqFile)
    shutil.copy(faiFile, refSeqIndexFile)

def remove_gene_lines(gff3_file, gff3_filtered):
    with open(gff3_file, 'r') as f:
        with open(gff3_filtered, 'w') as out:
            for line in f:
                if not line.startswith('#'):
                    feature_type = line.split('\t')[2].rstrip()
                    if feature_type == 'transcript' or feature_type == 'mRNA':
                        arr = line.split('\t')
                        # as we remove the gene features, we should also remove the Parent attribute (gene id) from the transcript
                        arr[8] = ';'.join([item for item in arr[8].split(';') if 'Parent=' not in item]).rstrip()
                        line = '\t'.join(arr) + '\n'
                    if feature_type == 'gene':
                        continue
                out.write(line)

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

def bedSort(inputFile, outputFile):
    array_call = ['sort', '-k1,1', '-k2,2n', '-k6,6', inputFile]
    p = _handleExceptionAndCheckCall(array_call, stdout=outputFile)
    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, trackName, outputFolder):
    if "bed" in dataType:
        fileType = 'bed'
        sortedFile = tempfile.NamedTemporaryFile(bufsize=0)
        bedSort(inputFile, sortedFile)
    elif "gff" in dataType:
        fileType = 'gff'
        filteredFile = tempfile.NamedTemporaryFile(bufsize=0)
        remove_gene_lines(inputFile, filteredFile.name)
        sortedFile = tempfile.NamedTemporaryFile(bufsize=0)
        gff3sort(filteredFile.name, sortedFile)
        # add .gff3.gz extension to Tabix GFF3 files, in order to enable creating name index with generate-names.pl
        trackName = trackName + '.gff3.gz'
    compressedFile = bgzip(sortedFile.name)
    tabixFile = createTabix(compressedFile, fileType)
    trackPath = os.path.join(outputFolder, trackName)
    trackIndexPath = os.path.join(outputFolder, trackName+'.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:

    track_json = json.dumps(track_json)
    new_track = subprocess.Popen(['echo', track_json], stdout=subprocess.PIPE)
    p = subprocess.call(['add-track-json.pl', trackList], stdin=new_track.stdout)
    return p

def prepare_refseqs(fastaFile, outputFolder):
    #array_call = ['prepare-refseqs.pl', '--fasta', fasta_file_name, '--out', outputFolder]
    createFastaIndex(fastaFile)
    array_call = ['prepare-refseqs.pl', '--indexed_fasta', fastaFile, '--out', outputFolder]
    p = _handleExceptionAndCheckCall(array_call)
    return p       

def generate_names(outputFolder, hashBits=4):
    array_call = ['generate-names.pl', '--hashBits', '4', '-v', '--out', outputFolder]
    p = _handleExceptionAndCheckCall(array_call)
    return p  
   
def validateFiles(input_file, chrom_sizes_file_name, file_type, options=None):
    """