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# Copyright 2008-2011 by Peter Cock.  All rights reserved. 

# 

# This code is part of the Biopython distribution and governed by its 

# license.  Please see the LICENSE file that should have been included 

# as part of this package. 

"""Bio.AlignIO support for "fasta-m10" output from Bill Pearson's FASTA tools. 

 

You are expected to use this module via the Bio.AlignIO functions (or the 

Bio.SeqIO functions if you want to work directly with the gapped sequences). 

 

This module contains a parser for the pairwise alignments produced by Bill 

Pearson's FASTA tools, for use from the Bio.AlignIO interface where it is 

refered to as the "fasta-m10" file format (as we only support the machine 

readable output format selected with the -m 10 command line option). 

 

This module does NOT cover the generic "fasta" file format originally 

developed as an input format to the FASTA tools.  The Bio.AlignIO and 

Bio.SeqIO both use the Bio.SeqIO.FastaIO module to deal with these files, 

which can also be used to store a multiple sequence alignments. 

""" 

 

from __future__ import print_function 

 

from Bio.Seq import Seq 

from Bio.SeqRecord import SeqRecord 

from Bio.Align import MultipleSeqAlignment 

from Bio.Alphabet import single_letter_alphabet, generic_dna, generic_protein 

from Bio.Alphabet import Gapped 

 

 

def _extract_alignment_region(alignment_seq_with_flanking, annotation): 

    """Helper function for the main parsing code (PRIVATE). 

 

    To get the actual pairwise alignment sequences, we must first 

    translate the un-gapped sequence based coordinates into positions 

    in the gapped sequence (which may have a flanking region shown 

    using leading - characters).  To date, I have never seen any 

    trailing flanking region shown in the m10 file, but the 

    following code should also cope with that. 

 

    Note that this code seems to work fine even when the "sq_offset" 

    entries are prsent as a result of using the -X command line option. 

    """ 

    align_stripped = alignment_seq_with_flanking.strip("-") 

    display_start = int(annotation['al_display_start']) 

    if int(annotation['al_start']) <= int(annotation['al_stop']): 

        start = int(annotation['al_start']) \ 

              - display_start 

        end = int(annotation['al_stop']) \ 

              - display_start + 1 

    else: 

        #FASTA has flipped this sequence... 

        start = display_start \ 

              - int(annotation['al_start']) 

        end = display_start \ 

              - int(annotation['al_stop']) + 1 

    end += align_stripped.count("-") 

    assert 0 <= start and start < end and end <= len(align_stripped), \ 

           "Problem with sequence start/stop,\n%s[%i:%i]\n%s" \ 

           % (alignment_seq_with_flanking, start, end, annotation) 

    return align_stripped[start:end] 

 

 

def FastaM10Iterator(handle, alphabet=single_letter_alphabet): 

    """Alignment iterator for the FASTA tool's pairwise alignment output. 

 

    This is for reading the pairwise alignments output by Bill Pearson's 

    FASTA program when called with the -m 10 command line option for machine 

    readable output.  For more details about the FASTA tools, see the website 

    http://fasta.bioch.virginia.edu/ and the paper: 

 

         W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448 

 

    This class is intended to be used via the Bio.AlignIO.parse() function 

    by specifying the format as "fasta-m10" as shown in the following code: 

 

        from Bio import AlignIO 

        handle = ... 

        for a in AlignIO.parse(handle, "fasta-m10"): 

            assert len(a) == 2, "Should be pairwise!" 

            print("Alignment length %i" % a.get_alignment_length()) 

            for record in a: 

                print("%s %s %s" % (record.seq, record.name, record.id)) 

 

    Note that this is not a full blown parser for all the information 

    in the FASTA output - for example, most of the header and all of the 

    footer is ignored.  Also, the alignments are not batched according to 

    the input queries. 

