Mercurial > repos > iuc > snpeff_datatypes
annotate snpeff.py @ 1:2b53f59de80c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/datatypes/snpeff_datatypes commit e511f2e85cd3d39f34fc0ed6e0ea5bc7b9a11e9e
| author | iuc |
|---|---|
| date | Thu, 14 Jan 2016 14:51:36 -0500 |
| parents | d78b2b2a3388 |
| children |
| rev | line source |
|---|---|
| 0 | 1 """ |
| 2 SnpEff datatypes | |
| 3 """ | |
| 4 import os,os.path,re,sys,gzip,logging | |
| 5 import galaxy.datatypes.data | |
| 6 from galaxy.datatypes.data import Text | |
| 7 from galaxy.datatypes.metadata import MetadataElement | |
| 8 | |
| 9 log = logging.getLogger(__name__) | |
| 10 | |
| 11 class SnpEffDb( Text ): | |
| 12 """Class describing a SnpEff genome build""" | |
| 13 file_ext = "snpeffdb" | |
| 14 MetadataElement( name="genome_version", default=None, desc="Genome Version", readonly=True, visible=True, no_value=None ) | |
| 15 MetadataElement( name="snpeff_version", default="SnpEff4.0", desc="SnpEff Version", readonly=True, visible=True, no_value=None ) | |
| 16 MetadataElement( name="regulation", default=[], desc="Regulation Names", readonly=True, visible=True, no_value=[], optional=True) | |
| 17 MetadataElement( name="annotation", default=[], desc="Annotation Names", readonly=True, visible=True, no_value=[], optional=True) | |
| 18 | |
| 19 def __init__( self, **kwd ): | |
| 20 Text.__init__( self, **kwd ) | |
| 21 | |
|
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2b53f59de80c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/datatypes/snpeff_datatypes commit e511f2e85cd3d39f34fc0ed6e0ea5bc7b9a11e9e
iuc
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0
diff
changeset
|
22 # The SnpEff version line was added in SnpEff version 4.1 |
| 0 | 23 def getSnpeffVersionFromFile(self, path): |
| 24 snpeff_version = None | |
| 25 try: | |
| 26 fh = gzip.open(path, 'rb') | |
| 27 buf = fh.read(100) | |
| 28 lines = buf.splitlines() | |
| 29 m = re.match('^(SnpEff)\s+(\d+\.\d+).*$',lines[0].strip()) | |
| 30 if m: | |
| 31 snpeff_version = m.groups()[0] + m.groups()[1] | |
| 32 fh.close() | |
| 33 except Exception, e: | |
| 34 pass | |
| 35 return snpeff_version | |
| 36 | |
| 37 def set_meta( self, dataset, **kwd ): | |
| 38 Text.set_meta(self, dataset, **kwd ) | |
| 39 data_dir = dataset.extra_files_path | |
| 40 ## search data_dir/genome_version for files | |
| 41 regulation_pattern = 'regulation_(.+).bin' | |
| 42 # annotation files that are included in snpEff by a flag | |
| 43 annotations_dict = {'nextProt.bin' : '-nextprot','motif.bin': '-motif'} | |
| 44 regulations = [] | |
| 45 annotations = [] | |
| 46 genome_version = None | |
| 47 snpeff_version = None | |
| 48 if data_dir and os.path.isdir(data_dir): | |
| 49 for root, dirs, files in os.walk(data_dir): | |
| 50 for fname in files: | |
| 51 if fname.startswith('snpEffectPredictor'): | |
| 52 # if snpEffectPredictor.bin download succeeded | |
| 53 genome_version = os.path.basename(root) | |
| 54 dataset.metadata.genome_version = genome_version | |
| 55 else: | |
| 56 m = re.match(regulation_pattern,fname) | |
| 57 if m: | |
| 58 name = m.groups()[0] | |
| 59 regulations.append(name) | |
| 60 elif fname in annotations_dict: | |
| 61 value = annotations_dict[fname] | |
| 62 name = value.lstrip('-') | |
| 63 annotations.append(name) | |
| 64 dataset.metadata.regulation = regulations | |
| 65 dataset.metadata.annotation = annotations | |
| 66 try: | |
| 67 fh = file(dataset.file_name,'w') | |
| 68 fh.write("%s\n" % genome_version if genome_version else 'Genome unknown') | |
| 69 fh.write("%s\n" % snpeff_version if snpeff_version else 'SnpEff version unknown') | |
| 70 if annotations: | |
| 71 fh.write("annotations: %s\n" % ','.join(annotations)) | |
| 72 if regulations: | |
| 73 fh.write("regulations: %s\n" % ','.join(regulations)) | |
| 74 fh.close() | |
| 75 except: | |
| 76 pass | |
| 77 |