diff --git a/rna_tools/tools/rna_alignment/rna_align_coverage.py b/rna_tools/tools/rna_alignment/rna_align_coverage.py new file mode 100644 index 000000000..33a703ed0 --- /dev/null +++ b/rna_tools/tools/rna_alignment/rna_align_coverage.py @@ -0,0 +1,72 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- +""" + +""" +from Bio import AlignIO +import argparse +from icecream import ic +import sys +ic.configureOutput(outputFunction=lambda *a: print(*a, file=sys.stderr)) +ic.configureOutput(prefix='> ') + + +def get_parser(): + parser = argparse.ArgumentParser( + description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) + parser.add_argument("-v", "--verbose", + action="store_true", help="be verbose") + parser.add_argument("sequence", help="", default="") # nargs='+') + parser.add_argument("stk", help="", default="") # nargs='+') + return parser + + +if __name__ == '__main__': + parser = get_parser() + args = parser.parse_args() + + verbose = args.verbose + + # Load the alignment + alignment = AlignIO.read(args.stk, "stockholm") + alignment_name = args.stk.split('/')[-1] + # Define the target sequence ID + target_id = args.sequence + + + # Find the target sequence + target_seq = None + for record in alignment: + if record.id == target_id: + target_seq = record.seq + break + + if target_seq is None: + print(f"Target sequence '{target_id}' not found in the alignment.") + else: + seq_len = 0 + cols_no_coverage = 0 + # Collect columns where the target sequence has no gaps + filtered_columns = [] + for col_index in range(alignment.get_alignment_length()): + if target_seq[col_index] != "-": + column = [record.seq[col_index] for record in alignment] + filtered_columns.append(column) + seq_len += 1 + + # Display filtered columns + if verbose: print(f"Columns where the target sequence '{target_id}' has no gaps:") + for col in filtered_columns: + if verbose: print(col, len(col)) + # Count the number of '-' + gap_count = col.count('-') + if verbose: print(f"Number of '-': {gap_count}") + ratio_per_col = gap_count/(len(col) - 1) + if verbose: print(f'ratio of gaps: {ratio_per_col}') # -1 target_sequence + if ratio_per_col > 0.5: + if verbose: print('WARNING: more than 50% gaps in column', cols_no_coverage) + cols_no_coverage +=1 + if verbose: print() + + ratio = round((1 - (cols_no_coverage / seq_len)) * 100) + print(f"Query {target_id} length {seq_len} in the alignment {alignment_name} number of columns with low coverage (<50%) for the query sequence {cols_no_coverage}; coverge for the query: {ratio}%") diff --git a/rna_tools/tools/rna_alignment/test.sh b/rna_tools/tools/rna_alignment/test.sh old mode 100644 new mode 100755 index c00b55354..e62c51373 --- a/rna_tools/tools/rna_alignment/test.sh +++ b/rna_tools/tools/rna_alignment/test.sh @@ -1 +1,9 @@ -python rna_align_foldability.py test_data/gmp_ref.sto test_data/gmp_foldability.csv --verbose +#python rna_align_fetch_seed.py RF00026 +#python rna_align_fetch_cm.py RF00026 +#python rna_align_subcols.py test_data/u6_isl_rfam.sto +#python rna_align_foldability.py test_data/gmp_ref.sto test_data/gmp_foldability.csv --verbose + +python rna_align_coverage.py xrRNA test_data/xrrna_rfam.sto +#easel alistat test_data/xrrna_rfam.sto +python rna_align_coverage.py u6isl test_data/u6_isl_rfam.sto + diff --git a/rna_tools/tools/rna_alignment/test_data/u6_isl_rfam.sto b/rna_tools/tools/rna_alignment/test_data/u6_isl_rfam.sto new file mode 100644 index 000000000..e275d37a9 --- /dev/null +++ b/rna_tools/tools/rna_alignment/test_data/u6_isl_rfam.sto @@ -0,0 +1,765 @@ +# STOCKHOLM 1.0 +#=GF AU Infernal 1.1.2 + +u6isl -------.........----...-....................--..---..---------.----..------.---....-----------.........................................................----UGGC.CCCUGCGCAA.GGAUGACA--...------..-------- +#=GR u6isl PP ...........................................................................................................................................................****.**********.********..................... +AB010698.1/46416-46518 GUCCC--.........UUCG...-....................GG..GAC..AUCUGAUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAUAAA.uCGAGAAAU +#=GR AB010698.1/46416-46518 PP *****...........****........................**..***..*********.****..******.***....***********.........................................................********.**********.**********...*****9.9******** +AARH01001853.1/272694-272592 GUCUC--.........UUCG...-....................GA..GAC..AUCUGAUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CACAAA.uCGAGAAAU +#=GR AARH01001853.1/272694-272592 PP *****...........****........................**..***..*********.****..******.***....***********.........................................................********.**********.**********...*****9.9******** +X60506.1/390-492 GUCCC--.........UUCG...-....................GG..GAC..AUCCGAUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CACAAA.uCGAGAAAU +#=GR X60506.1/390-492 PP *****...........****........................**..***..*********.****..******.***....***********.........................................................********.**********.**********...*****9.9******** +AC146705.11/15272-15374 GUCCC--.........UUCG...-....................GG..GAC..AUCCGAUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CACAAA.uCGAGAAAU +#=GR AC146705.11/15272-15374 PP *****...........****........................**..***..*********.****..******.***....