 

    Also note that there can be up to about 30 letters of flanking region 

    included in the raw FASTA output as contextual information.  This is NOT 

    part of the alignment itself, and is not included in the resulting 

    MultipleSeqAlignment objects returned. 

    """ 

    if alphabet is None: 

        alphabet = single_letter_alphabet 

 

    state_PREAMBLE = -1 

    state_NONE = 0 

    state_QUERY_HEADER = 1 

    state_ALIGN_HEADER = 2 

    state_ALIGN_QUERY = 3 

    state_ALIGN_MATCH = 4 

    state_ALIGN_CONS = 5 

 

    def build_hsp(): 

        if not query_tags and not match_tags: 

            raise ValueError("No data for query %r, match %r" 

                             % (query_id, match_id)) 

        assert query_tags, query_tags 

        assert match_tags, match_tags 

        evalue = align_tags.get("fa_expect", None) 

        q = "?"  # Just for printing len(q) in debug below 

        m = "?"  # Just for printing len(m) in debug below 

        tool = global_tags.get("tool", "").upper() 

        try: 

            q = _extract_alignment_region(query_seq, query_tags) 

            if tool in ["TFASTX"] and len(match_seq) == len(q): 

                m = match_seq 

                #Quick hack until I can work out how -, * and / characters 

                #and the apparent mix of aa and bp coordinates works. 

            else: 

                m = _extract_alignment_region(match_seq, match_tags) 

            assert len(q) == len(m) 

        except AssertionError as err: 

            print("Darn... amino acids vs nucleotide coordinates?") 

            print(tool) 

            print(query_seq) 

            print(query_tags) 

            print("%s %i" % (q, len(q))) 

            print(match_seq) 

            print(match_tags) 

            print("%s %i" % (m, len(m))) 

            print(handle.name) 

            raise err 

 

        assert alphabet is not None 

        alignment = MultipleSeqAlignment([], alphabet) 

 

        #TODO - Introduce an annotated alignment class? 

        #For now, store the annotation a new private property: 

        alignment._annotations = {} 

 

        #Want to record both the query header tags, and the alignment tags. 

        for key, value in header_tags.items(): 

            alignment._annotations[key] = value 

        for key, value in align_tags.items(): 

            alignment._annotations[key] = value 

 

        #Query 

        #===== 

        record = SeqRecord(Seq(q, alphabet), 

                           id=query_id, 

                           name="query", 

                           description=query_descr, 

                           annotations={"original_length": int(query_tags["sq_len"])}) 

        #TODO - handle start/end coordinates properly. Short term hack for now: 

        record._al_start = int(query_tags["al_start"]) 

        record._al_stop = int(query_tags["al_stop"]) 

        alignment.append(record) 

 

        #TODO - What if a specific alphabet has been requested? 

        #TODO - Use an IUPAC alphabet? 

        #TODO - Can FASTA output RNA? 

        if alphabet == single_letter_alphabet and "sq_type" in query_tags: 

            if query_tags["sq_type"] == "D": 

                record.seq.alphabet = generic_dna 

            elif query_tags["sq_type"] == "p": 

                record.seq.alphabet = generic_protein 

        if "-" in q: 

            if not hasattr(record.seq.alphabet, "gap_char"): 

                record.seq.alphabet = Gapped(record.seq.alphabet, "-") 

 

        #Match 

        #===== 

        record = SeqRecord(Seq(m, alphabet), 

                           id=match_id, 

                           name="match", 

                           description=match_descr, 

                           annotations={"original_length": int(match_tags["sq_len"])}) 

        #TODO - handle start/end coordinates properly. Short term hack for now: 

        record._al_start = int(match_tags["al_start"]) 

        record._al_stop = int(match_tags["al_stop"]) 

        alignment.append(record) 

 

