##########################################################################
#
#   MRC FGU Computational Genomics Group
#
#   $Id$
#
#   Copyright (C) 2009 <NAME>
#
#   This program is free software; you can redistribute it and/or
#   modify it under the terms of the GNU General Public License
#   as published by the Free Software Foundation; either version 2
#   of the License, or (at your option) any later version.
#
#   This program is distributed in the hope that it will be useful,
#   but WITHOUT ANY WARRANTY; without even the implied warranty of
#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#   GNU General Public License for more details.
#
#   You should have received a copy of the GNU General Public License
#   along with this program; if not, write to the Free Software
#   Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
##########################################################################
'''
MaliIO.py - 
======================================================

:Author: <NAME>
:Release: $Id$
:Date: |today|
:Tags: Python

Code
----

'''
import string
import sys
import re
try:
    import alignlib_lite
except ImportError:
    pass

# ------------------------------------------------------------------------


def writeFasta(outfile,
               mali,
               line_width=60,
               identifiers=None,
               skip_first=0,
               gap_char=None
               ):
    """print multiple alignment in fasta format.
    """

    mali_width = mali.getWidth()
    mali_length = mali.getLength()

    for x in range(skip_first, mali_width):
        if identifiers:
            outfile.write(">" + str(identifiers[x]) + "\n")
        else:
            outfile.write(">%i\n" % x)
        if not gap_char:
            outfile.write(mali.getRow(x).getString() + "\n")
        else:
            outfile.write(
                string.replace(mali.getRow(x).getString(), "-", gap_char) + "\n")

# ------------------------------------------------------------------------


def WriteMODELLER(outfile,
                  mali,
                  line_width=60,
                  identifiers=None,
                  skip_first=0,
                  gap_char=None
                  ):
    """print multiple alignment in PIR (MODELLER) format.
example:

>P1;5fd1
structureX:5fd1:1    : :106  : :ferredoxin:Azotobacter vinelandii: 1.90: 0.19
AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELA
EVWPNITEKKDPLPDAEDWDGVKGKLQHLER*
    """

    mali_width = mali.getWidth()
    mali_length = mali.getLength()

    for x in range(skip_first, mali_width):

        if identifiers:
            outfile.write(">" + str(identifiers[x]) + "\n")
        else:
            outfile.write(">%i\n" % x)

        if not gap_char:
            outfile.write(mali.getRow(x).getString() + "\n")
        else:
            outfile.write(
                string.replace(mali.getRow(x).getString(), "-", gap_char) + "\n")


# ------------------------------------------------------------------------
def writeClustalW(outfile, mali, line_width=60, identifiers=None):
    """print alignment in ClustalW format.
    (have to still look up the format, dsc can read it.)
    """

    mali_width = mali.getWidth()
    mali_length = mali.getLength()

    lines = []
    for x in range(0, mali_width):
        lines.append(mali.getRow(x).getString())

    outfile.write("CLUSTAL W(1.60) multiple sequence alignment\n")
    outfile.write("\n" * 5)

    for i in range(0, mali_length, line_width):
        i_to = i + line_width

        for x in range(0, mali_width):
            if identifiers:
                outfile.write("%-16s" % identifiers[x])
            else:
                outfile.write("%-16i" % x)

            outfile.write(lines[x][i:i_to] + "\n")

        outfile.write("\n" * 2)

# ------------------------------------------------------------------------


def readPicasso(infile):
    """read alignment in the non-defined picasso format.
    """

    mali = alignlib_lite.py_makeMultipleAlignment()

    while 1:
        line = infile.readline()
        if not line:
            break

        x = re.search("\d+\s+([A-Z\-\.]*)\s+\d+", line)
        if x:
            s = x.groups()[0]
            a = alignlib_lite.py_makeAlignatumFromString(s)
            a.thisown = 0
            mali.addAlignatum(a)

    return mali

# ------------------------------------------------------------------------


def compressAlignment(alignment, gap_character="-", ignore_beginning=0):
    """compress an alignment string.
    Lower-case characters at the beginning are ignored if so wished.
    --xxabBCDEfgHI
    becomes:
    -6+4

    This was necessary for radar output (e.g., 46497)
    """

