Skip to content

Instantly share code, notes, and snippets.

@sr320

sr320/From-Ensenada.md

Last active November 17, 2015 01:26
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save sr320/af21afb92c8fad8ec611 to your computer and use it in GitHub Desktop.
Save sr320/af21afb92c8fad8ec611 to your computer and use it in GitHub Desktop.
Download ZIP
Notebook post on panopea project
Raw
From-Ensenada.md

There have not been many posts recently, but that is not to say I have not been doing any science. Much of what I have been doing is numerous burst commits on the Panopea transcriptome paper / project. This can be found @ https://github.com/sr320/paper-pano-go.

You can see all the Jupyter nbs in this sub-directory. I will highlight some of my proudest cell moments here:

Ok the first one is so good I will just give you the whole thing except that I will provide just a little more comments ##

!wc -l analyses/Geoduck-transcriptome-v2.tab
  154407 analyses/Geoduck-transcriptome-v2.tab

!head -5 analyses/Geoduck_v2_blastn-NT.out
comp190_c0_seq1	gi	315593157	gb	CP002417.1		84.50	200	31	0	1	200	2271015	2271214	1e-47	  198	Bacteria	Variovorax paradoxus EPS, complete genome	595537	Variovorax paradoxus EPS	Variovorax paradoxus EPS	b-proteobacteria
comp1900_c0_seq1	gi	481319564	gb	CP003293.1		100.00	271	0	0	1	271	1334370	1334640	1e-138	  501	Bacteria	Propionibacterium acnes HL096PA1, complete genome	1134454	Propionibacterium acnes HL096PA1	Propionibacterium acnes HL096PA1	high GC Gram+
comp2164_c0_seq1	gi	221728669	gb	CP001392.1		98.47	261	4	0	1	261	721134	721394	2e-126	  460	Bacteria	Acidovorax ebreus TPSY, complete genome	535289	Acidovorax ebreus TPSY	Acidovorax ebreus TPSY	b-proteobacteria
comp2742_c0_seq1	gi	527256352	ref	XM_005146392.1		85.65	230	33	0	16	245	2293	2522	7e-61	  243	Eukaryota	PREDICTED: Melopsittacus undulatus exostosin-like glycosyltransferase 3 (EXTL3), mRNA	13146	Melopsittacus undulatus	budgerigar	birds
comp3315_c0_seq1	gi	156627645	gb	AC209228.1		79.13	206	36	6	3	202	76584	76380	1e-28	  135	Eukaryota	Populus trichocarpa clone POP075-L19, complete sequence	3694	Populus trichocarpa	black cottonwood	eudicots

#Lets subset above table to non Eukaryotes
#Here I am letting awk know we are dealing with tabs, 
#and I want to have all rows where column 17 is NOT Eukaryota.
!awk -F"\t" '$17 != "Eukaryota" {print $1, $17 ,$15}' analyses/Geoduck_v2_blastn-NT.out \
> analyses/Non-Eukaryota-Geoduck-v2

!sort analyses/Non-Eukaryota-Geoduck-v2 > analyses/Non-Eukaryota-Geoduck-v2.sorted

!sort analyses/Geoduck-transcriptome-v2.tab > analyses/Geoduck-transcriptome-v2.sorted

!head -2 analyses/Geoduck-transcriptome-v2.sorted
comp100000_c0_seq1		TGAATGTATGTTTGTGAACGTATGTATATGAATGTATGTATGTGAATGCATACCATCTGTATAAGTATAATCCGACCGGGAGATGTTTATTCACACAGTTTGGCATTATGACGTTTAACCTCTGAATTGGCGTCTCTTGCTACTGACCGCTTCACAGTGATGACCCATGTTGTCACTTCTAATCTATTTATGTATTGCTCTTTTATATTATACTATTAACGCTGTTAAAATACACTACCGCTAAACAAATAAGAGTTGTGGGTTTGAATCATTGGTGAGTGCAGGAACCTCAGCAGGTCATTAAGATTTACGTGTACGTCTATCCTAAACCTACATGTTTCAACTTTGTTGTTTTTCGGTTTCGTTCTCTGTACACAGCTCTTGAAACATACATAAAATACCATTTTATTAAAAAATATGTCTCTATTTAATGTTAAAACCTTTTTAAGAAAA
comp100001_c1_seq1		GCTTTACCAGTTGTTACAAACATTTTAATAGTTATAGTTAATATACACAACATTTTAAATTAACTAGTGTCGAGAACTTGAGTCGGACATAGAGAATTAAATGTTTGTTGAACTTTAGCCAAGCACTTTTATTCTATTACTTTTTGAAGTATTTAATACCTTAAAATAATGGAATACTCCTGTAGAGTCCTTGAAGCCATCAACAATTTACCAACCTCCAAATAAAATATGAATATATTTTACATGATGAATTTACATAATGGATATATCATTGATATCTGCCAAGTTAACTTCACCTACCATTTTTAAGCTTACTTTGACCATGTTAGTTGGTATTGTGTATATAACGAGTGGGAGGACATTCATACCTGGCATTTGTTTGGTCAAACTGACACAAGATTTATGTTTATTTCAAACCTATATATAAAACAAGTCTCAATGAATATCTTCCTAGGCACAAGACAATGCTGATAAAATGTCTTGTTCAAGGACA


