sequenzo 0.1.21__cp39-cp39-macosx_10_9_x86_64.whl

sequenzo/multidomain/cat.py

@@ -0,0 +1,431 @@
+"""
+@Author  : 李欣怡
+@File    : cat.py
+@Time    : 2025/4/8 09:06
+@Desc    : Build multidomain (MD) sequences of combined individual domain states (expanded alphabet),
+           derive multidomain indel and substitution costs from domain costs by means of an additive trick (CAT),
+           and compute OM pairwise distances using CAT costs.
+"""
+import numpy as np
+import pandas as pd
+from typing import List, Union, Optional
+import contextlib
+import io
+
+from sequenzo.define_sequence_data import SequenceData
+from sequenzo.dissimilarity_measures.utils import seqlength
+from sequenzo.dissimilarity_measures import get_distance_matrix, get_substitution_cost_matrix
+
+
+def compute_cat_distance_matrix(channels: List[SequenceData],
+                                method: Optional[str] = None,
+                                norm: str = "none",
+                                indel: Union[float, np.ndarray, List[Union[float, List[float]]]] = "auto",
+                                sm: Optional[Union[List[str], List[np.ndarray]]] = None,
+                                with_missing: Optional[Union[bool, List[bool]]] = None,
+                                full_matrix: bool = True,
+                                link: str = "sum",
+                                cval: float = 2,
+                                miss_cost: float = 2,
+                                cweight: Optional[List[float]] = None,
+                                what: str = "MDseq",
+                                ch_sep: str = "+"):
+    """
+            mulitdomain sequences analysis, you can get:
+            - multi-domain sequences ('MDseq')
+            - multi-domain substitution and indel costs ('cost')
+            - multi-domain distance_matrix ('diss')
+
+            :param channels: A list of domain state sequence stslist objects defined with the define_sequences_data function
+            :param method: Dissimilarity measure between sequences.
+            :param norm: The normalization method to use. Ignored if what is not "diss".
+            :param indel: An insertion/deletion cost or a vector of state dependent indel costs for each domain.
+            :param sm: A list with a substitution-cost matrix for each domain,
+                       or a list of method names for generating the domain substitution costs
+            :param with_missing: Whether consider missing values
+            :param full_matrix: the full distance matrix between MD sequences is returned.
+            :param link: Method to compute the "link" between domains.
+            :param cval: Domain substitution cost for "CONSTANT" matrix, for seqcost
+            :param miss_cost: Cost to substitute missing values at domain level, for seqcost
+            :param cweight: A vector of domain weights.
+            :param what: What output should be returned?
+            :param ch_sep: Separator used for building state names of the expanded alphabet.
+    """
+
+    # ==================
+    # Checking Arguments
+    # ==================
+    if what == "sm":
+        print("[!] what='sm' deprecated! Use what='cost' instead.")
+        what = "cost"
+    elif what == "seqmc":
+        print("[!] what='seqmc' deprecated! Use what='MDseq' instead.")
+        what = "MDseq"
+
+    valid_whats = ["MDseq", "cost", "diss"]
+    if what not in valid_whats:
+        raise ValueError(f"[!] 'what' should be one of {valid_whats}.")
+
+    if what == "diss" and not method:
+        raise ValueError("[!] A valid 'method' must be provided when what = 'diss'.")
+    if what == "cost" and sm is None:
+        raise ValueError("[!] 'sm' cannot be NULL when what = 'cost'.")
+
+    nchannels = len(channels)
+    if nchannels < 2:
+        raise ValueError("[!] Please specify at least two domains.")
+
+    # Check cweight
+    if cweight is None:
+        cweight = np.repeat(1.0, nchannels)
+
+    # If time varying sm are provided, all sm must be 3-dimensional
+    timeVarying = False
+    if isinstance(sm, list) and isinstance(sm[0], np.ndarray):
+        ndims = [arr.ndim for arr in sm]
+        if any(d == 3 for d in ndims) and not all(d == 3 for d in ndims):
+            raise ValueError("[!] One sm is 3-dimensional and some are not.")