        #This is still a very crude way of dealing with the alphabet: 

        if alphabet == single_letter_alphabet and "sq_type" in match_tags: 

            if match_tags["sq_type"] == "D": 

                record.seq.alphabet = generic_dna 

            elif match_tags["sq_type"] == "p": 

                record.seq.alphabet = generic_protein 

        if "-" in m: 

            if not hasattr(record.seq.alphabet, "gap_char"): 

                record.seq.alphabet = Gapped(record.seq.alphabet, "-") 

 

        return alignment 

 

    state = state_PREAMBLE 

    query_id = None 

    match_id = None 

    query_descr = "" 

    match_descr = "" 

    global_tags = {} 

    header_tags = {} 

    align_tags = {} 

    query_tags = {} 

    match_tags = {} 

    query_seq = "" 

    match_seq = "" 

    cons_seq = "" 

    for line in handle: 

        if ">>>" in line and not line.startswith(">>>"): 

            if query_id and match_id: 

                #This happens on old FASTA output which lacked an end of 

                #query >>><<< marker line. 

                yield build_hsp() 

            state = state_NONE 

            query_descr = line[line.find(">>>")+3:].strip() 

            query_id = query_descr.split(None, 1)[0] 

            match_id = None 

            header_tags = {} 

            align_tags = {} 

            query_tags = {} 

            match_tags = {} 

            query_seq = "" 

            match_seq = "" 

            cons_seq = "" 

        elif line.startswith("!! No "): 

            #e.g. 

            #!! No library sequences with E() < 0.5 

            #or on more recent versions, 

            #No sequences with E() < 0.05 

            assert state == state_NONE 

            assert not header_tags 

            assert not align_tags 

            assert not match_tags 

            assert not query_tags 

            assert match_id is None 

            assert not query_seq 

            assert not match_seq 

            assert not cons_seq 

            query_id = None 

        elif line.strip() in [">>><<<", ">>>///"]: 

            #End of query, possible end of all queries 

            if query_id and match_id: 

                yield build_hsp() 

            state = state_NONE 

            query_id = None 

            match_id = None 

            header_tags = {} 

            align_tags = {} 

            query_tags = {} 

            match_tags = {} 

            query_seq = "" 

            match_seq = "" 

            cons_seq = "" 

        elif line.startswith(">>>"): 

            #Should be start of a match! 

            assert query_id is not None 

            assert line[3:].split(", ", 1)[0] == query_id, line 

            assert match_id is None 

            assert not header_tags 

            assert not align_tags 

            assert not query_tags 

            assert not match_tags 

            assert not match_seq 

            assert not query_seq 

            assert not cons_seq 

            state = state_QUERY_HEADER 

        elif line.startswith(">>"): 

            #Should now be at start of a match alignment! 

            if query_id and match_id: 

                yield build_hsp() 

            align_tags = {} 

            query_tags = {} 

            match_tags = {} 

            query_seq = "" 

            match_seq = "" 

            cons_seq = "" 

            match_descr = line[2:].strip() 

            match_id = match_descr.split(None, 1)[0] 

            state = state_ALIGN_HEADER 

        elif line.startswith(">--"): 

            #End of one HSP 

            assert query_id and match_id, line 

            yield build_hsp() 

            #Clean up read for next HSP 

            #but reuse header_tags 

            align_tags = {} 

            query_tags = {} 

            match_tags = {} 

            query_seq = "" 

            match_seq = "" 

            cons_seq = "" 

            state = state_ALIGN_HEADER 

        elif line.startswith(">"): 

            if state == state_ALIGN_HEADER: 

                #Should be start of query alignment seq... 

                assert query_id is not None, line 

                assert match_id is not None, line 

                assert query_id.startswith(line[1:].split(None, 1)[0]), line 

                state = state_ALIGN_QUERY 

            elif state == state_ALIGN_QUERY: 

                #Should be start of match alignment seq 

                assert query_id is not None, line 

                assert match_id is not None, line 

                assert match_id.startswith(line[1:].split(None, 1)[0]), line 

                state = state_ALIGN_MATCH 

            elif state == state_NONE: 

