import logging
import os
import pysam
import subprocess
class AnnotationError(Exception):
pass
def ensureIndexed(bedPath, preset="bed", trySorting=True):
if not bedPath.endswith(".gz"):
if not os.path.exists(bedPath+".gz"):
logging.info("bgzf compressing {}".format(bedPath))
pysam.tabix_compress(bedPath, bedPath+".gz")
if not os.path.exists(bedPath+".gz"):
raise Exception("Failed to create compress {preset} file for {file}; make sure the {preset} file is "
"sorted and the directory is writeable".format(preset=preset, file=bedPath))
bedPath += ".gz"
if not os.path.exists(bedPath+".tbi"):
logging.info("creating tabix index for {}".format(bedPath))
pysam.tabix_index(bedPath, preset=preset)
if not os.path.exists(bedPath+".tbi"):
raise Exception("Failed to create tabix index file for {file}; make sure the {preset} file is "
"sorted and the directory is writeable".format(preset=preset, file=bedPath))
line = next(pysam.Tabixfile(bedPath).fetch())
if len(line.strip().split("\t")) < 6 and preset == "bed":
raise AnnotationError("BED files need to have at least 6 (tab-delimited) fields (including "
"chrom, start, end, name, score, strand; score is unused)")
if len(line.strip().split("\t")) < 9 and preset == "gff":
raise AnnotationError("GFF/GTF files need to have at least 9 tab-delimited fields")
return bedPath
# def sortFile(uncompressedPath, preset):
# if preset == "bed":
# fields = {"chrom":0, "start":1, "end":2}
# elif preset == "gff":
# fields = {"chrom":0, "start":3, "end":4}
# sortCommand = "sort -k{chrom}V -k{start}n -k{end}n".format(**fields)
# tabixCommand = "{sort} {path} | bgzip > {path}.gz".format(sort=sortCommand, path=uncompressedPath)
# logging.info("Trying to sort input annotation file with command:")
# logging.info(" {}".format(tabixCommand))
# subprocess.check_call(tabixCommand, shell=True)