***********.........................................................********.**********.**********...*****9.9******** +AASG02002949.1/2307-2409 GUCCC--.........UUCG...-....................GG..GAC..AUCCGAUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CACAAA.uCGAGAAAU +#=GR AASG02002949.1/2307-2409 PP *****...........****........................**..***..*********.****..******.***....***********.........................................................********.**********.**********...*****9.9******** +AACV01009611.1/38269-38167 GUCCC--.........UUCG...-....................GG..GAC..AUCCGAUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CACAAA.uCGAGAAAU +#=GR AACV01009611.1/38269-38167 PP *****...........****........................**..***..*********.****..******.***....***********.........................................................********.**********.**********...*****9.9******** +AAAA02013555.1/2292-2394 GUCCC--.........UUCG...-....................GG..GAC..AUCCGAUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CACAAA.uCGAGAAAU +#=GR AAAA02013555.1/2292-2394 PP *****...........****........................**..***..*********.****..******.***....***********.........................................................********.**********.**********...*****9.9******** +CR855100.1/43897-43999 GUCCC--.........UUCG...-....................GG..GAC..AUCCGAUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CACAAA.uCGAGAAAU +#=GR CR855100.1/43897-43999 PP *****...........****........................**..***..*********.****..******.***....***********.........................................................********.**********.**********...*****9.9******** +X52315.1/1-103 GUCUC--.........UUCG...-....................GA..GAC..AUCCGAUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CACAAA.uCGAGAAAU +#=GR X52315.1/1-103 PP *****...........****........................**..***..*********.****..******.***....***********.........................................................********.**********.**********...*****9.9******** +X51447.1/262-364 GUCCC--.........UUCG...-....................GG..GAC..AUCCGAUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CACAAA.uCGAGAAAU +#=GR X51447.1/262-364 PP *****...........****........................**..***..*********.****..******.***....***********.........................................................********.**********.**********...*****9.9******** +AAXJ01018701.1/864-762 ACCCC--.........UUCG...-....................GG..GGU..AUCCGAUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CACAAA.uCGAGAAGU +#=GR AAXJ01018701.1/864-762 PP *****...........****........................**..***..*********.****..******.***....***********.........................................................********.**********.**********...*****9.9******** +AAQA01000086.1/111608-111711 GUUCAU-.........UCCG...A....................UG..AAC..AUAUACUAA.AAUU..GGAACA.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAUU..CGUGAAGC +#=GR AAQA01000086.1/111608-111711 PP *****9..........9999...*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +L26849.1/150-253 GUUCAU-.........UCCG...A....................UG..AAC..AUAUACUAA.AAUU..GGAACA.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAUU..CGUGAAGC +#=GR L26849.1/150-253 PP *****9..........9999...*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +X51387.1/158-259 GUUCU--.........UCCG...-....................AG..AAC..AUAUACUAA.AAUU..GGAACA.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAUU..CGUGAAGC +#=GR X51387.1/158-259 PP *****...........9999........................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AANU01133867.1/371-269 ACCCC--.........CUCG...-....................GG..GGU..AUCCGAUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CACAAA.uCGAGAAGU +#=GR AANU01133867.1/371-269 PP *****...........9***........................**..***..*********.****..******.***....***********.........................................................********.**********.**********...*****9.9******** +X63066.1/363-465 GCCCC--.........UUCG...-....................GG..GAC..AUCCGAUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CACAAA.uCGAGAAAU +#=GR X63066.1/363-465 PP *****...........****........................**..***..*********.****..******.***....***********.........................................................********.**********.**********...*****9.9******** +AAAB01008807.1/5121648-5121542 GUCCUUG........cUUCG..gC....................AG..GAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAAU..CGUGAAGC +#=GR AAAB01008807.1/5121648-5121542 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AAWU01008690.1/11499-11605 GUCUUUG........cUUCG..gC....................AA..GAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAAU..CGUGAAGC +#=GR AAWU01008690.1/11499-11605 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AAGE02013372.1/83708-83814 GUCUUUG........cUUCG..gC....................AA..GAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAAU..CGUGAAGC +#=GR AAGE02013372.1/83708-83814 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AABU01002774.1/16804311-16804417 GUUCUUG........cUUCG..gC....................AG..AAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAAU..CGUGAAGC +#=GR AABU01002774.1/16804311-16804417 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AAGH01007200.1/1053-947 GUUCUUG........cUUCG..gC....................AG..AAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAAU..CGUGAAGC +#=GR AAGH01007200.1/1053-947 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AADE01001799.1/12821-12927 GUUCUUG........cUUCG..gC....................AG..AAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAAU..CGUGAAGC +#=GR AADE01001799.1/12821-12927 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AAEU02000254.1/81013-80907 GUUCUUG........cUUCG..gC....................AG..AAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAAU..CGUGAAGC +#=GR AAEU02000254.1/81013-80907 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AAPQ01001284.1/654-760 GUUCUUG........cUUCG..gC....................AG..AAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAAU..CGUGAAGC +#=GR AAPQ01001284.1/654-760 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AAPP01016905.1/3608-3714 GUUCUUG........cUUCG..gC....................AG..AAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAAU..CGUGAAGC +#=GR AAPP01016905.1/3608-3714 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AAQB01008633.1/461913-461807 GUUCUUG........cUUCG..gC....................AG..AAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAAU..CGUGAAGC +#=GR AAQB01008633.1/461913-461807 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AANI01001778.1/524-630 GUUCUUG........cUUCG..gC....................AG..AAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAAU..CGUGAAGC +#=GR AANI01001778.1/524-630 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AAIZ01003051.1/11867-11761 GUUCUUG........cUUCG..gC....................AG..AAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAAU..CGUGAAGC +#=GR AAIZ01003051.1/11867-11761 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AAPT01019380.1/23511-23405 GUUCUUG........cUUCG..gC....................AG..AAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAAU..CGUGAAGC +#=GR AAPT01019380.1/23511-23405 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AAPU01011102.1/63061-63167 GUUCUUG........cUUCG..gC....................AG..AAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAAU..CGUGAAGC +#=GR AAPU01011102.1/63061-63167 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AABS01000051.1/274751-274857 GUACUAG........cUUCG..gC....................AG..UAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAAU..CGUGAAGC +#=GR AABS01000051.1/274751-274857 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AAHY01132583.1/7739-7845 GUGCUCG........cUUCG..gC....................AG..CAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAAU..CGUGAAGC +#=GR AAHY01132583.1/7739-7845 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AAFC03115769.1/4330-4436 GUGCUCGc.......uUUGG...C....................AG..CAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAUU..CGUGAAGU +#=GR AAFC03115769.1/4330-4436 PP ********.......66666...*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AAPY01153714.1/3278-3172 GUGCUCGc.......uUUGG...C....................AG..CAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAUU..CGUGAAGU +#=GR AAPY01153714.1/3278-3172 PP ********.......66666...*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AALT01529386.1/701-595 GUGCUCG........cUUCG..gC....................AG..CAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAUU..CGUGAAGU +#=GR AALT01529386.1/701-595 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AAYZ01436191.1/1883-1777 GUGCUCG........cUUCG..gC....................AG..CAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAUU..CGUGAAGU +#=GR AAYZ01436191.1/1883-1777 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +BAAB01141103.1/711-817 GUACUUG........cUUCG..gC....................AG..UAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAAU..CGUGAAGC +#=GR BAAB01141103.1/711-817 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AAZX01000860.1/13921-13815 GUACUUG........cUUCG..gC....................AG..UAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAAU..CGUGAAGC +#=GR AAZX01000860.1/13921-13815 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AACY022149992.1/529-635 GUACUUG........cUUCG..gC....................AG..UAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAAU..CGUGAAGC +#=GR AACY022149992.1/529-635 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AATU01006594.1/28185-28081 GACCAC-.........UUCG...G....................UG..GUC..AUCCGUAAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAUAAA.uCGAGAAGU +#=GR AATU01006594.1/28185-28081 PP ******..........****...*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...*****9.9******** +ABAV01046662.1/5606-5712 GUGCUCG........cUUCG..gC....................AG..CAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAUU..CGUGAAGC +#=GR ABAV01046662.1/5606-5712 PP *******........*9999..8*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AAFR03037834.1/2280-2178 GUGCU--.........UCAG...C....................AG..CAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCACAA.GGAUGACAUG...CAAAUU..CGUGAAGC +#=GR AAFR03037834.1/2280-2178 PP *****...........9***...*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +ABDC01230141.1/8073-7967 GUGCUUGc.......uUUGG...C....................AG..CAC..AUAUACUAA.AAUU..GGAACA.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAUU..UGUGAAGU +#=GR ABDC01230141.1/8073-7967 PP ********.......66666...*....................**..***..*********.****..******.***....***********.........................................................********.