IPyRSSA (Integrative Python library for RNA Secondary Structure Analysis) is a set of Python library to analyze RNA secondary structure and SHAPE data.
Python 3 is supported now. Python 2 is not supported.
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| 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. |
| 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 |
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 |
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 |
| 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 |
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 |
Prerequisites: ROSETTA, it can be only run in cluster
| Function name | Usage |
|---|---|
| pred_3D_rosetta | Predict RNA 3D structure with ROSETTA |
| 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 |
| 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 |
| 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 |
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 |
import Alignment
| Function name | Usage |
|---|---|
| blast_seq | Use blastn to search sequence |
| annotate_seq | Given a sequence and blastdb, search and annotate the sequence |
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 |