BLASTer script improvements

I made some improvements in the BLASTer script, described below.

  • To deal with some NCBI updates I changed the rettype and retmode of the Entrez.efetch command.
  • Since I am now trying candidate genes from other species I set the reciprocal BLAST to the respective organism database. Now each locus shows each reciprocal BLAST separately, when needed.
  • The loci frame and strand is now stored and printed along.
  • Major output formatting adjustments.

An output example:

Locus_978_Transcript_1/1_Confidence_1.000_Length_2580 | frame: +1 | candidates: DDX4, vas, vasa, pl10

				gene                id                  accession           e-value
  Homo sapiens
				DDX4                54514               NP_001160005.1      3.78e-141
				DDX4                54514               NP_001136021.1      3.78e-141
				DDX4                54514               NP_077726.1         3.78e-141 <<
				DDX4                54514               NP_001160006.1      4.93e-141
				DDX3X               1654                NP_001180346.1      7.40e-121
				DDX3X               1654                NP_001347.3         7.40e-121
				DDX3X               1654                NP_001180345.1      7.40e-121
  Danio rerio
				vasa                30263               NP_571132.1         1.36e-146 <<
				ddx3                566947              NP_001119895.1      3.05e-122
				pl10                30116               NP_571016.2         1.16e-121 <<
				ddx42               503932              NP_001032894.2      5.45e-79
				ddx5                322206              NP_997777.1         4.32e-76
  Drosophila melanogaster
				bel                 45826               NP_536783.1         8.20e-120
				CG10077             38756               NP_648062.2         1.32e-77
				CG6418              39218               NP_648413.1         2.11e-75
				CG7878              40959               NP_649767.1         8.04e-75
				Rm62                40739               NP_731034.1         2.19e-72
				Rm62                40739               NP_731035.2         2.19e-72
				Rm62                40739               NP_731033.1         2.19e-72
				Rm62                40739               NP_001189182.1      2.19e-72
				Rm62                40739               NP_731032.1         2.19e-72
				Rm62                40739               NP_001163528.1      2.19e-72
				Rm62                40739               NP_731031.1         2.19e-72
				Rm62                40739               NP_524243.2         2.19e-72

Now the next steps will be to integrate better with the Zim Desktop Wiki.