def __main__():
#Parse Command Line
parser = optparse.OptionParser()
#I/O
parser.add_option( '-x', '--reference_xml', dest='reference_xml', help='Reference protein UniProt-XML file. Sequence variant peptide entries are appended to this database to generate the ouptut UniProt-XML protein database.' )
parser.add_option( '-p', '--protein_fasta', dest='protein_fasta', help='Reference protein FASTA file. Used to generate SAV peptide entries. If no UniProt-XML is specified, SAV and NSJ entries will be appended to this database to generate an output database. By default, this output will be a UniProt-XML protein database without PTM annotations. If --output-fasta is selected, the output will be a protein FASTA.')
parser.add_option( '-g', '--gene_model', dest='gene_model', default=None, help='GTF gene model file. Used to annotate NSJ peptide entries.')
parser.add_option( '-v', '--snpeff_vcf', dest='snpeff_vcf', help='SnpEff VCF file with HGVS annotations (else read from stdin).' )
parser.add_option( '-b', '--splice_bed', dest='splice_bed', help='BED file (tophat junctions.bed) with sequence column added.' )
parser.add_option( '-o', '--output', dest='output', help='Output file path. Outputs UniProt-XML format unless --output-fasta is selected.' )
parser.add_option( '-z', '--output_fasta', dest='output_fasta', action='store_true', default=False, help='Output a FASTA-format database. Place path for output file after the --output flag.')
#Peptide sequence construction
parser.add_option( '-l', '--leading_aa_num', dest='leading_aa_num', type='int', default=33, help='Leading number of AAs to output for SAV peptides. Default: 33.' )
parser.add_option( '-t', '--trailing_aa_num', dest='trailing_aa_num', type='int', default=33, help='Trailing number of AAs to output for SAV peptides. Default: 33.' )
#Filtering parameters
parser.add_option( '-D', '--nsj_depth_cutoff', dest='nsj_depth_cutoff', type='int', default=0, help='Keep only NSJs found with above this depth (BED score field). Default: 0.' )
parser.add_option( '-E', '--snv_depth_cutoff', dest='snv_depth_cutoff', type='int', default=0, help='Keep only SNVs found with above this depth (DP=# field). Default: 0.' )
parser.add_option( '-M', '--minimum_length', dest='minimum_length', type='int', default=0, help='Keep only sequence variant peptides with greater than or equal to this length. Default: 0.' )
#Simple entry
parser.add_option( '-Q', '--bed_score_name', dest='bed_score_name', default="depth", help='Include in the NSJ ID line score_name:score. Default: "depth."' )
parser.add_option( '-R', '--reference', dest='reference', default="None", help='Genome Reference Name for NSJ ID location. Automatically pulled from genome_build header in GTF if present.' )
(options, args) = parser.parse_args()
##INPUTS##
#Protein FASTA
try:
protein_fasta = os.path.abspath(options.protein_fasta)
protein_fasta = open(protein_fasta, 'r')
protein_fasta = refparse.read_protein_fasta(protein_fasta)
except Exception, e:
print >> sys.stderr, "failed: %s" % e
exit(2)
def setUp(self):
fastaLines = ""
fastaLines += ">ENSP00000381386 pep:known chromosome:GRCh37:22:24313554:24316773:-1 gene:ENSG00000099977 transcript:ENST00000398344 gene_biotype:protein_coding transcript_biotype:protein_coding"
fastaLines += "\nMPFLELDTNLPANRVPAGLEKRLCAAAASILGKPADRVNVTVRPGLAMALSGSTEPCAQL"
fastaLines += "\nSISSIGVVGTAEDNRSHSAHFFEFLTKELALGQDRILIRFFPLESWQIGKIGTVMTFL"
self.header = ">ENSP00000381386 pep:known chromosome:GRCh37:22:24313554:24316773:-1 gene:ENSG00000099977 transcript:ENST00000398344 gene_biotype:protein_coding transcript_biotype:protein_coding"
self.sequence = "MPFLELDTNLPANRVPAGLEKRLCAAAASILGKPADRVNVTVRPGLAMALSGSTEPCAQLSISSIGVVGTAEDNRSHSAHFFEFLTKELALGQDRILIRFFPLESWQIGKIGTVMTFL"
self.protein_fasta = open('fasta_entry.fasta', 'w')
self.protein_fasta.write(fastaLines)
self.protein_fasta.close()
self.protein_fasta = open('fasta_entry.fasta', 'r')
self.protein_fasta = refparse.read_protein_fasta(self.protein_fasta)
def __main__():
#Parse Command Line
parser = optparse.OptionParser()
#I/O
parser.add_option(
'-x',
'--reference_xml',
dest='reference_xml',
help=
'Reference protein UniProt-XML file. Sequence variant peptide entries are appended to this database to generate the ouptut UniProt-XML protein database.'