+
+        if ndims[0] == 3:
+            timeVarying = True
+
+    # Check indel
+    # Convert all elements in indel(list) to list
+    if isinstance(indel, (float, int)):
+        indel = [indel] * nchannels
+        indel = [[x] for x in indel]
+
+    if isinstance(indel, np.ndarray):
+        indel = [[x] for x in indel.tolist()]
+
+    if isinstance(indel, list) and isinstance(indel[0], (float, int)):
+        indel = [[x] for x in indel]
+
+    if len(indel) > 1 and any(indel == "auto" for indel in indel):
+        raise ValueError("[!] 'auto' not allowed in vector or list indel.")
+
+    if isinstance(indel, list) and len(indel) == 1:
+        raise ValueError("[!] When a list or vector, indel must be of length equal to number of domains.")
+
+    if isinstance(indel, list) and len(indel) != nchannels:
+        raise ValueError("[!] When a list or vector, indel must be of length equal to number of domains.")
+
+    # Check missing
+    has_miss = np.repeat(False, nchannels)
+
+    for i in range(nchannels):
+        channel = channels[i]
+        alphabet = channel.states
+
+        # Check separator
+        if any(ch_sep in str(s) for s in alphabet):
+            raise ValueError(f"[!] 'ch.sep' symbol ({ch_sep}) occurs in alphabet of at least one channel.")
+
+        has_miss[i] = channel.ismissing
+        if with_missing is not None and has_miss[i] != with_missing[i]:
+            with_missing[i] = has_miss[i]
+            print(f"[!] Bad with.missing value for domain {i + 1}. I set it as {has_miss[i]}.")
+
+    if with_missing is None:
+        with_missing = has_miss
+
+    if isinstance(with_missing, bool) or len(with_missing) == 1:
+        with_missing = np.repeat(with_missing, nchannels)
+
+    if len(with_missing) > 1 and len(with_missing) != nchannels:
+        raise ValueError("[!] When a vector, with.missing must be of length equal to number of domains.")
+
+    # Check number of sequences for each channel
+    first_len = channels[0].seqdata.shape[0]
+    if not all(channel.seqdata.shape[0] == first_len for channel in channels):
+        raise ValueError("[!] sequence objects have different numbers of rows.")
+
+    numseq = first_len
+
+    print(f"[>] {nchannels} domains with {numseq} sequences.")
+    # Actually LCP and RLCP are not included
+
+    # Check what : method, sm
+    if what == "diss":
+        metlist = ["OM", "LCS", "DHD", "HAM"]
+
+        if method not in metlist:
+            raise ValueError(f"[!] 'method' should be one of {metlist}.")
+        if not isinstance(sm, list):
+            raise ValueError(f"[!] 'sm' should be a list.")
+
+        if method == "LCS":
+            method = "OM"
+            sm = "CONSTANT"
+            indel = list(np.repeat(indel, nchannels))
+            cval = 2
+            miss_cost = 2
+
+        timeVarying = method == "DHD"
+
+        if sm is None:
+            costmethod = "CONSTANT"
+            if method == "DHD":
+                costmethod = "TRATE"
+            sm = list(np.repeat(costmethod, nchannels))
+
+    if len(sm) == 1 and sm[0] in ["CONSTANT", "TRATE", "INDELS", "INDELSLOG"]:
+        sm = list(np.repeat(sm, nchannels))
+
+    # Checking correct numbers of info per channel
+    if what != "MDseq":
+        if len(sm) != nchannels or len(cweight) != nchannels:
+            raise ValueError("[!] You must supply one weight, one substitution matrix, and one indel per domain.")
+
+    # Checking that all channels have the same length
+    slength1 = seqlength(channels[1])
+    for i in range(1, nchannels):
+        if not np.array_equal(slength1, seqlength(channels[i])):
+            print("[!] Cases with sequences of different length across domains.")
+            break
+
+    substmat_list = []  # subsitution matrix
+    indel_list = []  # indels per channel
+    alphabet_list = []  # alphabet for each channel
+    alphsize_list = []  # alphabet size per channel
+    maxlength_list = np.zeros(nchannels)  # seqlenth of each channels
+
+    # Storing number of columns and cnames
+    for i in range(nchannels):
+        maxlength_list[i] = channels[i].seqdata.shape[1]
+    max_index = np.argmax(maxlength_list)
+    md_cnames = channels[max_index].seqdata.columns
+
+    print("[>] Building MD sequences of combined states.")