                #Can get > as the last line of a histogram 

                pass 

            else: 

                assert False, "state %i got %r" % (state, line) 

        elif line.startswith("; al_cons"): 

            assert state == state_ALIGN_MATCH, line 

            state = state_ALIGN_CONS 

            #Next line(s) should be consensus seq... 

        elif line.startswith("; "): 

            if ": " in line: 

                key, value = [s.strip() for s in line[2:].split(": ", 1)] 

            else: 

                import warnings 

                #Seen in lalign36, specifically version 36.3.4 Apr, 2011 

                #Fixed in version 36.3.5b Oct, 2011(preload8) 

                warnings.warn("Missing colon in line: %r" % line) 

                try: 

                    key, value = [s.strip() for s in line[2:].split(" ", 1)] 

                except ValueError: 

                    raise ValueError("Bad line: %r" % line) 

            if state == state_QUERY_HEADER: 

                header_tags[key] = value 

            elif state == state_ALIGN_HEADER: 

                align_tags[key] = value 

            elif state == state_ALIGN_QUERY: 

                query_tags[key] = value 

            elif state == state_ALIGN_MATCH: 

                match_tags[key] = value 

            else: 

                assert False, "Unexpected state %r, %r" % (state, line) 

        elif state == state_ALIGN_QUERY: 

            query_seq += line.strip() 

        elif state == state_ALIGN_MATCH: 

            match_seq += line.strip() 

        elif state == state_ALIGN_CONS: 

            cons_seq += line.strip("\n") 

        elif state == state_PREAMBLE: 

            if line.startswith("#"): 

                global_tags["command"] = line[1:].strip() 

            elif line.startswith(" version "): 

                global_tags["version"] = line[9:].strip() 

            elif " compares a " in line: 

                global_tags["tool"] = line[:line.find(" compares a ")].strip() 

            elif " searches a " in line: 

                global_tags["tool"] = line[:line.find(" searches a ")].strip() 

        else: 

            pass 

 

 

if __name__ == "__main__": 

    print("Running a quick self-test") 

 

    #http://emboss.sourceforge.net/docs/themes/alnformats/align.simple 

    simple_example = \ 

"""# /opt/fasta/fasta34 -Q -H -E 1 -m 10 NC_002127.faa NC_009649.faa 

FASTA searches a protein or DNA sequence data bank 

version 34.26 January 12, 2007 

Please cite: 

W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448 

 

Query library NC_002127.faa vs NC_009649.faa library 

searching NC_009649.faa library 

 

  1>>>gi|10955263|ref|NP_052604.1| plasmid mobilization [Escherichia coli O157:H7 s 107 aa - 107 aa 

vs  NC_009649.faa library 

 

  45119 residues in   180 sequences 

  Expectation_n fit: rho(ln(x))= 6.9146+/-0.0249; mu= -5.7948+/- 1.273 

mean_var=53.6859+/-13.609, 0's: 0 Z-trim: 1  B-trim: 9 in 1/25 

Lambda= 0.175043 

 

FASTA (3.5 Sept 2006) function [optimized, BL50 matrix (15:-5)] ktup: 2 

join: 36, opt: 24, open/ext: -10/-2, width:  16 

Scan time:  0.000 

The best scores are:                                      opt bits E(180) 

gi|152973457|ref|YP_001338508.1| ATPase with chape ( 931)   71 24.9    0.58 

gi|152973588|ref|YP_001338639.1| F pilus assembly  ( 459)   63 23.1    0.99 

 

>>>gi|10955263|ref|NP_052604.1|, 107 aa vs NC_009649.faa library 

; pg_name: /opt/fasta/fasta34 

; pg_ver: 34.26 

; pg_argv: /opt/fasta/fasta34 -Q -H -E 1 -m 10 NC_002127.faa NC_009649.faa 

; pg_name: FASTA 

; pg_ver: 3.5 Sept 2006 

; pg_matrix: BL50 (15:-5) 