)
parser.add_option(
'-p',
'--protein_fasta',
dest='protein_fasta',
help=
'Reference protein FASTA file. Used to generate SAV peptide entries. If no UniProt-XML is specified, SAV and NSJ entries will be appended to this database to generate an output database. By default, this output will be a UniProt-XML protein database without PTM annotations. If --output-fasta is selected, the output will be a protein FASTA.'
)
parser.add_option(
'-g',
'--gene_model',
dest='gene_model',
default=None,
help='GTF gene model file. Used to annotate NSJ peptide entries.')
parser.add_option(
'-v',
'--snpeff_vcf',
dest='snpeff_vcf',
help='SnpEff VCF file with HGVS annotations (else read from stdin).')
parser.add_option('-c',
'--cufflinks_bed',
dest='cufflinks_bed',
help='Reconstructed transcripts in bed format.')
parser.add_option(
'-b',
'--splice_bed',
dest='splice_bed',
help='BED file (tophat junctions.bed) with sequence column added.')
parser.add_option(
'-o',
'--output',
dest='output',
help='Output file path. Outputs UniProt-XML and FASTA format databases.'
)
# parser.add_option( '-z', '--output_fasta', dest='output_fasta', action='store_true', default=False, help='Output a FASTA-format database. Place path for output file after the --output flag.')
# parser.add_option( '-m', '--threads', dest='threads', type='int', default=)
#Peptide sequence construction
parser.add_option(
'-l',
'--leading_aa_num',
dest='leading_aa_num',
type='int',
default=33,
help='Leading number of AAs to output for SAV peptides. Default: 33.')
parser.add_option(
'-t',
'--trailing_aa_num',
dest='trailing_aa_num',
type='int',
default=33,
help='Trailing number of AAs to output for SAV peptides. Default: 33.')
#Filtering parameters
parser.add_option(
'-D',
'--nsj_depth_cutoff',
dest='nsj_depth_cutoff',
type='int',
default=0,
help=
'Keep only NSJs found with above this depth (BED score field). Default: 0.'
)
parser.add_option(
'-E',
'--snv_depth_cutoff',
dest='snv_depth_cutoff',
type='int',
default=0,
help=
'Keep only SNVs found with above this depth (DP=# field). Default: 0.')
parser.add_option(
'-M',
'--minimum_length',
dest='minimum_length',
type='int',
default=0,
help=
'Keep only sequence variant peptides with greater than or equal to this length. Default: 0.'
)
#Simple entry
parser.add_option(
'-Q',
'--bed_score_name',
dest='bed_score_name',
default="depth",
help='Include in the NSJ ID line score_name:score. Default: "depth."')
parser.add_option(
'-R',
'--reference',
dest='reference',
default="None",
help=
'Genome Reference Name for NSJ ID location. Automatically pulled from genome_build header in GTF if present.'
)
(options, args) = parser.parse_args()
##INPUTS##
#Protein FASTA
try:
protein_fasta = os.path.abspath(options.protein_fasta)
protein_fasta = open(protein_fasta, 'r')
protein_fasta = refparse.read_protein_fasta(protein_fasta)
except Exception, e:
print >> sys.stderr, "failed: %s" % e
exit(2)