**********.**********...******..******** +AANN01390182.1/1050-1156 GUGCUUG........cUUCG..gC....................AG..CAC..AUAUACUAA.AAUU..GGAACG.AUA....CAGAGAAGAUU.........................................................AGCAUGGC.CCCUGCGCAA.GGAUGACACG...CAAAUU..CGUGAAGC +#=GR AANN01390182.1/1050-1156 PP 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............GUUCCAUAUUUUU +#=GR AAEX03005034.1/14917-14815 PP ............************* +AC242743.1/25579-25465 agacc..uacgg-GUCUCAAUAUUU +#=GR AC242743.1/25579-25465 PP *****..****5.555555555555 +BAAB01206473.1/1073-967 ............GUUCCACAUUUUU +#=GR BAAB01206473.1/1073-967 PP ............************* +M24606.1/401-507 ............GUUCCACAUUUUU +#=GR M24606.1/401-507 PP ............************* +AL844509.2/1632740-1632633 ............AAUGUAAUUUUUU +#=GR AL844509.2/1632740-1632633 PP ............************* +AC188639.6/7118-7225 ............GUUCCAUAUUUUU +#=GR AC188639.6/7118-7225 PP ............************* +#=GC SS_cons ............::::::::::::: +#=GC RF ............guuccauaUUUUU +// diff --git a/rna_tools/tools/rna_alignment/test_data/xrrna_rfam.sto b/rna_tools/tools/rna_alignment/test_data/xrrna_rfam.sto new file mode 100644 index 000000000..bf58eafef --- /dev/null +++ b/rna_tools/tools/rna_alignment/test_data/xrrna_rfam.sto @@ -0,0 +1,189 @@ +# STOCKHOLM 1.0 +#=GF AU Infernal 1.1.2 + +xrRNA GggaguauaaaGAACACuAGCCGAGC............AAAC...GAAAGUUGCAAGCAUCGGAAG.UCAAgucuuucacaucagccggacacacaaaauagauuucaaauuucuagcaggauuugcaucaggcuuucuugccgcaaucccaauuucaguagccgguauuuacuuagucuaccucaaaaucucacccacg +#=GR xrRNA PP 577777777777888888********............****...*******************99.9999********************************************************************************************************************************* +NC_001726.1/2661-2711 G..........UCACGU.AGCUAGUA............---C...-CAGGUUGCAAUA-CUAGA-G.CGUU................................................................................................................................. +#=GR NC_001726.1/2661-2711 PP *..........******.********...............*....**********77.*****.7.7777................................................................................................................................. +NC_035451.1/3370-3423 G..........UAACGUcAGCCGCCA............---A...CACAGUUGCAA-GAGCGGAAG.ACGU................................................................................................................................. +#=GR NC_035451.1/3370-3423 PP *..........***************...............9...9**********.*********.****................................................................................................................................. +NC_000874.1/3464-3517 G..........CAUCCCgAGCCACCA............---U...AUAGGUUGCAA-GAGUGGAAC.GGGA................................................................................................................................. +#=GR NC_000874.1/3464-3517 PP *..........***************...............9...***********.*********.****................................................................................................................................. +NC_025837.1/3484-3536 U..........UUGAACcAGCGAACA............---A...UUCAGUUGCGA-GAUUCGAGG.UUUC................................................................................................................................. +#=GR NC_025837.1/3484-3536 PP *..........***************...............*...***********.*********.****................................................................................................................................. +NC_031747.1/3736-3788 G..........ACAGAU.AGCCGGUA............U--C...AGUUGUUGCAAUAGCCGGA-G.UCUU................................................................................................................................. +#=GR NC_031747.1/3736-3788 PP *..........******.********............7..8...*******************.*.****................................................................................................................................. +NC_010809.1/3332-3387 A..........GAACACuAGCCGGAA............AUAC...-GUUGUUGCAAUUGCCGGAAG.UUUA................................................................................................................................. +#=GR NC_010809.1/3332-3387 PP *..........***************............****....********************.****................................................................................................................................. +NC_018571.2/3455-3510 U..........CAUAACuAGCCGGAA............AUAC...-GUUGUUGCAAUUGCCGGAAG.UUAA................................................................................................................................. +#=GR NC_018571.2/3455-3510 PP *..........**99999********............****....********************.****................................................................................................................................. +NC_004751.1/3564-3618 -..........AAAACU.AGCCGGAC............AAAC...GUAAGUUGCAAGUGCCGGAAG.UCA-................................................................................................................................. +#=GR NC_004751.1/3564-3618 PP ...........666666.********............****...