+
+    # ================================
+    # Building the New Sequence Object
+    # ================================
+    maxlength = int(np.max(maxlength_list))
+    newseqdata = np.full((numseq, maxlength), "", dtype='U256')
+
+    for i in range(nchannels):
+        seqchan = channels[i].values.copy()
+
+        for j in range(maxlength):
+            if j < maxlength_list[i]:
+                newcol = seqchan[:, j].astype(str)
+
+                # TraMineR default missing value is legal, and we already do this.
+                # newseqdataNA[,j] <- newseqdataNA[,j] & newCol == void
+
+                # SequenceData has no attributes void, so we default fill with missing value (np.nan)
+                # if (fill.with.miss == TRUE & has.miss[i] & any(newCol == void)) {
+                #     newCol[newCol == void] < - nr
+                # }
+
+            else:
+                newcol = np.repeat("", numseq)
+
+            if i > 0:
+                newseqdata[:, j] = np.char.add(np.char.add(newseqdata[:, j], ch_sep), newcol)
+            else:
+                newseqdata[:, j] = newcol
+
+    states_space = list(np.unique(newseqdata))
+
+    print("  - OK.")
+
+    if what == "MDseq":
+        return newseqdata
+    else:
+        # ==================================================
+        # Building Substitution Matrix and Indel Per Channel
+        # ==================================================
+        for i in range(nchannels):
+            channel = channels[i]
+
+            if not isinstance(channel, SequenceData):
+                raise ValueError("[!] Channel ", i,
+                                 " is not a state sequence object, use 'seqdef' function to create one.")
+
+            # Since states is prepared for the upcoming MD states
+            # And MD uses numeric representations, we use numbers here instead of the original string states.
+            states = np.arange(1, len(channel.states) + 1).astype(str).tolist()
+
+            # Checking missing values
+            if with_missing[i]:
+                print("[>] Including missing value as an additional state.")
+            else:
+                if channel.ismissing:
+                    raise ValueError("[!] Found missing values in channel ", i,
+                                     ", set with.missing as TRUE for that channel.")
+
+            # Check states
+            alphabet_list.append(states)
+            alphsize_list.append(len(states))
+
+            # Pre-progress indel
+            if indel != "auto" and len(indel[i]) == 1:
+                indel[i] = np.repeat(indel[i], alphsize_list[i])
+
+            # Substitution matrix generation method is given
+            if isinstance(sm[i], str):
+                print(f"[>] Computing substitution cost matrix for domain {i}.")
+
+                with contextlib.redirect_stdout(io.StringIO()):
+                    costs = get_substitution_cost_matrix(channel, sm[i],
+                                                         with_missing=has_miss[i],
+                                                         time_varying=timeVarying, cval=cval,
+                                                         miss_cost=miss_cost)
+                substmat_list.append(costs['sm'])
+
+                if "auto" == indel:
+                    costs['indel'] = np.repeat(costs['indel'], alphsize_list[i])
+                    indel_list.append(costs['indel'])
+                else:
+                    indel_list.append(indel[i])
+
+            else:  # Provided sm
+                substmat_list.append(sm[i])
+
+                if "auto" == indel:
+                    indel_list.append(np.repeat(np.max(sm[i]) / 2, alphsize_list[i]))
+                else:
+                    indel_list.append(indel[i])
+
+            # Mutliply by channel weight
+            substmat_list[i] = cweight[i] * substmat_list[i]
+
+        if "auto" == indel:
+            indel = indel_list
+
+        # =============================================
+        # Building the New CAT Substitution Cost Matrix
+        # =============================================
+        print("[>] Computing MD substitution and indel costs with additive trick.")