    # subsitute all initial lower case characters with a gap
    if ignore_beginning:
        x = re.search("[A-Z]", alignment)
        if x:
            alignment = gap_character * x.start() + alignment[x.start():]

    d = 0
    if alignment[0] == gap_character:
        gap = 1
    else:
        gap = 0

    result = ""

    for char in alignment:
        if char == gap_character and not gap:
            result += "+%i" % d
            d = 1
            gap = 1
            continue

        if char != gap_character and gap:
            result += "-%i" % d
            d = 1
            gap = 0
            continue

        d = d + 1

    if gap:
        result = result + "-%i" % d
    else:
        result = result + "+%i" % d

    return result

# ------------------------------------------------------------------------


def readFasta(infile, pattern_identifier="\S+"):
    """read alignment in fasta format.
    """

    mali = {}
    id = None
    fragments = []
    identifiers = []
    for line in infile:
        if line[0] == "#":
            continue
        if line[0] == ">":
            if id:
                mali[id] = re.sub("\s", "", string.join(fragments, ""))
            id = re.search("^(%s)" % pattern_identifier, line[1:-1]).group(0)
            identifiers.append(id)
            fragments = []
            continue
        fragments.append(line[:-1])

    if id:
        mali[id] = re.sub("\s", "", string.join(fragments, ""))
    return convertGaps(mali), identifiers

# ------------------------------------------------------------------------


def readPlain(infile):

    mali = {}
    for line in infile:
        if line[0] == "#":
            continue
        data = line[:-1].split("\t")
        identifiers.append(data[3])
        mali[data[3]] = data[2]

    return convertGaps(mali), identifiers

# ------------------------------------------------------------------------


def readMali(infile, format="fasta"):

    if format == "fasta":
        return readFasta(infile)
    elif format == "plain":
        return readPlain(infile)
    else:
        raise ValueError, "unknown format %s" % format

# ------------------------------------------------------------------------


def convertGaps(mali, old_gap=".", new_gap="-"):
    """convert gaps characters in mali.
    """
    for id in mali.keys():
        mali[id] = string.replace(mali[id], old_gap, new_gap,)
    return mali

# ------------------------------------------------------------------------


def removeGappedColumns(mali, gap_char="-"):
    """remove all gapped columns in mali."""

    if len(mali) == 0:
        return mali

    keys = mali.keys()
    lmali = len(mali[keys[0]])
    wmali = len(keys)

    gaps_per_column = [0] * lmali

    for m in mali.values():
        for x in range(lmali):
            if m[x] == gap_char:
                gaps_per_column[x] += 1

    new_mali = {}

    for k in keys:
        s = []
        m = mali[k]
        for x in range(lmali):
            if gaps_per_column[x] < wmali:
                s += m[x]
        new_mali[k] = string.join(s, "")

    return new_mali

# ------------------------------------------------------------------------


def getSubset(mali, identifiers, not_in_set=False):
    """return subset of mali which only contains identifiers."""

    new_mali = {}

    if not_in_set:
        for k, v in mali.items():
            if k not in identifiers:
                new_mali[k] = v
    else:
        for k, v in mali.items():
            if k in identifiers:
                new_mali[k] = v

    return new_mali

# ------------------------------------------------------------------------


def getFrameColumnsForMaster(mali, master, gap_char="-"):
    """get columns in frame according to master.
    """
    columns = []
    sequence = mali[master]
    x = 0
    while x < len(sequence):
        c = 0
        codon = []
        while x < len(sequence) and c < 3:
            if sequence[x] != gap_char:  # and sequence[x] in string.uppercase:
                codon.append(x)
                c += 1
            x += 1

        if len(codon) == 3:
            columns.append(codon)

    return columns

# ------------------------------------------------------------------------


def getFrameColumnsForMasterPattern(mali, identifiers, master_pattern, gap_char="-"):
    """get columns in frame for all masters matching the pattern.
    """
    columns = []
    for id in identifiers:
        if re.search(master_pattern, id):
            columns += getFrameColumnsForMaster(mali, id)

    if len(columns) == 0:
        columns += getFrameColumnsForMaster(mali, identifiers[0])

    # sort all columns by tuple. The "shortest" codon will be first (1,2,3)
    # before (1,2,100)
    columns.sort()

    # select codons
    frame_columns = []
    last_codon = columns[0]
    for codon in columns[1:]:
        # skip identical codons
        if codon == last_codon:
            continue

        # take first (shortest) codon in case of identical first residue
        if codon[0] == last_codon[0]:
            continue