*******************77.777.................................................................................................................................. +NC_021484.1/3332-3389 C..........UCAAGUcAGCCAGGC............AAAU...UCGAGUUGCAAGCACUGGAUG.ACCU................................................................................................................................. +#=GR NC_021484.1/3332-3389 PP *..........***************............****...*********************.****................................................................................................................................. +LN865080.1/843-898 C..........AUAGCC.AGCCACAC............AUAC...ACAAGUUGCAAGUAGUGGA-G.GUUC................................................................................................................................. +#=GR LN865080.1/843-898 PP 9..........999999.********............****...*******************.9.9999................................................................................................................................. +NC_006265.1/3306-3359 -..........GAAGCU.AGCCGAGA............AACA...CGUUGUUGCAAUCGUCGGA-A.GCAA................................................................................................................................. +#=GR NC_006265.1/3306-3359 PP ...........999***.********............****...*******************.9.99**................................................................................................................................. +NC_034247.1/3465-3519 C..........UCAGUU.AGCCGGAA............AGUC...-GCUGUUGCAAUUGCCGGAAA.ACUU................................................................................................................................. +#=GR NC_034247.1/3465-3519 PP *..........******.********............****....********************.****................................................................................................................................. +NC_010732.1/3457-3513 A..........UAAACU.AGCCAAGC............AUAC...RUCAGUUGCRAGCGUUGGAAG.UUCA................................................................................................................................. +#=GR NC_010732.1/3457-3513 PP 9..........999999.********............****...*********************.****................................................................................................................................. +NC_003688.1/3317-3374 A..........GAACACuAGCCAAGC............ACAC...ACGAGUUGCAAGCAUUGGAAG.UCUG................................................................................................................................. +#=GR NC_003688.1/3317-3374 PP *..........***************............****...*********************.****................................................................................................................................. +NC_036803.1/3442-3498 U..........AUAACU.AGCCAAGC............AUAC...AUCAGUUGCAAGCGUUGGAAG.UUCA................................................................................................................................. +#=GR NC_036803.1/3442-3498 PP 9..........999999.********............****...*********************.****................................................................................................................................. +JX427534.1/587-643 U..........AUAACU.AGCCAAGC............AUAC...AUCAGUUGCAAGCAUUGGAAG.UUCA................................................................................................................................. +#=GR JX427534.1/587-643 PP 9..........999999.********............****...*********************.****................................................................................................................................. +NC_004756.1/3344-3398 -..........-AACACuAGCCGAGC............AAAC...GAAAGUUGCAAGCAUCGGA-A.GUCA................................................................................................................................. +#=GR NC_004756.1/3344-3398 PP ............**************............****...*******************.9.9999................................................................................................................................. +NC_002766.1/3422-3478 U..........ACAAAC.AGCCGGGU............AAAC...AUCAGUUGCAAACACCGGAAG.UUUU................................................................................................................................. +#=GR NC_002766.1/3422-3478 PP *..........******.********............****...*********************.****................................................................................................................................. +NC_029906.1/3325-3382 C..........UGAAGCuAGCCAGAC............AUAC...GUGAGUUGCAAGUACUGGAUA.GCUU................................................................................................................................. +#=GR NC_029906.1/3325-3382 PP *..........***************............****...*******************99.****................................................................................................................................. +MN204612.1/3410-3464 G..........AAACAU.AGCCUCAC............AUAC...-ACAGUUGCAAGUGGAGGAGU.GUUU................................................................................................................................. +#=GR MN204612.1/3410-3464 PP *..........******.********............****....******************99.****................................................................................................................................. +MK482114.1/3574-3626 -..........