; pg_open-ext: -10 -2 

; pg_ktup: 2 

; pg_optcut: 24 

; pg_cgap: 36 

; mp_extrap: 60000 180 

; mp_stats:  Expectation_n fit: rho(ln(x))= 6.9146+/-0.0249; mu= -5.7948+/- 1.273  mean_var=53.6859+/-13.609, 0's: 0 Z-trim: 1  B-trim: 9 in 1/25  Lambda= 0.175043 

; mp_KS: -0.0000 (N=0) at 8159228 

>>gi|152973457|ref|YP_001338508.1| ATPase with chaperone activity, ATP-binding subunit [Klebsiella pneumoniae subsp. pneumoniae MGH 78578] 

; fa_frame: f 

; fa_initn:  65 

; fa_init1:  43 

; fa_opt:  71 

; fa_z-score: 90.3 

; fa_bits: 24.9 

; fa_expect:   0.58 

; sw_score: 71 

; sw_ident: 0.250 

; sw_sim: 0.574 

; sw_overlap: 108 

>gi|10955263| .. 

; sq_len: 107 

; sq_offset: 1 

; sq_type: p 

; al_start: 5 

; al_stop: 103 

; al_display_start: 1 

--------------------------MTKRSGSNT-RRRAISRPVRLTAE 

ED---QEIRKRAAECGKTVSGFLRAAALGKKVNSLTDDRVLKEVM----- 

RLGALQKKLFIDGKRVGDREYAEVLIAITEYHRALLSRLMAD 

>gi|152973457|ref|YP_001338508.1| .. 

; sq_len: 931 

; sq_type: p 

; al_start: 96 

; al_stop: 195 

; al_display_start: 66 

SDFFRIGDDATPVAADTDDVVDASFGEPAAAGSGAPRRRGSGLASRISEQ 

SEALLQEAAKHAAEFGRS------EVDTEHLLLALADSDVVKTILGQFKI 

KVDDLKRQIESEAKR-GDKPF-EGEIGVSPRVKDALSRAFVASNELGHSY 

VGPEHFLIGLAEEGEGLAANLLRRYGLTPQ 

>>gi|152973588|ref|YP_001338639.1| F pilus assembly protein [Klebsiella pneumoniae subsp. pneumoniae MGH 78578] 

; fa_frame: f 

; fa_initn:  33 

; fa_init1:  33 

; fa_opt:  63 

; fa_z-score: 86.1 

; fa_bits: 23.1 

; fa_expect:   0.99 

; sw_score: 63 

; sw_ident: 0.266 

; sw_sim: 0.656 

; sw_overlap: 64 

>gi|10955263| .. 

; sq_len: 107 

; sq_offset: 1 

; sq_type: p 

; al_start: 32 

; al_stop: 94 

; al_display_start: 2 

TKRSGSNTRRRAISRPVRLTAEEDQEIRKRAAECGKTVSGFLRAAALGKK 

VNSLTDDRVLKEV-MRLGALQKKLFIDGKRVGDREYAEVLIAITEYHRAL 

LSRLMAD 

>gi|152973588|ref|YP_001338639.1| .. 

; sq_len: 459 

; sq_type: p 

; al_start: 191 

; al_stop: 248 

; al_display_start: 161 

VGGLFPRTQVAQQKVCQDIAGESNIFSDWAASRQGCTVGG--KMDSVQDK 

ASDKDKERVMKNINIMWNALSKNRLFDG----NKELKEFIMTLTGTLIFG 

ENSEITPLPARTTDQDLIRAMMEGGTAKIYHCNDSDKCLKVVADATVTIT 

SNKALKSQISALLSSIQNKAVADEKLTDQE 

  2>>>gi|10955264|ref|NP_052605.1| hypothetical protein pOSAK1_02 [Escherichia coli O157:H7 s 126 aa - 126 aa 

vs  NC_009649.faa library 

 

