GitHub - tgorkovets/2015_histone_seq

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Name		Name	Last commit message	Last commit date
Latest commit History 1 Commits
inp_data		inp_data
results		results
02_def_refseq.py		02_def_refseq.py
03_redef_variants.py		03_redef_variants.py
0_get_seq.py		0_get_seq.py
1_conservation.py		1_conservation.py
1_example_aln_H2A.py		1_example_aln_H2A.py
2_H2AZ_cellular.py		2_H2AZ_cellular.py
2_H2A_ca_cellular.py		2_H2A_ca_cellular.py
2_H2B_ca_cellular.py		2_H2B_ca_cellular.py
L_hist_aln.py		L_hist_aln.py
L_seq_subset.py		L_seq_subset.py
example_cons_ent_unw.png		example_cons_ent_unw.png
example_cons_sofp_psic_renorm1.png		example_cons_sofp_psic_renorm1.png
example_cons_sofp_unw.png		example_cons_sofp_unw.png
example_cons_sofp_unw_renorm1.png		example_cons_sofp_unw_renorm1.png
example_h2a.html		example_h2a.html
example_motifs_H2A.svg		example_motifs_H2A.svg
readme.txt		readme.txt

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#Histone seq analysis project
Extract useful information form histone sequence DB.
#Data structure
inp_data - input data
L_.... - libraries with examples that perform core functions.
we might want to move some of them to MYSOFT and to CBC.
int_data - intermediate data.
taxdump - NCBI taxonomy dump.

#inp_data
seqs.csv - dump of HistoneDB 2.0 database as of October 31, 2015
with some fixes: deleted 694915110, 334187383, all NOGI
features.json - our features file from HistoneDB 2.0.

#Pipeline files
0_get_seq.py - downloads the sequences and saves them as pickle int_data/fasta_dict.p. key is the gi.


#Libraries
L_seq_subset.py - routines that subset histone sequnces, by variants, by seq features, by taxonomy.