--CAGCuAGCCCGGA............AUUU...-GUUGUUGCAAUCGCGGGAAA.AGAA................................................................................................................................. +#=GR MK482114.1/3574-3626 PP .............55555********............****....********************.**55................................................................................................................................. +LC428360.1/3278-3332 -..........GAAGUU.AGCCCUAC............AUAC...GUAAGUUGCAAGUAAGGGA-A.ACAA................................................................................................................................. +#=GR LC428360.1/3278-3332 PP ...........******.********............****...*******************.*.****................................................................................................................................. +LC424839.1/3422-3477 -..........CGGAGUgAGCCAGAC............AUAC...GCAAGCUGCAAGUACUGGA-C.ACUA................................................................................................................................. +#=GR LC424839.1/3422-3477 PP ...........***************............****...*******************.*.****................................................................................................................................. +MK333461.1/3445-3501 C..........UUAGUU.AGCCAAGC............AUAC...AUCAGUUGCAAGCGUUGGAAA.CUUA................................................................................................................................. +#=GR MK333461.1/3445-3501 PP *..........******.********............****...*********************.****................................................................................................................................. +MH645154.1/3368-3424 -..........UAUAGUaAGCCAAGC............AUAC...AUCAGUUGCAAGCAUUGGAAU.ACUU................................................................................................................................. +#=GR MH645154.1/3368-3424 PP ...........***************............****...*********************.****................................................................................................................................. +MK050791.1/3409-3465 U..........ACAGAC.AGCCAGAC............ACAC...GCAAGUUGCAAGUACUGGAAGuCUUA................................................................................................................................. +#=GR MK050791.1/3409-3465 PP *..........******.********............****...*********************99999................................................................................................................................. +LR584020.1/3338-3392 -..........GAAGUU.AGCCCUAC............AUAC...GUAAGUUGCAAGUAAGGGA-A.ACAA................................................................................................................................. +#=GR LR584020.1/3338-3392 PP ...........******.********............****...*******************.*.****................................................................................................................................. +L39983.1/338-394 A..........UAAAAC.AGCCGGGU............AAAC...AUCAGUUGCAAACACCGGAAG.UUUU................................................................................................................................. +#=GR L39983.1/338-394 PP *..........******.********............****...*********************.****................................................................................................................................. +NC_028793.1/3525-3581 G..........AAAACU.AGCCAAGC............ACAC...GCGAGUUGCAAGCAUUGGAAG.UUCA................................................................................................................................. +#=GR NC_028793.1/3525-3581 PP 8..........888888.********............****...*********************.****................................................................................................................................. +KT963000.1/3530-3585 -..........UACACU.AGCCAAGC............AAAC...ACGAGUUGCAAGCAUUGGAAG.UAAA................................................................................................................................. +#=GR KT963000.1/3530-3585 PP ...........******.********............****...*********************.****................................................................................................................................. +NC_034265.1/3498-3554 A..........UAAGCU.AGCCAAGC............AUAC...ACGAGUUGCAAGCAUUGGAAG.UUCA................................................................................................................................. +#=GR NC_034265.1/3498-3554 PP 6..........666666.********............****...*********************.****................................................................................................................................. +NC_034207.1/3516-3572 C..........ACGAUC.AGCCAAGC............AUAC...AUCAGUUGCAAGCGUUGGAGA.UCAC................................................................................................................................. +#=GR NC_034207.1/3516-3572 PP *..........******.********............****...*********************.