#variables to set
fa="../data/fa/Ahyacinthus_v1.fasta"
db="/Applications/BLAST/ncbi-blast-2.2.29\+/db/uniprot_sprot_r2013_12"
sqls="/Users/sr320/sqlshare-pythonclient/tools/"
usr="sr320@washington.edu"
sp="Ahyacinthus"
!head -2 {fa}
>contig27 CAAAATTCCAGCACTCCGTTTTGCATGGTAAACTTGTCTTAGTAGGACACTGTGGAAGATGTACAGCGCAAGACATCACAGTTGCAAGCGCCGACGAACAGCTGTTAAACTCTCCTCTCATATTCTCGAACAAACCAAATATTTCTTCCTCTCTGTTGTTGCTAACCTTTGAATATATGAAGCTGGCATTAGCACAGGACTCAAAGTTTCCGCCGAGCAGTTT
!fgrep -c ">" {fa}
33496
!/Applications/BLAST/ncbi-blast-2.2.29\+/bin/blastx \
-query {fa} \
-db {db} \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6 \
-evalue 1E-05 \
-num_threads 3 \
-out ../analyses/{sp}_sprot.tab
Selenocysteine (U) at position 123 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 266 replaced by X Selenocysteine (U) at position 132 replaced by X Selenocysteine (U) at position 265 replaced by X Selenocysteine (U) at position 134 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 266 replaced by X Selenocysteine (U) at position 124 replaced by X Selenocysteine (U) at position 130 replaced by X Selenocysteine (U) at position 263 replaced by X Selenocysteine (U) at position 128 replaced by X Selenocysteine (U) at position 261 replaced by X Selenocysteine (U) at position 160 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 266 replaced by X Selenocysteine (U) at position 130 replaced by X Selenocysteine (U) at position 263 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 122 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 131 replaced by X Selenocysteine (U) at position 132 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 128 replaced by X Selenocysteine (U) at position 261 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 122 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 132 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 666 replaced by X Selenocysteine (U) at position 494 replaced by X Selenocysteine (U) at position 648 replaced by X Selenocysteine (U) at position 612 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 510 replaced by X Selenocysteine (U) at position 523 replaced by X Selenocysteine (U) at position 523 replaced by X Selenocysteine (U) at position 525 replaced by X Selenocysteine (U) at position 642 replaced by X Selenocysteine (U) at position 651 replaced by X Selenocysteine (U) at position 18 replaced by X Selenocysteine (U) at position 13 replaced by X Selenocysteine (U) at position 17 replaced by X Selenocysteine (U) at position 17 replaced by X Selenocysteine (U) at position 15 replaced by X Selenocysteine (U) at position 17 replaced by X Selenocysteine (U) at position 15 replaced by X Selenocysteine (U) at position 15 replaced by X Selenocysteine (U) at position 25 replaced by X Selenocysteine (U) at position 16 replaced by X Selenocysteine (U) at position 13 replaced by X Selenocysteine (U) at position 16 replaced by X Selenocysteine (U) at position 16 replaced by X Selenocysteine (U) at position 19 replaced by X Selenocysteine (U) at position 16 replaced by X Selenocysteine (U) at position 7 replaced by X Selenocysteine (U) at position 16 replaced by X Selenocysteine (U) at position 21 replaced by X Selenocysteine (U) at position 24 replaced by X Selenocysteine (U) at position 60 replaced by X Selenocysteine (U) at position 63 replaced by X Selenocysteine (U) at position 63 replaced by X Selenocysteine (U) at position 121 replaced by X Selenocysteine (U) at position 123 replaced by X Selenocysteine (U) at position 121 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 130 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 266 replaced by X Selenocysteine (U) at position 132 replaced by X Selenocysteine (U) at position 265 replaced by X Selenocysteine (U) at position 134 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 266 replaced by X Selenocysteine (U) at position 124 replaced by X Selenocysteine (U) at position 130 replaced by X Selenocysteine (U) at position 263 replaced by X Selenocysteine (U) at position 128 replaced by X Selenocysteine (U) at position 261 replaced by X Selenocysteine (U) at position 160 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 266 replaced by X Selenocysteine (U) at position 130 replaced by X Selenocysteine (U) at position 263 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 122 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 131 replaced by X Selenocysteine (U) at position 132 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 25 replaced by X Selenocysteine (U) at position 60 replaced by X Selenocysteine (U) at position 63 replaced by X Selenocysteine (U) at position 63 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 666 replaced by X Selenocysteine (U) at position 494 replaced by X Selenocysteine (U) at position 648 replaced by X Selenocysteine (U) at position 612 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 510 replaced by X Selenocysteine (U) at position 523 replaced by