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0
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1
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2 optional inputs : species, pi, glycan , cell type
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3 file type - for now msa
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4 outputs : json of everything. *.msa files .
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5 possibly if images are selected then bundle all as an html.
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6
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7 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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8
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9 basic functional version
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10 python cfg_get_glycan_from_cells.py -s Human -p "Crocker,Paul"
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11
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12 gets the msa
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13 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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14 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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15 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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16 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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17
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18 writes out output.json with other info
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19
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20 prints messages on stdout:
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21 no msa for Human T-Cells Crocker,Paul N-Linked
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22 no msa for Human VG37 Crocker,Paul O-Linked
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23
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24
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25 because any number of the outputs can be generated, Number of Output datasets cannot be determined until tool run
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26 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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27 Another option is to use an html file and link to all the data (2)
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28 I am trying part 1 first.
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