# joining with -v suppressing joined lines
!join -v 1 analyses/Geoduck-transcriptome-v2.sorted \
analyses/Non-Eukaryota-Geoduck-v2.sorted | wc -l
  153982

!join -v 1 analyses/Geoduck-transcriptome-v2.sorted \
analyses/Non-Eukaryota-Geoduck-v2.sorted \
> ../data-results/Geoduck-transcriptome-v3.tab

!head -2 ../data-results/Geoduck-transcriptome-v3.tab
comp100000_c0_seq1 TGAATGTATGTTTGTGAACGTATGTATATGAATGTATGTATGTGAATGCATACCATCTGTATAAGTATAATCCGACCGGGAGATGTTTATTCACACAGTTTGGCATTATGACGTTTAACCTCTGAATTGGCGTCTCTTGCTACTGACCGCTTCACAGTGATGACCCATGTTGTCACTTCTAATCTATTTATGTATTGCTCTTTTATATTATACTATTAACGCTGTTAAAATACACTACCGCTAAACAAATAAGAGTTGTGGGTTTGAATCATTGGTGAGTGCAGGAACCTCAGCAGGTCATTAAGATTTACGTGTACGTCTATCCTAAACCTACATGTTTCAACTTTGTTGTTTTTCGGTTTCGTTCTCTGTACACAGCTCTTGAAACATACATAAAATACCATTTTATTAAAAAATATGTCTCTATTTAATGTTAAAACCTTTTTAAGAAAA
comp100001_c1_seq1 GCTTTACCAGTTGTTACAAACATTTTAATAGTTATAGTTAATATACACAACATTTTAAATTAACTAGTGTCGAGAACTTGAGTCGGACATAGAGAATTAAATGTTTGTTGAACTTTAGCCAAGCACTTTTATTCTATTACTTTTTGAAGTATTTAATACCTTAAAATAATGGAATACTCCTGTAGAGTCCTTGAAGCCATCAACAATTTACCAACCTCCAAATAAAATATGAATATATTTTACATGATGAATTTACATAATGGATATATCATTGATATCTGCCAAGTTAACTTCACCTACCATTTTTAAGCTTACTTTGACCATGTTAGTTGGTATTGTGTATATAACGAGTGGGAGGACATTCATACCTGGCATTTGTTTGGTCAAACTGACACAAGATTTATGTTTATTTCAAACCTATATATAAAACAAGTCTCAATGAATATCTTCCTAGGCACAAGACAATGCTGATAAAATGTCTTGTTCAAGGACA

#Going from tab back to fasta!
!awk '{print ">"$1"\n"$2}' ../data-results/Geoduck-transcriptome-v3.tab \
> ../data-results/Geoduck-transcriptome-v3.fa

!fgrep -c ">" ../data-results/Geoduck-transcriptome-v3.fa
153982

tldr:

'$c != string`  join -v  awk '{print ">"$1"\n"$2}'

One more tidbit- I wanted to see how many blast hits were in the opposite direction "- frame".

thus:

!awk '($10-$9) < 0 {print $1, "\t", ($10-$9)}' \
../data-results/Geoduck-tranv2-blastx_sprot.tab \
> analyses/Geoduck-tranv2-minus_direction.tab
!head analyses/Geoduck-tranv2-minus_direction.tab
!wc -l analyses/Geoduck-tranv2-minus_direction.tab

comp95_c0_seq1 	 -230
comp146_c0_seq1 	 -173
comp195_c0_seq1 	 -185
comp296_c0_seq1 	 -200
comp455_c1_seq1 	 -197
comp943_c0_seq1 	 -218
comp1059_c0_seq1 	 -227
comp1683_c0_seq1 	 -206
comp1868_c0_seq1 	 -308
comp1910_c1_seq1 	 -248
   10413 analyses/Geoduck-tranv2-minus_direction.tab
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment