view get_data/cfg/NOTES @ 1:0a5e0df17054 draft default tip

Uploaded

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−optional inputs : species, pi, glycan , cell type
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−file type - for now msa
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−outputs : json of everything. *.msa files . 
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−possibly if images are selected then bundle all as an html.
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−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
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−basic functional version
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−python cfg_get_glycan_from_cells.py  -s Human -p "Crocker,Paul" 
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−gets the msa 
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−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
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−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
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−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
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−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
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−writes out output.json with other info
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−prints messages on stdout:
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−no msa for  Human T-Cells Crocker,Paul N-Linked
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−no msa for  Human VG37 Crocker,Paul O-Linked
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−because any number of the outputs can be generated, Number of Output datasets cannot be determined until tool run
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−However ... these discovered datasets cannot be used with workflows and require the user to refresh their history before they are shown. (1)
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−Another option is to use an html file and link to all the data (2)
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−I am trying part 1 first.