        # if not overlapping, keep
        if codon[0] > last_codon[2]:
            frame_columns.append(last_codon)

        # if overlapping, but out of register: skip
        last_codon = codon

    frame_columns.append(last_codon)

    return frame_columns

# ------------------------------------------------------------------------


def getMapFromMali(seq1, seq2, gap_char="-"):
    """build map of positions between mali."""
    xpos = 0
    ypos = 0

    map_a2b = alignlib_lite.py_makeAlignataVector()
    # build map between genomic sequences:
    for p in range(len(seq1)):

        if seq1[p] != gap_char and \
           seq2[p] != gap_char and \
           seq1[p] in string.uppercase and \
           seq2[p] in string.uppercase:
            map_a2b.addPairExplicit(xpos + 1, ypos + 1, 0)

        if seq1[p] != gap_char:
            xpos += 1
        if seq2[p] != gap_char:
            ypos += 1
    return map_a2b


# ------------------------------------------------------------------------
def getCodonSequence(sequence, frame_columns, gap_char="-", remove_stops=True):
    """return a pruned sequence given frame columns.

    everything not in frame is deleted, only complete codons are kept.
    """

    fragments = []
    nstops, ncodons, naligned = 0, 0, 0
    for a, b, c in frame_columns:
        codon = sequence[a] + sequence[b] + sequence[c]

        codon_is_aligned = False
        codon_is_ok = True
        for x in codon:
            # a codon will be masked, if it either
            # 1. contains a gap character
            # 2. is an unaligned character (lowercase)
            residue_is_unaligned = (x == gap_char) or \
                                   (x in string.lowercase)
            codon_is_aligned = codon_is_aligned or not residue_is_unaligned
            codon_is_ok = codon_is_ok and not residue_is_unaligned

        if codon_is_aligned:
            naligned += 1

        if codon_is_ok:
            ncodons += 1
            if string.upper(codon) in ("TAG", "TAA", "TGA"):
                if remove_stops:
                    fragments.append(gap_char * 3)
                else:
                    fragments.append(codon)
                nstops += 1
            else:
                fragments.append(codon)
        else:
            fragments.append(gap_char * 3)

    return string.join(fragments, ""), naligned, ncodons, nstops

# ------------------------------------------------------------------------


def getPercentIdentity(seq1, seq2, gap_char="-"):
    """get number of identical residues between seq1 and seq2."""

    ntotal = 0
    nidentical = 0
    for a in range(len(seq1)):
        if seq1[a] != gap_char and seq2[a] != gap_char:
            ntotal += 1
            if seq1[a] == seq2[a]:
                nidentical += 1

    if ntotal == 0:
        return 0.0
    return float(nidentical) / ntotal


if __name__ == '__main__':

    c = pairsdblib.ConnectionPicasso()
    c.Connect()

    import pairsdblib
    mali = pairsdblib.makeMultipleAlignmentNeighbours(c, 54, "pairsdb_90x90")

    writeClustalW(sys.stdout, mali)

    c.Disconnect()

##########################################################################
#
#   MRC FGU Computational Genomics Group
#
#   $Id$
#
#   Copyright (C) 2009 <NAME>
#
#   This program is free software; you can redistribute it and/or
#   modify it under the terms of the GNU General Public License
#   as published by the Free Software Foundation; either version 2
#   of the License, or (at your option) any later version.
#
#   This program is distributed in the hope that it will be useful,
#   but WITHOUT ANY WARRANTY; without even the implied warranty of
#   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#   GNU General Public License for more details.
#
#   You should have received a copy of the GNU General Public License
#   along with this program; if not, write to the Free Software
#   Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
##########################################################################
'''
MaliIO.py - 
======================================================

:Author: <NAME>
:Release: $Id$
:Date: |today|
:Tags: Python

Code
----

'''
import string
import sys
import re
try:
    import alignlib_lite
except ImportError:
    pass

# ------------------------------------------------------------------------


def writeFasta(outfile,
               mali,
               line_width=60,
               identifiers=None,
               skip_first=0,
               gap_char=None
               ):
    """print multiple alignment in fasta format.
    """

    mali_width = mali.getWidth()
    mali_length = mali.getLength()

    for x in range(skip_first, mali_width):
        if identifiers:
            outfile.write(">" + str(identifiers[x]) + "\n")
        else:
            outfile.write(">%i\n" % x)
        if not gap_char:
            outfile.write(mali.getRow(x).getString() + "\n")
        else:
            outfile.write(
                string.replace(mali.getRow(x).getString(), "-", gap_char) + "\n")

# ------------------------------------------------------------------------


def WriteMODELLER(outfile,
                  mali,
                  line_width=60,
                  identifiers=None,
                  skip_first=0,
                  gap_char=None
                  ):
    """print multiple alignment in PIR (MODELLER) format.
example:

>P1;5fd1
structureX:5fd1:1    : :106  : :ferredoxin:Azotobacter vinelandii: 1.90: 0.19
AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELA
EVWPNITEKKDPLPDAEDWDGVKGKLQHLER*
    """

    mali_width = mali.getWidth()
    mali_length = mali.getLength()

    for x in range(skip_first, mali_width):

        if identifiers:
            outfile.write(">" + str(identifiers[x]) + "\n")
        else:
            outfile.write(">%i\n" % x)

        if not gap_char:
            outfile.write(mali.getRow(x).getString() + "\n")
        else:
            outfile.write(
                string.replace(mali.getRow(x).getString(), "-", gap_char) + "\n")


# ------------------------------------------------------------------------
def writeClustalW(outfile, mali, line_width=60, identifiers=None):
    """print alignment in ClustalW format.
    (have to still look up the format, dsc can read it.)
    """

    mali_width = mali.getWidth()
    mali_length = mali.getLength()

    lines = []
    for x in range(0, mali_width):
        lines.append(mali.getRow(x).getString())

    outfile.write("CLUSTAL W(1.60) multiple sequence alignment\n")
    outfile.write("\n" * 5)

    for i in range(0, mali_length, line_width):
        i_to = i + line_width

        for x in range(0, mali_width):
            if identifiers:
                outfile.write("%-16s" % identifiers[x])
            else:
                outfile.write("%-16i" % x)

            outfile.write(lines[x][i:i_to] + "\n")

        outfile.write("\n" * 2)

# ------------------------------------------------------------------------


def readPicasso(infile):
    """read alignment in the non-defined picasso format.
    """

    mali = alignlib_lite.py_makeMultipleAlignment()

    while 1:
        line = infile.readline()
        if not line:
            break

        x = re.search("\d+\s+([A-Z\-\.]*)\s+\d+", line)
        if x:
            s = x.groups()[0]
            a = alignlib_lite.py_makeAlignatumFromString(s)
            a.thisown = 0
            mali.addAlignatum(a)

    return mali

# ------------------------------------------------------------------------


def compressAlignment(alignment, gap_character="-", ignore_beginning=0):
    """compress an alignment string.
    Lower-case characters at the beginning are ignored if so wished.
    --xxabBCDEfgHI
    becomes:
    -6+4

    This was necessary for radar output (e.g., 46497)
    """

    # subsitute all initial lower case characters with a gap
    if ignore_beginning:
        x = re.search("[A-Z]", alignment)
        if x:
            alignment = gap_character * x.start() + alignment[x.start():]

    d = 0
    if alignment[0] == gap_character:
        gap = 1
    else:
        gap = 0

    result = ""

    for char in alignment:
        if char == gap_character and not gap:
            result += "+%i" % d
            d = 1
            gap = 1
            continue

        if char != gap_character and gap:
            result += "-%i" % d
            d = 1
            gap = 0
            continue

        d = d + 1

    if gap:
        result = result + "-%i" % d
    else:
        result = result + "+%i" % d

    return result

# ------------------------------------------------------------------------


def readFasta(infile, pattern_identifier="\S+"):
    """read alignment in fasta format.
    """

    mali = {}
    id = None
    fragments = []
    identifiers = []
    for line in infile:
        if line[0] == "#":
            continue
        if line[0] == ">":
            if id:
                mali[id] = re.sub("\s", "", string.join(fragments, ""))
            id = re.search("^(%s)" % pattern_identifier, line[1:-1]).group(0)
            identifiers.append(id)
            fragments = []
            continue
        fragments.append(line[:-1])

    if id:
        mali[id] = re.sub("\s", "", string.join(fragments, ""))
    return convertGaps(mali), identifiers

# ------------------------------------------------------------------------


def readPlain(infile):

    mali = {}
    for line in infile:
        if line[0] == "#":
            continue
        data = line[:-1].split("\t")
        identifiers.append(data[3])
        mali[data[3]] = data[2]

    return convertGaps(mali), identifiers

# ------------------------------------------------------------------------


def readMali(infile, format="fasta"):

    if format == "fasta":
        return readFasta(infile)
    elif format == "plain":
        return readPlain(infile)
    else:
        raise ValueError, "unknown format %s" % format