****................................................................................................................................. +NC_027703.1/3484-3543 -..........UACAUAcAGCCGGGC............AUAC...CGUAGUUGCAAGCGCCGGA-A.AGUAuc............................................................................................................................... +#=GR NC_027703.1/3484-3543 PP ...........5555555********............****...*******************.6.66667*............................................................................................................................... +KC960436.1/599-653 U..........AAAGCC.AGCCGAGU............----uagACUUGUUGCAAACGUCGGAGG.CUAA................................................................................................................................. +#=GR KC960436.1/599-653 PP *..........******.********................6667********************.****................................................................................................................................. +MF136435.1/2804-2858 U..........AAACAC.AGCCAAUA............---A...UCUUGUUGCAAUAGUUGGAGU.GUUC................................................................................................................................. +#=GR MF136435.1/2804-2858 PP *..........******.********...............9...9********************.****................................................................................................................................. +NC_008249.1/3486-3539 A..........CAGAGAuAGCCGACU............---A...ACUAGUUGCGA-GAUCGGA-G.UCUC................................................................................................................................. +#=GR NC_008249.1/3486-3539 PP *..........***************...............*...***********.*******.*.****................................................................................................................................. +NC_034246.1/3377-3430 U..........CAGAAUcAGCCCUAC............---A...UCAAGUUGCGAGUGAGGGA-G.AUUC................................................................................................................................. +#=GR NC_034246.1/3377-3430 PP *..........***************...............9...9******************.*.****................................................................................................................................. +NC_014545.1/3448-3504 C..........CUGAGCuAGCUCUUA............---A...UCUUGUUGCAUUAGAGAGAAGcUUAA................................................................................................................................. +#=GR NC_014545.1/3448-3504 PP *..........***************...............9...9******************999****................................................................................................................................. +LN865083.1/839-907 G..........AAACAC.AGCCGGCAaauaaacuuaaaAUAA...GUAGGUUGCAA-GAUCGGAGU.GUAC................................................................................................................................. +#=GR LN865083.1/839-907 PP 9..........999999.************************...***********.*******88.8887................................................................................................................................. +MH323436.1/3743-3795 C..........UCCAGU.AGCUGAAG............---C...GAAAGUUGCAACUGUCAGAAC.UGU-................................................................................................................................. +#=GR MH323436.1/3743-3795 PP *..........******.********...............*...*********************.***.................................................................................................................................. +NC_034836.1/4190-4264 -..........-CCCCCcAGCCGAAA............GUUC...-UAGGUUGCAAUUGUCGGU-G.GGCUccggcguaag....................................................................................................................... +#=GR NC_034836.1/4190-4264 PP ............777777********............****....******************.8.88888*********....................................................................................................................... +NC_032224.1/3354-3415 C..........GAGAGUcAGCCAAAC............AAAC...ACAAGUUGCAAGUGUUGGA-G.ACUCau............................................................................................................................... +#=GR NC_032224.1/3354-3415 PP *..........***************............****...*******************.9.999999............................................................................................................................... +NC_033229.1/3703-3758 -..........CAAAAUcAGCCACAC............AUAC...ACAAGUUGCGAGUAGUGGA-G.AUUC................................................................................................................................. +#=GR NC_033229.1/3703-3758 PP ...........8888888********............****...*******************.9.9999................................................................................................................................. +URS00021ED9C7_12045/1-51 -..........GGAACU.AGCUCAGC............AUAC...ACGAGUUGCAAGCAUGGGAAG.UUCA................................................................................................................................. +#=GR URS00021ED9C7_12045/1-51 PP ...........555555.********............****...*********************.****................................................................................................................................. +#=GC SS_cons :..........:<<<<<.