  45119 residues in   180 sequences 

  Expectation_n fit: rho(ln(x))= 7.1374+/-0.0246; mu= -7.6540+/- 1.313 

mean_var=51.1189+/-13.171, 0's: 0 Z-trim: 1  B-trim: 8 in 1/25 

Lambda= 0.179384 

 

FASTA (3.5 Sept 2006) function [optimized, BL50 matrix (15:-5)] ktup: 2 

join: 36, opt: 24, open/ext: -10/-2, width:  16 

Scan time:  0.000 

The best scores are:                                      opt bits E(180) 

gi|152973462|ref|YP_001338513.1| hypothetical prot ( 101)   58 22.9    0.29 

 

>>>gi|10955264|ref|NP_052605.1|, 126 aa vs NC_009649.faa library 

; pg_name: /opt/fasta/fasta34 

; pg_ver: 34.26 

; pg_argv: /opt/fasta/fasta34 -Q -H -E 1 -m 10 NC_002127.faa NC_009649.faa 

; pg_name: FASTA 

; pg_ver: 3.5 Sept 2006 

; pg_matrix: BL50 (15:-5) 

; pg_open-ext: -10 -2 

; pg_ktup: 2 

; pg_optcut: 24 

; pg_cgap: 36 

; mp_extrap: 60000 180 

; mp_stats:  Expectation_n fit: rho(ln(x))= 7.1374+/-0.0246; mu= -7.6540+/- 1.313  mean_var=51.1189+/-13.171, 0's: 0 Z-trim: 1  B-trim: 8 in 1/25  Lambda= 0.179384 

; mp_KS: -0.0000 (N=0) at 8159228 

>>gi|152973462|ref|YP_001338513.1| hypothetical protein KPN_pKPN3p05904 [Klebsiella pneumoniae subsp. pneumoniae MGH 78578] 

; fa_frame: f 

; fa_initn:  50 

; fa_init1:  50 

; fa_opt:  58 

; fa_z-score: 95.8 

; fa_bits: 22.9 

; fa_expect:   0.29 

; sw_score: 58 

; sw_ident: 0.289 

; sw_sim: 0.632 

; sw_overlap: 38 

>gi|10955264| .. 

; sq_len: 126 

; sq_offset: 1 

; sq_type: p 

; al_start: 1 

; al_stop: 38 

; al_display_start: 1 

------------------------------MKKDKKYQIEAIKNKDKTLF 

IVYATDIYSPSEFFSKIESDLKKKKSKGDVFFDLIIPNGGKKDRYVYTSF 

NGEKFSSYTLNKVTKTDEYN 

>gi|152973462|ref|YP_001338513.1| .. 

; sq_len: 101 

; sq_type: p 

; al_start: 44 

; al_stop: 81 

; al_display_start: 14 

DALLGEIQRLRKQVHQLQLERDILTKANELIKKDLGVSFLKLKNREKTLI 

VDALKKKYPVAELLSVLQLARSCYFYQNVCTISMRKYA 

  3>>>gi|10955265|ref|NP_052606.1| hypothetical protein pOSAK1_03 [Escherichia coli O157:H7 s 346 aa - 346 aa 

vs  NC_009649.faa library 

 

  45119 residues in   180 sequences 

  Expectation_n fit: rho(ln(x))= 6.0276+/-0.0276; mu= 3.0670+/- 1.461 

mean_var=37.1634+/- 8.980, 0's: 0 Z-trim: 1  B-trim: 14 in 1/25 

Lambda= 0.210386 

 

FASTA (3.5 Sept 2006) function [optimized, BL50 matrix (15:-5)] ktup: 2 

join: 37, opt: 25, open/ext: -10/-2, width:  16 

Scan time:  0.020 

The best scores are:                                      opt bits E(180) 

gi|152973545|ref|YP_001338596.1| putative plasmid  ( 242)   70 27.5   0.082 

 