# ------------------------------------------------------------------------


def convertGaps(mali, old_gap=".", new_gap="-"):
    """convert gaps characters in mali.
    """
    for id in mali.keys():
        mali[id] = string.replace(mali[id], old_gap, new_gap,)
    return mali

# ------------------------------------------------------------------------


def removeGappedColumns(mali, gap_char="-"):
    """remove all gapped columns in mali."""

    if len(mali) == 0:
        return mali

    keys = mali.keys()
    lmali = len(mali[keys[0]])
    wmali = len(keys)

    gaps_per_column = [0] * lmali

    for m in mali.values():
        for x in range(lmali):
            if m[x] == gap_char:
                gaps_per_column[x] += 1

    new_mali = {}

    for k in keys:
        s = []
        m = mali[k]
        for x in range(lmali):
            if gaps_per_column[x] < wmali:
                s += m[x]
        new_mali[k] = string.join(s, "")

    return new_mali

# ------------------------------------------------------------------------


def getSubset(mali, identifiers, not_in_set=False):
    """return subset of mali which only contains identifiers."""

    new_mali = {}

    if not_in_set:
        for k, v in mali.items():
            if k not in identifiers:
                new_mali[k] = v
    else:
        for k, v in mali.items():
            if k in identifiers:
                new_mali[k] = v

    return new_mali

# ------------------------------------------------------------------------


def getFrameColumnsForMaster(mali, master, gap_char="-"):
    """get columns in frame according to master.
    """
    columns = []
    sequence = mali[master]
    x = 0
    while x < len(sequence):
        c = 0
        codon = []
        while x < len(sequence) and c < 3:
            if sequence[x] != gap_char:  # and sequence[x] in string.uppercase:
                codon.append(x)
                c += 1
            x += 1

        if len(codon) == 3:
            columns.append(codon)

    return columns

# ------------------------------------------------------------------------


def getFrameColumnsForMasterPattern(mali, identifiers, master_pattern, gap_char="-"):
    """get columns in frame for all masters matching the pattern.
    """
    columns = []
    for id in identifiers:
        if re.search(master_pattern, id):
            columns += getFrameColumnsForMaster(mali, id)

    if len(columns) == 0:
        columns += getFrameColumnsForMaster(mali, identifiers[0])

    # sort all columns by tuple. The "shortest" codon will be first (1,2,3)
    # before (1,2,100)
    columns.sort()

    # select codons
    frame_columns = []
    last_codon = columns[0]
    for codon in columns[1:]:
        # skip identical codons
        if codon == last_codon:
            continue

        # take first (shortest) codon in case of identical first residue
        if codon[0] == last_codon[0]:
            continue

        # if not overlapping, keep
        if codon[0] > last_codon[2]:
            frame_columns.append(last_codon)

        # if overlapping, but out of register: skip
        last_codon = codon

    frame_columns.append(last_codon)

    return frame_columns

# ------------------------------------------------------------------------


def getMapFromMali(seq1, seq2, gap_char="-"):
    """build map of positions between mali."""
    xpos = 0
    ypos = 0

    map_a2b = alignlib_lite.py_makeAlignataVector()
    # build map between genomic sequences:
    for p in range(len(seq1)):

        if seq1[p] != gap_char and \
           seq2[p] != gap_char and \
           seq1[p] in string.uppercase and \
           seq2[p] in string.uppercase:
            map_a2b.addPairExplicit(xpos + 1, ypos + 1, 0)

        if seq1[p] != gap_char:
            xpos += 1
        if seq2[p] != gap_char:
            ypos += 1
    return map_a2b


# ------------------------------------------------------------------------
def getCodonSequence(sequence, frame_columns, gap_char="-", remove_stops=True):
    """return a pruned sequence given frame columns.