+
+        # Build new subsitution matrix and new alphabet
+        alphabet = states_space
+        alphabet_size = len(alphabet)
+        newindel = None
+
+        # Recomputing the substitution matrix
+        if not timeVarying:
+            newsm = np.zeros((alphabet_size, alphabet_size))
+            newindel = np.zeros(alphabet_size)
+
+            # To reduce redundancy, we simply merged the code for retrieving sm and indel
+            statelisti = alphabet[alphabet_size - 1].split(ch_sep)
+            for i in range(nchannels):
+                state = statelisti[i]
+                ipos = alphabet_list[i].index(state)
+
+                newindel[alphabet_size - 1] += indel[i][ipos] * cweight[i]
+
+            for i in range(alphabet_size - 1):
+                statelisti = alphabet[i].split(ch_sep)
+
+                for chan in range(nchannels):
+                    state = statelisti[chan]
+                    ipos = alphabet_list[chan].index(state)
+
+                    newindel[i] += indel[chan][ipos] * cweight[chan]
+
+                for j in range(i + 1, alphabet_size):
+                    cost = 0
+                    statelistj = alphabet[j].split(ch_sep)
+
+                    for chan in range(nchannels):
+                        ipos = alphabet_list[chan].index(statelisti[chan]) + 1
+                        jpos = alphabet_list[chan].index(statelistj[chan]) + 1
+                        cost += substmat_list[chan].iloc[ipos, jpos]
+
+                    newsm[i, j] = cost
+                    newsm[j, i] = cost
+
+        else:
+            # Recomputing time varying substitution
+            newsm = np.zeros((maxlength, alphabet_size, alphabet_size))
+
+            for t in range(maxlength):
+                for i in range(alphabet_size - 1):
+                    statelisti = alphabet[i].split(ch_sep)
+
+                    for j in range(i + 1, alphabet_size):
+                        cost = 0
+                        statelistj = alphabet[j].split(ch_sep)
+
+                        for chan in range(nchannels):
+                            ipos = alphabet_list[chan].index(statelisti[chan])
+                            jpos = alphabet_list[chan].index(statelistj[chan])
+
+                            cost += substmat_list[chan][t, ipos, jpos]
+
+                        newsm[t, i, j] = cost
+                        newsm[t, j, i] = cost
+
+        print("  - OK.")
+
+        # Indel as sum
+        if newindel is None:
+            newindel = np.sum(cweight * cweight[:, np.newaxis], axis=0)
+
+        # If we want the mean of cost
+        if link == "mean":
+            newindel = newindel / np.sum(cweight)
+            newsm = newsm / np.sum(cweight)
+
+        if what == "cost":
+            return {
+                "sm": newsm,
+                "indel": newindel,
+                "alphabet": alphabet,
+                "cweight": cweight
+            }
+
+        if what == "diss":
+            if np.any(np.isnan(newsm)) or np.any(np.isnan(newindel)):
+                raise ValueError("NA values found in substitution or indel costs. Cannot compute MD distances.")
+
+            print("[>] Computing MD distances using additive trick.")
+
+            # This step will hide the state concatenation,
+            # And the returned result will convert the MD strings into numbers.
+            # for example : '1+2+3' --> 1, '1+4+6' --> 2
+            newseqdata_df = pd.DataFrame(newseqdata, columns=md_cnames)
+            newseqdata_df.insert(0, channels[0].id_col, channels[0].ids)
+
+            # Reconstruct multi-domain labels for composite states
+            domain_labels = [channel.labels for channel in
+                             channels]  # e.g., [["At home", "Left home"], ["No child", "Child"]]
+
+            md_labels = []
+            for md_state in states_space:
+                parts = md_state.split(ch_sep)  # e.g., ["0", "1"]
+                if len(parts) != len(domain_labels):
+                    md_labels.append(md_state)  # fallback if structure doesn't match
+                else:
+                    label_parts = []
+                    for val, dom_lab in zip(parts, domain_labels):
+                        try:
+                            label_parts.append(dom_lab[int(val)])
+                        except (ValueError, IndexError):
+                            label_parts.append(str(val))  # fallback if unexpected value
+                    md_labels.append(" + ".join(label_parts))
+
+            with contextlib.redirect_stdout(io.StringIO()):
+                newseqdata_seq = SequenceData(newseqdata_df,
+                                              time=md_cnames,
+                                              states=states_space,
+                                              labels=md_labels,
+                                              id_col=channels[0].id_col)
+
+            newindel = np.max(newindel)
+            with contextlib.redirect_stdout(io.StringIO()):
+                diss_matrix = get_distance_matrix(newseqdata_seq,
+                                                  method=method,
+                                                  norm=norm,
+                                                  indel=newindel,
+                                                  sm=newsm,
+                                                  with_missing=False,
+                                                  full_matrix=full_matrix)
+            print("  - OK.")
+
+            diss_matrix = pd.DataFrame(diss_matrix, index=channels[0].ids, columns=channels[0].ids)
+            return diss_matrix