Mercurial > repos > chrisb > gap_all_glycan_tools
comparison get_data/cfg/NOTES @ 0:89592faa2875 draft
Uploaded
| author | chrisb |
|---|---|
| date | Wed, 23 Mar 2016 14:35:56 -0400 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:89592faa2875 |
|---|---|
| 1 | |
| 2 optional inputs : species, pi, glycan , cell type | |
| 3 file type - for now msa | |
| 4 outputs : json of everything. *.msa files . | |
| 5 possibly if images are selected then bundle all as an html. | |
| 6 | |
| 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 | |
| 8 | |
| 9 basic functional version | |
| 10 python cfg_get_glycan_from_cells.py -s Human -p "Crocker,Paul" | |
| 11 | |
| 12 gets the msa | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 17 | |
| 18 writes out output.json with other info | |
| 19 | |
| 20 prints messages on stdout: | |
| 21 no msa for Human T-Cells Crocker,Paul N-Linked | |
| 22 no msa for Human VG37 Crocker,Paul O-Linked | |
| 23 | |
| 24 | |
| 25 because any number of the outputs can be generated, Number of Output datasets cannot be determined until tool run | |
| 26 However ... these discovered datasets cannot be used with workflows and require the user to refresh their history before they are shown. (1) | |
| 27 Another option is to use an html file and link to all the data (2) | |
| 28 I am trying part 1 first. |