    everything not in frame is deleted, only complete codons are kept.
    """

    fragments = []
    nstops, ncodons, naligned = 0, 0, 0
    for a, b, c in frame_columns:
        codon = sequence[a] + sequence[b] + sequence[c]

        codon_is_aligned = False
        codon_is_ok = True
        for x in codon:
            # a codon will be masked, if it either
            # 1. contains a gap character
            # 2. is an unaligned character (lowercase)
            residue_is_unaligned = (x == gap_char) or \
                                   (x in string.lowercase)
            codon_is_aligned = codon_is_aligned or not residue_is_unaligned
            codon_is_ok = codon_is_ok and not residue_is_unaligned

        if codon_is_aligned:
            naligned += 1

        if codon_is_ok:
            ncodons += 1
            if string.upper(codon) in ("TAG", "TAA", "TGA"):
                if remove_stops:
                    fragments.append(gap_char * 3)
                else:
                    fragments.append(codon)
                nstops += 1
            else:
                fragments.append(codon)
        else:
            fragments.append(gap_char * 3)

    return string.join(fragments, ""), naligned, ncodons, nstops

# ------------------------------------------------------------------------


def getPercentIdentity(seq1, seq2, gap_char="-"):
    """get number of identical residues between seq1 and seq2."""

    ntotal = 0
    nidentical = 0
    for a in range(len(seq1)):
        if seq1[a] != gap_char and seq2[a] != gap_char:
            ntotal += 1
            if seq1[a] == seq2[a]:
                nidentical += 1

    if ntotal == 0:
        return 0.0
    return float(nidentical) / ntotal


if __name__ == '__main__':

    c = pairsdblib.ConnectionPicasso()
    c.Connect()

    import pairsdblib
    mali = pairsdblib.makeMultipleAlignmentNeighbours(c, 54, "pairsdb_90x90")

    writeClustalW(sys.stdout, mali)

    c.Disconnect()

########################################################################## # #   MRC FGU Computational Genomics Group # #   $Id$ # #   Copyright (C) 2009 <NAME> # #   This program is free software; you can redistribute it and/or #   modify it under the terms of the GNU General Public License #   as published by the Free Software Foundation; either version 2 #   of the License, or (at your option) any later version. # #   This program is distributed in the hope that it will be useful, #   but WITHOUT ANY WARRANTY; without even the implied warranty of #   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the #   GNU General Public License for more details. # #   You should have received a copy of the GNU General Public License #   along with this program; if not, write to the Free Software #   Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA. ########################################################################## MaliIO.py -  ======================================================  :Author: <NAME> :Release: $Id$ :Date: |today| :Tags: Python  Code ---- # ------------------------------------------------------------------------ print multiple alignment in fasta format. # ------------------------------------------------------------------------ print multiple alignment in PIR (MODELLER) format. example:  >P1;5fd1 structureX:5fd1:1    : :106  : :ferredoxin:Azotobacter vinelandii: 1.90: 0.19 AFVVTDNCIKCKYTDCVEVCPVDCFYEGPNFLVIHPDECIDCALCEPECPAQAIFSEDEVPEDMQEFIQLNAELA EVWPNITEKKDPLPDAEDWDGVKGKLQHLER* # ------------------------------------------------------------------------ print alignment in ClustalW format.     (have to still look up the format, dsc can read it.) # ------------------------------------------------------------------------ read alignment in the non-defined picasso format. # ------------------------------------------------------------------------ compress an alignment string.     Lower-case characters at the beginning are ignored if so wished.     --xxabBCDEfgHI     becomes:     -6+4      This was necessary for radar output (e.g., 46497) # subsitute all initial lower case characters with a gap # ------------------------------------------------------------------------ read alignment in fasta format. # ------------------------------------------------------------------------ # ------------------------------------------------------------------------ # ------------------------------------------------------------------------ convert gaps characters in mali. # ------------------------------------------------------------------------ remove all gapped columns in mali. # ------------------------------------------------------------------------ return subset of mali which only contains identifiers. # ------------------------------------------------------------------------ get columns in frame according to master. # and sequence[x] in string.uppercase: # ------------------------------------------------------------------------ get columns in frame for all masters matching the pattern. # sort all columns by tuple. The "shortest" codon will be first (1,2,3) # before (1,2,100) # select codons # skip identical codons # take first (shortest) codon in case of identical first residue # if not overlapping, keep # if overlapping, but out of register: skip # ------------------------------------------------------------------------ build map of positions between mali. # build map between genomic sequences: # ------------------------------------------------------------------------ return a pruned sequence given frame columns.      everything not in frame is deleted, only complete codons are kept. # a codon will be masked, if it either # 1. contains a gap character # 2. is an unaligned character (lowercase) # ------------------------------------------------------------------------ get number of identical residues between seq1 and seq2.