IPyRSSA

IPyRSSA (Integrative Python library for RNA Secondary Structure Analysis) is a set of Python library to analyze RNA secondary structure and SHAPE data.

New

Python 3 is supported now. Python 2 is not supported.

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General module

`import General`

Function name	Usage
load_fasta	Read fasta file
write_fasta	Write fasta file
load_dot	Read dotBracket file
write_dot	Write dotBracket file
load_shape	Read SHAPE .out file
load_SHAPEMap	Read SHAPEmap file
load_ct	Read .ct file
write_ct	Write .ct file
init_pd_rect	Build a dataframe
init_list_rect	Build a list matrix
find_all_match	Find all match regions with a regex
bi_search	Binary search
calc_shape_gini	Calculate SHAPE gini index
calc_shape_structure_ROC	Calculate the ROC points structure and shape scores
calc_AUC	Calculate AUC with ROC points
calc_AUC_v2	Calculate AUC with dot and shape_list
seq_entropy	Calculate the entropy of the sequence.

Colors module

`import Colors`

Function name	Usage
format or f	Format a colorful text
color_SHAPE	Convert SHAPE list to colorful blocks
color_Seq_SHAPE	Convert sequence to colorful sequence
browse_shape	Print and compare single/multiple shape scores example
browse_multi_shape	Align multiple sequences and print shape scores example

Cluster module

`import Cluster`

Warning: This module can only be used on loginviewxx/mgtxx

Function name	Usage
new_job	Get a job handle
handle.set_job_depends	The job will be executed when parameter jobs done
handle.submit	Submit the job to queue
handle.has_finish	Return True if finished
handle.job_status	Return one of Not_Found, DONE, RUN, PEND, EXIT
handle.wait	Wait the job to finish
handle.kill	Kill the job

Seq module

`import Seq`

Prerequisites: pyliftover, pysam

Function name	Usage
reverse_comp	Get reversed complementary sequence of raw sequence
flat_seq	Flatten the long sequence to multiline sequence
format_gene_type	Classify the raw gene type in annotation to common gene type
Class:seqClass	A class to fetch sequence from big genome
lift_genome	Convert the genome version (hg19=>hg38)
search_subseq_from_genome	Search a pattern in genome region

Structure module

`import Structure`

Function name	Usage
predict_structure	Prediction secondary structure combine SHAPE or not
bi_fold	Prediction RNA interaction
search_TT_cross_linking	Search TT cross linking sites in structure
dyalign	Predict a common secondary structure for two sequences
multialign	Predict a common secondary structure for multiple sequences
estimate_energy	Calculate the folding free energy change of a structure
partition	Calculate the partition function
maxExpect	Calculate the max-expect structure
evaluate_dot	Evaluate the Sensitivty and PPV for a predicted structure relative to target structure
calc_structure_similarity	Calculate the structure similarity,distance
dot2ct	Dotbracket to list
dot2bpmap	Dotbracket to dictionary
parse_pseudoknot	Parse pseudoknot with ctList
ct2dot	ctList to dotbracket
write_ctFn	Save dot-bracket structure to .ct file
dot2align	Convert secondary structure to aligned sequence.
dot_from_ctFile	Read a dotbracket from .ct file
trim_stem	Trim a stem loop
find_stem_loop	Find stem loop from secondary structure
find_bulge_interiorLoop	Find bulges and interior loops from secondary structure
calcSHAPEStructureScore	Calculate strcuture - SHAPE agreement score for stem loop
sliding_score_stemloop	Find stem-loops in RNA with a sliding window
multi_alignment	Multiple sequence alignment with muscle
kalign_alignment	Multiple sequence alignment with kalign
global_search	Global align short sequences to multiple long sequences
align_find	Find the unaligned sequence region from aligned sequence
locate_homoseq	Locate homologous region in multiple sequences
dot_to_alignDot	Dotbracket to aligned dotbracket
shape_to_alignSHAPE	SHAPE list to aligned SHAPE list
annotate_covariation	Annotate raw sequence to colorful sequence by highlight the covariation sites
dot_F1	Compare predicted structure and true structure and calculate the F1 score
parse_structure	Given a dot-bracket structure, parse structure into all kinds of single-stranded bases and paired bases
refine_structure_interior	Check and make some some canonical base pairs in interior loops paired
refine_structure_stackingclosing	Check and make some some canonical base pairs in stacking end paired
refine_structure_hairpinclosing	Check and make some some canonical base pairs in hairpin paired

Visual module

`import Visual`

Prerequisites: java, VARNA (http://varna.lri.fr)

Function name	Usage
Plot_RNAStructure_Shape	Plot the RNA structure combine with SHAPE scores
Plot_RNAStructure_Base	Plot the RNA structure with different colors for ATCG
Plot_RNAStructure_highlight	Plot the RNA structure and highlight some regions
Map_rRNA_Shape	Output rRNA structure with PostScript format
get_rRNA_refseq	Return reference rRNA sequence

Rosetta module

`from D3 import Rosetta `

Prerequisites: ROSETTA, it can be only run in cluster

Function name	Usage
pred_3D_rosetta	Predict RNA 3D structure with ROSETTA

MCSym module

`from D3 import MCSym `

Function name	Usage
upload_MCSym_job	Upload MCSym RNA 3D structure prediction job
get_MCSym_status	Get the status of the job
minimize_MCSym_newThread	Minimize the pdbs
score_MCSym_newThread	Score and ranking pdbs
fetch_top_MCSym_pdb_newThread	Download top scored pdbs

HDOCK module

`from D3 import HDOCK`

Function name	Usage
upload_HDOCK_job	Upload HDOCK RNA-protein docking job
get_HDOCK_status	Get the status of the job
guess_HDOCK_time_left	guess the time to leave
fetch_HDOCK_results	Download all results
fetch_HDOCK_top10_results	Download top 10 results

Figures module

`import Figures`

Function name	Usage
stackedBarPlot	Plot a stacked bar figure
violinPlot	Plot a violin figure
piePlot	Plot a pie figure
boxPlot	Plot a box figure
cdf	Plot a CDF curve

GPU module

import GPU

Function name	Usage
get_gpu_processes	Get process handles running on GPU
get_gpu_list	Get a list of available gpu
get_free_gpus	Get a list of GPU id without process run on it

Alignment

import Alignment

Function name	Usage
blast_seq	Use blastn to search sequence
annotate_seq	Given a sequence and blastdb, search and annotate the sequence

Covariation

import Covariation

Function name	Usage
dot2sto	Covert dot to stockholm file
cmbuild	Create .cm file with stockholm alignment
cmcalibrate	Calibrate a .cm file
cmsearch	Call cmsearch programe to search aligned sequence agaist cm model
R_scape	Call R-scape to call covariation base pairs
read_RScape_result	Read the R-scape result
get_alignedPos2cleanPos_dict	Get a distionary {align_pos: raw_pos}
call_covariation	Give sequence and dot. Run covariation pipeline
calc_MI	Calculate the Mutual information for aligned sequences
calc_RNAalignfold	Calculate the RNAalifold covariation score for aligned sequences
calc_RNAalignfold_stack	Calculate the RNAalifold covariation score (consider stack) for aligned sequences
collect_columns	Given multialignment, return alignment columns
calc_covBP_from_sto	Given multialignment, return covariation score for each column pair