X Selenocysteine (U) at position 523 replaced by X Selenocysteine (U) at position 525 replaced by X Selenocysteine (U) at position 642 replaced by X Selenocysteine (U) at position 651 replaced by X Selenocysteine (U) at position 65 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 49 replaced by X Selenocysteine (U) at position 53 replaced by X Selenocysteine (U) at position 49 replaced by X Selenocysteine (U) at position 49 replaced by X Selenocysteine (U) at position 49 replaced by X Selenocysteine (U) at position 54 replaced by X Selenocysteine (U) at position 93 replaced by X Selenocysteine (U) at position 84 replaced by X Selenocysteine (U) at position 93 replaced by X Selenocysteine (U) at position 93 replaced by X Selenocysteine (U) at position 93 replaced by X Selenocysteine (U) at position 93 replaced by X Selenocysteine (U) at position 60 replaced by X Selenocysteine (U) at position 63 replaced by X Selenocysteine (U) at position 63 replaced by X Selenocysteine (U) at position 93 replaced by X Selenocysteine (U) at position 84 replaced by X Selenocysteine (U) at position 93 replaced by X Selenocysteine (U) at position 93 replaced by X Selenocysteine (U) at position 84 replaced by X Selenocysteine (U) at position 93 replaced by X Selenocysteine (U) at position 93 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 666 replaced by X Selenocysteine (U) at position 494 replaced by X Selenocysteine (U) at position 648 replaced by X Selenocysteine (U) at position 612 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 510 replaced by X Selenocysteine (U) at position 523 replaced by X Selenocysteine (U) at position 523 replaced by X Selenocysteine (U) at position 525 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 667 replaced by X Selenocysteine (U) at position 665 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 666 replaced by X Selenocysteine (U) at position 494 replaced by X Selenocysteine (U) at position 648 replaced by X Selenocysteine (U) at position 612 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 510 replaced by X Selenocysteine (U) at position 523 replaced by X Selenocysteine (U) at position 523 replaced by X Selenocysteine (U) at position 525 replaced by X Selenocysteine (U) at position 642 replaced by X Selenocysteine (U) at position 651 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 85 replaced by X Selenocysteine (U) at position 74 replaced by X Selenocysteine (U) at position 121 replaced by X Selenocysteine (U) at position 123 replaced by X Selenocysteine (U) at position 121 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 130 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 266 replaced by X Selenocysteine (U) at position 132 replaced by X Selenocysteine (U) at position 265 replaced by X Selenocysteine (U) at position 134 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 266 replaced by X Selenocysteine (U) at position 124 replaced by X Selenocysteine (U) at position 130 replaced by X Selenocysteine (U) at position 263 replaced by X Selenocysteine (U) at position 128 replaced by X Selenocysteine (U) at position 261 replaced by X Selenocysteine (U) at position 160 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 266 replaced by X Selenocysteine (U) at position 130 replaced by X Selenocysteine (U) at position 263 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 122 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 131 replaced by X Selenocysteine (U) at position 132 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 131 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 93 replaced by X Selenocysteine (U) at position 92 replaced by X Selenocysteine (U) at position 92 replaced by X Selenocysteine (U) at position 92 replaced by X Selenocysteine (U) at position 92 replaced by X Selenocysteine (U) at position 92 replaced by X Selenocysteine (U) at position 92 replaced by X Selenocysteine (U) at position 92 replaced by X Selenocysteine (U) at position 93 replaced by X Selenocysteine (U) at position 93 replaced by X Selenocysteine (U) at position 44 replaced by X Selenocysteine (U) at position 44 replaced by X Selenocysteine (U) at position 38 replaced by X Selenocysteine (U) at position 642 replaced by X Selenocysteine (U) at position 651 replaced by X Selenocysteine (U) at position 52 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 49 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 52 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 46 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 43 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 64 replaced by X Selenocysteine (U) at position 28 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 667 replaced by X Selenocysteine (U) at position 665 replaced by X Selenocysteine (U) at position 93 replaced by X Selenocysteine (U) at position 95 replaced by X Selenocysteine (U) at position 95 replaced by X Selenocysteine (U) at position 95 replaced by X