--<<<<<<............____...___________>>->>>>->>.>>>:................................................................................................................................. +#=GC RF u..........uaaacu.AGCCgagC............AUAC...acaAGUUGCAAGcAucGGAag.uuua................................................................................................................................. + +xrRNA ugcggagcaucguuA-------.----- +#=GR xrRNA PP *****6666666666............. +NC_001726.1/2661-2711 ..............AGUCCUGG.GGCGU +#=GR NC_001726.1/2661-2711 PP ..............********.***** +NC_035451.1/3370-3423 ..............AGUCUGUG.UCAAA +#=GR NC_035451.1/3370-3423 PP ..............********.***** +NC_000874.1/3464-3517 ..............AGUCCUAU.AGAUA +#=GR NC_000874.1/3464-3517 PP ..............********.***** +NC_025837.1/3484-3536 ..............AGUCUGAA.UCAU- +#=GR NC_025837.1/3484-3536 PP ..............********.****. +NC_031747.1/3736-3788 ..............AGUCAACG.UACA- +#=GR NC_031747.1/3736-3788 PP ..............********.****. +NC_010809.1/3332-3387 ..............AGCCAAC-.UACAA +#=GR NC_010809.1/3332-3387 PP ..............*******..99999 +NC_018571.2/3455-3510 ..............AGUCAAC-.UACAA +#=GR NC_018571.2/3455-3510 PP ..............*******..99999 +NC_004751.1/3564-3618 ..............AGUCUUAC.ACACA +#=GR NC_004751.1/3564-3618 PP ..............********.***** +NC_021484.1/3332-3389 ..............AGUCUCGA.UACAU +#=GR NC_021484.1/3332-3389 PP ..............********.***** +LN865080.1/843-898 ..............AGUCUUGU.UACCA +#=GR LN865080.1/843-898 PP ..............********.***** +NC_006265.1/3306-3359 ..............AGCCAAC-.UACAA +#=GR NC_006265.1/3306-3359 PP ..............*******..99999 +NC_034247.1/3465-3519 ..............AGUCAGCU.ACAC- +#=GR NC_034247.1/3465-3519 PP ..............********.8888. +NC_010732.1/3457-3513 ..............AGUCUGAU.UACCA +#=GR NC_010732.1/3457-3513 PP ..............********.***** +NC_003688.1/3317-3374 ..............AGUCUCGU.UACCA +#=GR NC_003688.1/3317-3374 PP ..............********.***** +NC_036803.1/3442-3498 ..............AGUCUGAU.UACCA +#=GR NC_036803.1/3442-3498 PP ..............********.***** +JX427534.1/587-643 ..............AGUCUGAU.UACCA +#=GR JX427534.1/587-643 PP ..............********.***** +NC_004756.1/3344-3398 ..............AGUCUUUC.ACAUC +#=GR NC_004756.1/3344-3398 PP ..............********.***** +NC_002766.1/3422-3478 ..............AGUCUGAU.UACAC +#=GR NC_002766.1/3422-3478 PP ..............********.***** +NC_029906.1/3325-3382 ..............AGUCUCAC.ACAUU +#=GR NC_029906.1/3325-3382 PP ..............********.***** +MN204612.1/3410-3464 ..............AGUCUGUU.ACCA- +#=GR MN204612.1/3410-3464 PP ..............********.****. +MK482114.1/3574-3626 ..............AGUCAAC-.UACAU +#=GR MK482114.1/3574-3626 PP ..............5555555..44444 +LC428360.1/3278-3332 ..............AGUCUUAC.ACCCG +#=GR LC428360.1/3278-3332 PP ..............********.***** +LC424839.1/3422-3477 ..............AGCCUUGC.ACAUA +#=GR LC424839.1/3422-3477 PP ..............********.***** +MK333461.1/3445-3501 ..............AGUCUGAU.UACCU +#=GR MK333461.1/3445-3501 PP ..............********.***** +MH645154.1/3368-3424 ..............AGCCUGAU.UACCA +#=GR MH645154.1/3368-3424 PP ..............********.***** +MK050791.1/3409-3465 ..............AGUCUUGU.UACA- +#=GR MK050791.1/3409-3465 PP ..............********.****. +LR584020.1/3338-3392 ..............AGUCUUAC.ACCCG +#=GR LR584020.1/3338-3392 PP ..............********.***** +L39983.1/338-394 ..............AGUCUGAU.UACAU +#=GR L39983.1/338-394 PP ..............********.***** +NC_028793.1/3525-3581 ..............AGUCUCGC.UACAA +#=GR NC_028793.1/3525-3581 PP ..............********.***** +KT963000.1/3530-3585 ..............AGUCUCGU.UACAA +#=GR KT963000.1/3530-3585 PP ..............********.***** +NC_034265.1/3498-3554 ..............AGCCUCGU.UACAU +#=GR NC_034265.1/3498-3554 PP ..............********.***** +NC_034207.1/3516-3572 ..............AGUCUGAU.UACCA +#=GR NC_034207.1/3516-3572 PP ..............********.***** +NC_027703.1/3484-3543 ............ugAGUCUACG.UACCG +#=GR NC_027703.1/3484-3543 PP ............**********.***** +KC960436.1/599-653 ..............AGUCAAG-.CACUA +#=GR KC960436.1/599-653 PP ..............*******..99999 +MF136435.1/2804-2858 ..............AGCCAAGAuGCCCC +#=GR MF136435.1/2804-2858 PP ..............*********99999 +NC_008249.1/3486-3539 ..............AGUCUAGUuCAUUG +#=GR NC_008249.1/3486-3539 PP ..............********9999** +NC_034246.1/3377-3430 ..............AGCCUUGA.UUCAG +#=GR NC_034246.1/3377-3430 PP ..............********.***** +NC_014545.1/3448-3504 ..............AGUCAAGAuCACAG +#=GR NC_014545.1/3448-3504 PP ..............************** +LN865083.1/839-907 .............aAGUCCUAC.AACAG +#=GR LN865083.1/839-907 PP .............9********.***** +MH323436.1/3743-3795 ..............AGUCUUUC.ACACA +#=GR MH323436.1/3743-3795 PP ..............********.***** +NC_034836.1/4190-4264 ...cucaaauauacAGGCCUAG.CAUAA +#=GR NC_034836.1/4190-4264 PP ...*******************.***** +NC_032224.1/3354-3415 ...........ucuAGUCUUGU.UAACA +#=GR NC_032224.1/3354-3415 PP ...........***********.***** +NC_033229.1/3703-3758 ..............AGUCUUGU.UACCA +#=GR NC_033229.1/3703-3758 PP ..............********.***** +URS00021ED9C7_12045/1-51 ..............AGCCUCGU.----- +#=GR URS00021ED9C7_12045/1-51 PP ..............*******9...... +#=GC SS_cons ..............::::::::.::::: +#=GC RF ..............AGUCUugu.uACaa +//