mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Daniel Blankenberg
a3390c3dc4
TODO: Allow annotations to be specified for all species in the file, not just the 'primary' organism (as specified by the dbkey). Metadata for sequences will need to be fleshed out more first (i.e. store all species present in the file).
89 lines
2.8 KiB
Python
89 lines
2.8 KiB
Python
#!/usr/bin/env python2.4
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"""
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Script that Creates a zip file for use by GMAJ
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"""
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import os, sys, zipfile
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import pkg_resources; pkg_resources.require( "bx-python" )
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from bx.align import maf
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out_file = sys.argv[1]
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maf_file = sys.argv[2]
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dbkey = sys.argv[3]
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if dbkey == "?": dbkey="unspecified"
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exons_file = sys.argv[4]
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highlights_file = sys.argv[5]
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underlays_file = sys.argv[6]
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repeats_file = sys.argv[7]
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links_file = sys.argv[8]
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def get_species_names( input_filename ):
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species={}
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file_in = open(input_filename, 'r')
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maf_reader = maf.Reader( file_in )
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for i, m in enumerate( maf_reader ):
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l = m.components
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for c in l:
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spec, chrom = maf.src_split( c.src )
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try:
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if chrom not in species[spec]:
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species[spec].append(chrom)
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except:
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species[spec] = [chrom]
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file_in.close()
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return species
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#open new zip file
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out_file = zipfile.ZipFile(out_file, "w") #, ZIP_DEFLATED)
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#determine organisms located in maf file.
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species = get_species_names( maf_file )
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GMAJ_str = "#:gmaj\n\ntitle = \"GMAJ through Galaxy\"\nalignfile = input.maf\nnowarn = bed_blocks bed_thick bed_name repeat_type_missing bed_name_prefix\ntabext = .%s\n" % (dbkey)
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if dbkey in species and len(species[dbkey])>0:
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GMAJ_str = GMAJ_str + "refseq = "+dbkey+"."+species[dbkey][0]+"\n"
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else:
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print "There was a problem setting the reference sequence."
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GMAJ_str = GMAJ_str + "\n"
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count = 0
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for key in species:
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for chr in species[key]:
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GMAJ_str = GMAJ_str + "seq "+str(count)+":\nseqname = "+key+"."+chr+"\n"
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if key == dbkey:
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if os.path.isfile(exons_file):
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GMAJ_str = GMAJ_str + "exons = exons."+dbkey+"\n"
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if os.path.isfile(highlights_file):
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GMAJ_str = GMAJ_str + "highlights = highlights."+dbkey+"\n"
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if os.path.isfile(underlays_file):
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GMAJ_str = GMAJ_str + "underlays = underlays."+dbkey+"\n"
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if os.path.isfile(repeats_file):
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GMAJ_str = GMAJ_str + "repeats = repeats."+dbkey+"\n"
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if os.path.isfile(links_file):
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GMAJ_str = GMAJ_str + "links = links."+dbkey+"\n"
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GMAJ_str = GMAJ_str + "\n"
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count += 1
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out_file.writestr("input.gmaj",GMAJ_str)
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#add maf file
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out_file.write(maf_file, "input.maf")
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if os.path.isfile(exons_file):
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out_file.write(exons_file, "exons."+dbkey)
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if os.path.isfile(highlights_file):
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out_file.write(highlights_file, "highlights."+dbkey)
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if os.path.isfile(underlays_file):
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out_file.write(underlays_file, "underlays."+dbkey)
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if os.path.isfile(repeats_file):
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out_file.write(repeats_file, "repeats."+dbkey)
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if os.path.isfile(links_file):
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out_file.write(links_file, "links."+dbkey)
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out_file.close()
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print "GMAJ bundle file created"
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