Selenocysteine (U) at position 95 replaced by X Selenocysteine (U) at position 95 replaced by X Selenocysteine (U) at position 95 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 52 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 49 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 52 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 46 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 40 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 129 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 64 replaced by X Selenocysteine (U) at position 28 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 666 replaced by X Selenocysteine (U) at position 494 replaced by X Selenocysteine (U) at position 648 replaced by X Selenocysteine (U) at position 612 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 510 replaced by X Selenocysteine (U) at position 523 replaced by X Selenocysteine (U) at position 523 replaced by X Selenocysteine (U) at position 525 replaced by X Selenocysteine (U) at position 642 replaced by X Selenocysteine (U) at position 651 replaced by X Selenocysteine (U) at position 106 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 494 replaced by X Selenocysteine (U) at position 648 replaced by X Selenocysteine (U) at position 612 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 498 replaced by X Selenocysteine (U) at position 510 replaced by X Selenocysteine (U) at position 523 replaced by X Selenocysteine (U) at position 523 replaced by X Selenocysteine (U) at position 525 replaced by X Selenocysteine (U) at position 642 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 13 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 106 replaced by X Selenocysteine (U) at position 121 replaced by X Selenocysteine (U) at position 123 replaced by X Selenocysteine (U) at position 121 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 126 replaced by X Selenocysteine (U) at position 130 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 266 replaced by X Selenocysteine (U) at position 132 replaced by X Selenocysteine (U) at position 265 replaced by X Selenocysteine (U) at position 134 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 266 replaced by X Selenocysteine (U) at position 124 replaced by X Selenocysteine (U) at position 130 replaced by X Selenocysteine (U) at position 263 replaced by X Selenocysteine (U) at position 128 replaced by X Selenocysteine (U) at position 261 replaced by X Selenocysteine (U) at position 160 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 266 replaced by X Selenocysteine (U) at position 130 replaced by X Selenocysteine (U) at position 263 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 122 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 131 replaced by X 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at position 124 replaced by X Selenocysteine (U) at position 130 replaced by X Selenocysteine (U) at position 263 replaced by X Selenocysteine (U) at position 128 replaced by X Selenocysteine (U) at position 261 replaced by X Selenocysteine (U) at position 160 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 266 replaced by X Selenocysteine (U) at position 130 replaced by X Selenocysteine (U) at position 263 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 122 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 133 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 144 replaced by X Selenocysteine (U) at position 131 replaced by X Selenocysteine (U) at position 132 replaced by X Selenocysteine (U) at position 387 replaced by X Selenocysteine (U) at position 387 replaced by X Selenocysteine (U) at position 388 replaced by X Selenocysteine (U) at position 387 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 642 replaced by X Selenocysteine (U) at position 651 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 387 replaced by X Selenocysteine (U) at position 387 replaced by X Selenocysteine (U) at position 388 replaced by X Selenocysteine (U) at position 387 replaced by X Selenocysteine (U) at position 637 replaced by X Selenocysteine (U) at position 690 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 47 replaced by X Selenocysteine (U) at position 43 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 129 replaced by X Selenocysteine (U) at position 129 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X Selenocysteine (U) at position 73 replaced by X
!ls ../analyses/A*
../analyses/Ahyacinthus_sprot.tab ../analyses/Ahyacinthus_v1_CG.tab ../analyses/Ahyacinthus_v1.tab ../analyses/Ahyacinthus_v1_CpG.tab ../analyses/Ahyacinthus_v1_C-G.tab ../analyses/Ahyacinthus_v1_G.tab ../analyses/Ahyacinthus_v1_C.tab ../analyses/Ahyacinthus_v1_len.tab
!wc -l ../analyses/{sp}_sprot.tab
11607 ../analyses/Ahyacinthus_sprot.tab
!tr '|' "\t" <../analyses/{sp}_sprot.tab> ../analyses/{sp}_sprot_sql.tab
!head -1 ../analyses/{sp}_sprot.tab
!echo SQLShare ready version has Pipes converted to Tabs ....
