moved data to mim_seq and added package_data for data folder

MANIFEST.in

@@ -5,7 +5,5 @@ include mim_seq/ccaPlots.R
 include mim_seq/modPlot.R
 include mim_seq/modifications
 include mim_seq/facet_share.R
-recursive-include data *
-recursive-include docs *
 include *.fastq.gz
 include sampleData_HEKvsK562.txt

mim_seq/data/additionalMods.txt

@@ -0,0 +1,31 @@
+Homo sapiens	Ala-CGC	m1A58;m2,2G26
+Homo sapiens	Ala-TGC	m1A58;m2,2G26
+Homo sapiens	Cys-GCA	m1A58;m1G37
+Homo sapiens	Asp-GTC	m1G9
+Homo sapiens	Glu-CTC	m1G9
+Homo sapiens	Gly-TCC	m1A58
+Homo sapiens	His-GTG	m1G37
+Homo sapiens	Ile-TAT	m1A58;m2,2G26;m1G9
+Homo sapiens	Leu-CAG	m3C47
+Homo sapiens	Leu-TAG	m1A58;m1G37;m2,2G26
+Homo sapiens	Met-CAT	m3C20
+Homo sapiens	Arg-CCG	m2,2G26
+Homo sapiens	Arg-TCG	m1A58;m1G37;m2,2G26;m1G9
+Homo sapiens	Ser-CGA	m1A58;m2,2G26;m3C32;m3C47
+Homo sapiens	Ser-TGA	m2,2G26;m3C32;m3C47
+Homo sapiens	Thr-CGT	m1A58;m2,2G26;m1G9;m3C32
+Homo sapiens	Thr-TGT	m1A58;m2,2G26;m1G9;m3C32
+Homo sapiens	Val-TAC	m1A58
+Homo sapiens	Arg-ACG	I34
+Homo sapiens	Ile-AAT	I34
+Homo sapiens	Leu-AAG	I34
+Homo sapiens	Pro-AGG	I34
+Homo sapiens	Ser-AGA	I34
+Homo sapiens	Thr-AGT	I34
+Homo sapiens	Val-AAC	I34
+Mus musculus	Ala-AGC	I34
+Mus musculus	Pro-AGG	I34
+Mus musculus	Thr-AGT	I34
+Mus musculus	Ser-AGA	I34
+Mus musculus	Leu-AAG	I34
+Saccharomyces cerevisiae	Gln-TTG	mcm5s2U34

mim_seq/data/ce11-tRNAs/ce11-mitotRNAs.fa

@@ -0,0 +1,44 @@
+>mtdbD00024812|Caenorhabditis_elegans|6239|Ala|TGC
+GGGATTTTAGTTTAATAAAAATATATGTTTTGCATACATAAGATAATAATTCTA
+>mtdbD00024802|Caenorhabditis_elegans|6239|Arg|ACG
+AGATGTAAAATAGATATTACTATGTTTGGTTACGGTCCAAAAAGATGCACATCTT
+>mtdbD00024796|Caenorhabditis_elegans|6239|Asn|GTT
+TAAGAGTTAGTTTAATATAGAATTGTTGACTGTTAATCAAAAGGTGTACCTCTTAA
+>mtdbD00024809|Caenorhabditis_elegans|6239|Asp|GTC
+AAAGTTTTAGTATAAAAAAGTATATTTTATTGTCAATAAAAAGGTAAAAACTTTA
+>mtdbD00024807|Caenorhabditis_elegans|6239|Cys|GCA
+GAAACCTTAGTATAATTTTAGTATATTTAATTGCAAATTAAATGGTATTGGTTTTT
+>mtdbD00024803|Caenorhabditis_elegans|6239|Gln|TTG
+TGCGATCTAGTTTAGAAAAAATATTTGTTTTTGGTGCAAAAGAGTTTGATTGCAT
+>mtdbD00024794|Caenorhabditis_elegans|6239|Glu|TTC
+GAGATAATAGTATAAATAAGTATGTTTCTTTTTCGCAGAAATGGTTTTTTATCTTA
+>mtdbD00024810|Caenorhabditis_elegans|6239|Gly|TCC
+GATTCTTTAGTATAATTCAGTATGTTTGACTTCCAATCAAAAGGTTTTGAGGATTA
+>mtdbD00024811|Caenorhabditis_elegans|6239|His|GTG
+AGCTTAATAGTTTATATTAAAATGTTTACTTGTGGTGTAAGAGAATATAGAGCTT
+>mtdbD00024801|Caenorhabditis_elegans|6239|Ile|GAT
+ACTTTTCTAGTAAAATATATTATATTATCTTGATAAGGTAAAGTTCCAGTTGGGAGAAGTA
+>mtdbD00024805|Caenorhabditis_elegans|6239|Leu1|TAG
+ACATGTCTAGTATAAGTTAATACATTAGATTTAGGTTCTAAAGATTTGTGATATGTT
+>mtdbD00024799|Caenorhabditis_elegans|6239|Leu2|TAA
+GTTGATATAGCATAAGAAGTGCATTTGTTTTAAGCGCAAAAGATATCCGTCAACT
+>mtdbD00024798|Caenorhabditis_elegans|6239|Lys|TTT
+AAGATGTTAACTTAAGTTTTAAAGTGCCAAACTTTTAATTTGGAAATGGTGGACCACATCTTA
+>mtdbD00024808|Caenorhabditis_elegans|6239|Met|CAT
+AGTAAGATAGGATAATTAAGTCTGTAAGGTTCATACCCTTGAGGTGGTTTTCTCTTATTA
+>mtdbD00024804|Caenorhabditis_elegans|6239|Phe|GAA
+ACTCTTTTAGTTTATAATTAAAATATGGCCCTGAAGAGGCTAAGAATATTAGGAGTA
+>mtdbD00024791|Caenorhabditis_elegans|6239|Pro|TGG
+CAGTAAATAGTTTAATAAAAATATAGCATTTGGGTTGCTAAGATATTATTACTGA
+>mtdbD00024800|Caenorhabditis_elegans|6239|Ser1|TCT
+AACGAGTTCATAAAGCAAGTCTTCTAAATTTGTTCTAGGTTAAATCCTGCTCGTTT
+>mtdbD00024795|Caenorhabditis_elegans|6239|Ser2|TGA
+AAACTATTTTTAAATATGTTTTGAAAACATGTTTTGAGGTAACTCGTAGTTTT
+>mtdbD00024806|Caenorhabditis_elegans|6239|Thr|TGT
+GCTATGATAGTTTAATTTAGAATATATAACTTGTAATTATAAGGTTTCTAGTAGCT
+>mtdbD00024793|Caenorhabditis_elegans|6239|Trp|TCA
+ACAGATATAAGTTAAGTTTAAACTATTGATCTTCAAAATCAAAAATTTATTTCTGTA
+>mtdbD00024797|Caenorhabditis_elegans|6239|Tyr|GTA
+AAGAGTTTAGTTTAAGTTAAAACGTTAGATTGTAAATCTAAAGATTATTGCTCTTG
+>mtdbD00024792|Caenorhabditis_elegans|6239|Val|TAC
+GAATTTTTAGTTTAATTTAGAATGTATCACTTACAATGATGGGGTTTAAAATTCT