Changeset 271


Ignore:
Timestamp:
Nov 19, 2009, 3:12:18 PM (11 years ago)
Author:
jjbot
Message:

Commit voor Evert 2

File:
1 edited

Legend:

Unmodified
Added
Removed
  • parsers/gene_extras.py

    r196 r271  
    1515   
    1616    # fieldname (fn) defenitions for all the csv files
    17     fn_gene2go = [
     17    FN_GENE2GO = [
    1818        "tax_id", "GeneID", "GO_ID", "Evidence",
    1919        "Qualifier", "GO_term", "PubMed", "Category"
    2020    ]
    21     fn_gene2refseq = [
     21    FN_GENE2REFSEQ = [
    2222        "tax_id", "GeneID", "status", "RNA_nucleotide_accession.version",
    2323        "RNA_nucleotide_gi", "protein_accession.version", "protein_gi",
     
    2626        "end_position_on_the_genomic_accession", "orientation", "assembly"
    2727    ]
    28     fn_gene_goup = [
     28    FN_GENE_GROUP = [
    2929        "tax_id", "GeneID", "relationship", "Other_tax_id", "Other_GeneID"
     30    ]
     31
     32    FN_GENE2ACCESSION = [
     33        "tax_id", "GeneID", "status", "RNA_nucleotide_accession.version",
     34        "RNA_nucleotide_gi", "protein_accession.version" "protein_gi",
     35        "genomic_nucleotide_accession.version", "genomic_nucleotide_gi",
     36        "start_position_on_the_genomic_accession",
     37        "end_position_on_the_genomic_accession", "orientation", "assembly"
    3038    ]
    3139
     
    6371
    6472    def parseGene2GO(self, filename):
    65         return liner.parse(filename, self.fn_gene2go, delimiter="\t", hasheader=True)
     73        return liner.parse(filename, self.FN_GENE2GO, delimiter="\t", hasheader=True)
    6674
    6775    def parseGene2RefSeq(self, filename):
    68         return liner.parse(filename, self.fn_gene2refseq, delimiter="\t", hasheader=True)
     76        return liner.parse(filename, self.FN_GENE2REFSEQ, delimiter="\t", hasheader=True)
    6977
    7078    def parseGene_group(self, filename):
    71         return liner.parse(filename, self.fn_gene_group, delimiter="\t", hasheader=True)
     79        return liner.parse(filename, self.FN_GENE_GROUP, delimiter="\t", hasheader=True)
     80
     81    def parseGene2Accession(self, filename, species_id=None):
     82        if species_id:
     83           
     84        else:
     85            return liner.parse(filename, self.FN_GENE2ACCESSION, delimiter="\t", hasheader=True)
     86   
     87    def _gene2accessionSpeciesFilter(self, species_id):
     88        vars =
     89        if
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