!head -1 ../analyses/{sp}_sprot_sql.tab
contig211 sp|Q96JB1|DYH8_HUMAN 77.53 89 20 0 1 267 2533 2621 4e-44 158 SQLShare ready version has Pipes converted to Tabs .... contig211 sp Q96JB1 DYH8_HUMAN 77.53 89 20 0 1 267 2533 2621 4e-44 158
!python {sqls}singleupload.py \
-d _blast_sprot \
../analyses/{sp}_sprot_sql.tab
processing chunk line 0 to 11607 (0.00473690032959 s elapsed) pushing ../analyses/Ahyacinthus_sprot_sql.tab... parsing 1D98A2E5... finished _blast_sprot
!python {sqls}fetchdata.py \
-s "SELECT Column1 as ContigID, term, GOSlim_bin, aspect, ProteinName \
FROM [{usr}].[_blast_sprot]md \
left join \
[samwhite@washington.edu].[UniprotProtNamesReviewed_yes20130610]sp \
on md.Column3=sp.SPID \
left join \
[sr320@washington.edu].[SPID and GO Numbers]go \
on md.Column3=go.SPID \
left join \
[sr320@washington.edu].[GO_to_GOslim]slim on go.GOID=slim.GO_id \
where aspect like 'P'" \
-f tsv \
-o ../analyses/{sp}_sprot_GOdescriptions.tab
!head ../analyses/{sp}_sprot_GOdescriptions.tab
!grep -c "stress response" ../analyses/{sp}_sprot_GOdescriptions.tab
2356
!grep "stress response" ../analyses/{sp}_sprot_GOdescriptions.tab \
> ../analyses/{sp}_sprot_GOdescriptions-stress.tab
!cut -f2 ../analyses/{sp}_sprot_GOdescriptions-stress.tab | sort | uniq -c
12 "DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest" 9 "DNA damage response, signal transduction by p53 class mediator resulting in induction of apoptosis" 5 "DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator" 6 "DNA damage response, signal transduction by p53 class mediator" 8 "DNA damage response, signal transduction resulting in induction of apoptosis" 6 "DNA damage response, signal transduction" 1 "base-excision repair, AP site formation" 4 "base-excision repair, gap-filling" 3 "blood coagulation, intrinsic pathway" 4 "complement activation, alternative pathway" 10 "complement activation, classical pathway" 2 "complement activation, lectin pathway" 1 "defense response to fungus, incompatible interaction" 5 "negative regulation of DNA damage response, signal transduction by p53 class mediator" 2 "nucleotide-excision repair, DNA damage recognition" 4 "nucleotide-excision repair, DNA damage removal" 2 "nucleotide-excision repair, DNA duplex unwinding" 4 "nucleotide-excision repair, DNA gap filling" 3 "nucleotide-excision repair, DNA incision" 2 "nucleotide-excision repair, DNA incision, 5'-to lesion" 1 "nucleotide-excision repair, preincision complex assembly" 4 "positive regulation of DNA damage response, signal transduction by p53 class mediator" 2 "regulation of complement activation, lectin pathway" 1 "sterol depletion response, sterol regulatory element binding protein nuclear translocation" 2 "wound healing, spreading of epidermal cells" 9 DNA damage checkpoint 4 DNA damage induced protein phosphorylation 1 DNA dealkylation 1 DNA double-strand break processing 4 DNA ligation during DNA repair 1 DNA recombinase assembly 223 DNA repair 2 DNA strand renaturation 8 DNA synthesis during DNA repair 4 ER overload response 1 ER-nuclear sterol response pathway 3 G1 DNA damage checkpoint 11 G2/M transition DNA damage checkpoint 23 JNK cascade 1 JUN phosphorylation 13 MyD88-dependent toll-like receptor signaling pathway 9 MyD88-independent toll-like receptor signaling pathway 4 activation of JNKK activity 18 activation of JUN kinase activity 5 activation of innate immune response 15 activation of signaling protein activity involved in unfolded protein response 3 acute inflammatory response 17 acute-phase response 2 age-dependent response to oxidative stress 1 age-dependent response to reactive oxygen species 3 aggregation involved in sorocarp development 1 angiogenesis involved in wound healing 1 antibacterial humoral response 1 antibacterial peptide secretion 12 autophagic vacuole formation 2 autophagic vacuole fusion 2 axon extension involved in regeneration 3 axon regeneration 2 axon regeneration in the peripheral nervous system 19 base-excision repair 8 behavioral fear response 3 behavioral response to pain 110 blood coagulation 4 bypass DNA synthesis 1 callose deposition in cell wall during defense response 1 cell surface pattern recognition receptor signaling pathway 4 cellular defense response 1 cellular