diff get_data/cfg/NOTES @ 0:89592faa2875 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_data/cfg/NOTES	Wed Mar 23 14:35:56 2016 -0400
@@ -0,0 +1,28 @@
+
+optional inputs : species, pi, glycan , cell type
+file type - for now msa
+outputs : json of everything. *.msa files . 
+possibly if images are selected then bundle all as an html.
+
+For now only interested in msa files. Ignoring everything else. i.e. if a match has no msa I do nothing serious just print to stdout
+
+basic functional version
+python cfg_get_glycan_from_cells.py  -s Human -p "Crocker,Paul" 
+
+gets the msa 
+Human_B-Cells_Crocker_N-Linked_10000007.msa  Human_K562_Crocker_N-Linked_7301.msa   Human_Monocytes_Crocker_N-Linked_10000006.msa             Human_T-Cells_Crocker_O-Linked_10000011.msa
+Human_B-Cells_Crocker_O-Linked_10000008.msa  Human_K562_Crocker_O-Linked_7302.msa   Human_Monocytes_Crocker_O-Linked_10000005.msa             Human_THP-1_Crocker_N-Linked_7309.msa
+Human_HL-60_Crocker_N-Linked_7330.msa        Human_KG-1a_Crocker_N-Linked_7317.msa  Human_Natural Killer Cells_Crocker_N-Linked_10000012.msa  Human_VG37_Crocker_N-Linked_7305.msa
+Human_HL-60_Crocker_O-Linked_7314.msa        Human_KG-1a_Crocker_O-Linked_7318.msa  Human_Natural Killer Cells_Crocker_O-Linked_10000013.msa
+
+writes out output.json with other info
+
+prints messages on stdout:
+no msa for  Human T-Cells Crocker,Paul N-Linked
+no msa for  Human VG37 Crocker,Paul O-Linked
+
+
+because any number of the outputs can be generated, Number of Output datasets cannot be determined until tool run
+However ... these discovered datasets cannot be used with workflows and require the user to refresh their history before they are shown. (1)
+Another option is to use an html file and link to all the data (2)
+I am trying part 1 first.