>>>gi|10955265|ref|NP_052606.1|, 346 aa vs NC_009649.faa library 

; pg_name: /opt/fasta/fasta34 

; pg_ver: 34.26 

; pg_argv: /opt/fasta/fasta34 -Q -H -E 1 -m 10 NC_002127.faa NC_009649.faa 

; pg_name: FASTA 

; pg_ver: 3.5 Sept 2006 

; pg_matrix: BL50 (15:-5) 

; pg_open-ext: -10 -2 

; pg_ktup: 2 

; pg_optcut: 25 

; pg_cgap: 37 

; mp_extrap: 60000 180 

; mp_stats:  Expectation_n fit: rho(ln(x))= 6.0276+/-0.0276; mu= 3.0670+/- 1.461  mean_var=37.1634+/- 8.980, 0's: 0 Z-trim: 1  B-trim: 14 in 1/25  Lambda= 0.210386 

; mp_KS: -0.0000 (N=0) at 8159228 

>>gi|152973545|ref|YP_001338596.1| putative plasmid SOS inhibition protein A [Klebsiella pneumoniae subsp. pneumoniae MGH 78578] 

; fa_frame: f 

; fa_initn:  52 

; fa_init1:  52 

; fa_opt:  70 

; fa_z-score: 105.5 

; fa_bits: 27.5 

; fa_expect:  0.082 

; sw_score: 70 

; sw_ident: 0.279 

; sw_sim: 0.651 

; sw_overlap: 43 

>gi|10955265| .. 

; sq_len: 346 

; sq_offset: 1 

; sq_type: p 

; al_start: 197 

; al_stop: 238 

; al_display_start: 167 

DFMCSILNMKEIVEQKNKEFNVDIKKETIESELHSKLPKSIDKIHEDIKK 

QLSC-SLIMKKIDVEMEDYSTYCFSALRAIEGFIYQILNDVCNPSSSKNL 

GEYFTENKPKYIIREIHQET 

>gi|152973545|ref|YP_001338596.1| .. 

; sq_len: 242 

; sq_type: p 

; al_start: 52 

; al_stop: 94 

; al_display_start: 22 

IMTVEEARQRGARLPSMPHVRTFLRLLTGCSRINSDVARRIPGIHRDPKD 

RLSSLKQVEEALDMLISSHGEYCPLPLTMDVQAENFPEVLHTRTVRRLKR 

QDFAFTRKMRREARQVEQSW 

>>><<< 

 

 

579 residues in 3 query   sequences 

45119 residues in 180 library sequences 

Scomplib [34.26] 

start: Tue May 20 16:38:45 2008 done: Tue May 20 16:38:45 2008 

Total Scan time:  0.020 Total Display time:  0.010 

 

Function used was FASTA [version 34.26 January 12, 2007] 

 

""" 

 

    from Bio._py3k import StringIO 

 

    alignments = list(FastaM10Iterator(StringIO(simple_example))) 

    assert len(alignments) == 4, len(alignments) 

    assert len(alignments[0]) == 2 

    for a in alignments: 

        print("Alignment %i sequences of length %i" \ 

              % (len(a), a.get_alignment_length())) 

        for r in a: 

            print("%s %s %i" % (r.seq, r.id, r.annotations["original_length"])) 

        #print(a.annotations) 

    print("Done") 

 

    import os 

    path = "../../Tests/Fasta/" 

    files = sorted(f for f in os.listdir(path) if os.path.splitext(f)[-1] == ".m10") 

    for filename in files: 

        if os.path.splitext(filename)[-1] == ".m10": 

            print("") 

            print(filename) 

            print("=" * len(filename)) 

            for i, a in enumerate(FastaM10Iterator(open(os.path.join(path, filename)))): 

                print("#%i, %s" % (i+1, a)) 

                for r in a: 

                    if "-" in r.seq: 

                        assert r.seq.alphabet.gap_char == "-" 

                    else: 

                        assert not hasattr(r.seq.alphabet, "gap_char")