response to amino acid starvation 4 cellular response to glucose starvation 18 cellular response to heat 6 cellular response to hydrogen peroxide 18 cellular response to oxidative stress 3 cellular response to reactive oxygen species 14 cellular response to starvation 2 cellular response to stress 1 cellular response to unfolded protein 2 cellular response to water deprivation 3 chronic inflammatory response 1 collateral sprouting of injured axon 9 complement activation 1 culmination during sorocarp development 15 defense response 6 defense response to Gram-negative bacterium 9 defense response to Gram-positive bacterium 24 defense response to bacterium 6 defense response to fungus 8 defense response to protozoan 14 defense response to virus 29 double-strand break repair 17 double-strand break repair via homologous recombination 3 double-strand break repair via nonhomologous end joining 33 endoplasmic reticulum unfolded protein response 1 error-free postreplication DNA repair 3 fear response 6 fibrinolysis 3 fin regeneration 30 hydrogen peroxide catabolic process 2 hyperosmotic response 1 hypotonic response 1 induction by symbiont of defense-related host nitric oxide production 5 induction of bacterial agglutination 52 inflammatory response 2 inflammatory response to antigenic stimulus 105 innate immune response 1 innate immune response in mucosa 2 intra-S DNA damage checkpoint 1 leukocyte chemotaxis during inflammatory response 3 leukocyte migration during inflammatory response 3 leukotriene production during acute inflammatory response 7 macroautophagy 2 meiotic mismatch repair 1 melanization defense response 3 melanotic encapsulation of foreign target 10 mismatch repair 8 mitotic cell cycle G2/M transition DNA damage checkpoint 4 multicellular organismal response to stress 1 natural killer cell degranulation 6 natural killer cell mediated cytotoxicity 5 negative regulation of JNK cascade 4 negative regulation of JUN kinase activity 1 negative regulation of axon extension involved in regeneration 1 negative regulation of blood coagulation 1 negative regulation of defense response 1 negative regulation of defense response to virus 4 negative regulation of fibrinolysis 7 negative regulation of inflammatory response 2 negative regulation of inflammatory response to antigenic stimulus 2 negative regulation of innate immune response 9 negative regulation of macroautophagy 1 negative regulation of platelet activation 1 negative regulation of respiratory burst during acute inflammatory response 2 negative regulation of stress-activated MAPK cascade 1 negative regulation of toll-like receptor 2 signaling pathway 2 negative regulation of transcription from RNA polymerase II promoter in response to UV-induced DNA damage 4 negative regulation of translation in response to stress 2 negative regulation of translational initiation in response to stress 1 non-photoreactive DNA repair 1 nucleotide-binding oligomerization domain containing 2 signaling pathway 4 nucleotide-binding oligomerization domain containing signaling pathway 24 nucleotide-excision repair 2 pathogen-associated molecular pattern dependent induction by symbiont of host innate immunity 7 pattern recognition receptor signaling pathway 16 plasma membrane repair 52 platelet activation 1 platelet aggregation 10 positive regulation of DNA repair 19 positive regulation of JNK cascade 19 positive regulation of JUN kinase activity 1 positive regulation of acute inflammatory response 2 positive regulation of axon regeneration 1 positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria 4 positive regulation of blood coagulation 1 positive regulation of chronic inflammatory response to non-antigenic stimulus 5 positive regulation of defense response to virus by host 2 positive regulation of epithelial cell proliferation involved in wound healing 1 positive regulation of fibrinolysis 6 positive regulation of inflammatory response 4 positive regulation of innate immune response 1 positive regulation of macroautophagy 1 positive regulation of natural killer cell mediated cytotoxicity 1 positive regulation of respiratory burst during acute inflammatory response 1 positive regulation of sterol regulatory element binding protein target gene transcription involved in sterol depletion response 3 positive regulation of stress-activated MAPK cascade 1 positive regulation of toll-like receptor 4 signaling pathway 1 positive regulation of toll-like receptor signaling pathway 5 postreplication repair 6 pyrimidine dimer repair 1 pyrimidine dimer repair by nucleotide-excision repair 4 regulation of DNA repair 10 regulation of JNK cascade 1 regulation of JUN kinase activity 1 regulation of aggregation involved in sorocarp development 1 regulation of axon regeneration 4 regulation of blood coagulation 2 regulation of cellular defense response 5 regulation of defense response to virus 3 regulation of defense response to virus by virus 1 regulation of double-strand break repair via homologous recombination 1 regulation of eIF2 alpha phosphorylation by heme 9 regulation of inflammatory response 5 regulation of innate immune response 1 regulation of response to interferon-gamma 1 regulation of response to osmotic stress 1 regulation of response to stress 2 regulation of stress-activated MAPK cascade 6 regulation of transcription from RNA polymerase II promoter in response to oxidative stress 2 regulation of transcription in response to stress 1 regulation of translation in response to stress 5 regulation of translational initiation in response to stress 2 replication fork processing 1 respiratory burst during defense response 234 response to DNA damage stimulus 7 response to axon injury 16 response to cold 15 response to endoplasmic reticulum stress 3 response to fluid shear stress 22 response to heat 2 response to herbicide 23 response to hydrogen peroxide 5 response to hydroperoxide 4 response to hyperoxia 59 response to hypoxia 2 response to interferon-gamma 2 response to laminar fluid shear stress 3 response to nitrosative stress 8 response to osmotic stress 96 response to oxidative stress 3 response to oxygen radical 17 response to pain 4 response to reactive oxygen species 5 response to salt stress 13 response to starvation 1 response to sterol depletion 89 response to stress 5 response to superoxide 3 response to type I interferon 35 response to unfolded protein 3 response to water deprivation 25 response to wounding 1 satellite cell maintenance involved in skeletal muscle regeneration 2 sensory epithelium regeneration 4 single strand break repair 1 skeletal muscle regeneration 3 sorocarp development 3 sorocarp morphogenesis 1 sorocarp stalk development 13 stress-activated MAPK cascade 1 stress-activated protein kinase signaling pathway 1 systemic acquired resistance 15 tissue regeneration 10 toll-like receptor 1 signaling pathway 11 toll-like receptor 2 signaling pathway 10 toll-like receptor 3 signaling pathway 11 toll-like receptor 4 signaling pathway 1 toll-like receptor 5 signaling pathway 1 toll-like receptor 7 signaling pathway 17 toll-like receptor signaling pathway 16 transcription-coupled nucleotide-excision repair 1 virus induced gene silencing 33 wound healing
pylab inline
Populating the interactive namespace from numpy and matplotlib
#FIXME - below I added '[Haliotis_kam]'
from pandas import *
gs = read_table('../analyses/Ahyacinthus_sprot_GOdescriptions.tab')
gs
<class 'pandas.core.frame.DataFrame'> Int64Index: 55343 entries, 0 to 55342 Data columns (total 5 columns): ContigID 55343 non-null values term 55343 non-null values GOSlim_bin 55343 non-null values aspect 55343 non-null values ProteinName 55296 non-null values dtypes: object(5)
gs.groupby('GOSlim_bin').ContigID.count().plot(kind='barh', color=list('y'))
savefig('../analyses/Ahyacinthus_GOSlim.png', bbox_inches='tight')
!python {sqls}fetchdata.py \
-s "SELECT Distinct \
Column1 as ContigID, GOSlim_bin \
FROM [{usr}].[_blast_sprot]md \
left join \
[sr320@washington.edu].[SPID and GO Numbers]go \
on md.Column3=go.SPID \
left join \
[sr320@washington.edu].[GO_to_GOslim]slim on go.GOID=slim.GO_id \
where aspect like 'P'" \
-f tsv \
-o ../analyses/{sp}_GOslim.tab
!head ../analyses/{sp}_GOslim.tab
from pandas import *
slim = read_table('../analyses/Ahyacinthus_GOslim.tab')
slim.groupby('GOSlim_bin').ContigID.count().plot(kind='barh', color=list('y'))
savefig('../analyses/Ahyacinthus_GOSlim-distinct.png', bbox_inches='tight')