--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cpt_putative_isp/spaninFuncs.py	Fri Jun 17 13:07:15 2022 +0000
@@ -0,0 +1,469 @@
+"""
+PREMISE
+### Functions/Classes that are used in both generate-putative-osp.py and generate-putative-isp.py
+###### Main premise here is to make the above scripts a little more DRY, as well as easily readable for execution.
+###### Documentation will ATTEMPT to be thourough here
+"""
+
+import re
+from Bio import SeqIO
+from Bio import Seq
+from collections import OrderedDict
+
+# Not written in OOP for a LITTLE bit of trying to keep the complication down in case adjustments are needed by someone else.
+# Much of the manipulation is string based; so it should be straightforward as well as moderately quick
+################## GLobal Variables
+Lys = "K"
+
+
+def check_back_end_snorkels(seq, tmsize):
+    """
+        Searches through the backend of a potential TMD snorkel. This is the 2nd part of a TMD snorkel lysine match.
+        --> seq : should be the sequence fed from the "search_region" portion of the sequence
+        --> tmsize : size of the potential TMD being investigated
+    """
+    found = []
+    if seq[tmsize - 4] == Lys and re.search(("[FIWLVMYCATGS]"), seq[tmsize - 5]):
+        found = "match"
+        return found
+    elif seq[tmsize - 3] == Lys and re.search(("[FIWLVMYCATGS]"), seq[tmsize - 4]):
+        found = "match"
+        return found
+    elif seq[tmsize - 2] == Lys and re.search(("[FIWLVMYCATGS]"), seq[tmsize - 3]):
+        found = "match"
+        return found
+    elif seq[tmsize - 1] == Lys and re.search(("[FIWLVMYCATGS]"), seq[tmsize - 2]):
+        found = "match"
+        return found
+    else:
+        found = "NOTmatch"
+        return found
+
+
+def prep_a_gff3(fa, spanin_type, org):
+    """
+        Function parses an input detailed 'fa' file and outputs a 'gff3' file
+        ---> fa = input .fa file
+        ---> output = output a returned list of data, easily portable to a gff3 next
+        ---> spanin_type = 'isp' or 'osp'
+    """
+    with org as f:
+        header = f.readline()
+        orgacc = header.split(" ")
+        orgacc = orgacc[0].split(">")[1].strip()
+    fa_zip = tuple_fasta(fa)
+    data = []
+    for a_pair in fa_zip:
+        # print(a_pair)
+        if re.search(("(\[1\])"), a_pair[0]):
+            strand = "+"
+        elif re.search(("(\[-1\])"), a_pair[0]):
+            strand = "-"  # column 7
+        start = re.search(("[\d]+\.\."), a_pair[0]).group(0).split("..")[0]  # column 4
+        end = re.search(("\.\.[\d]+"), a_pair[0]).group(0).split("..")[1]  # column 5
+        orfid = re.search(("(ORF)[\d]+"), a_pair[0]).group(0)  # column 1
+        if spanin_type == "isp":
+            methodtype = "CDS"  # column 3
+            spanin = "isp"
+        elif spanin_type == "osp":
+            methodtype = "CDS"  # column 3
+            spanin = "osp"
+        elif spanin_type == "usp":
+            methodtype = "CDS"
+            spanin = "usp"
+        else:
+            raise "need to input spanin type"
+        source = "cpt.py|putative-*.py"  # column 2
+        score = "."  # column 6
+        phase = "."  # column 8
+        attributes = "ID=" +orgacc+ "|"+ orfid + ";ALIAS=" + spanin + ";SEQ="+a_pair[1]  # column 9
+        sequence = [[orgacc, source, methodtype, start, end, score, strand, phase, attributes]]
+        data += sequence
+    return data
+
+
+def write_gff3(data, output="results.gff3"):
+    """
+        Parses results from prep_a_gff3 into a gff3 file
+        ---> input : list from prep_a_gff3
+        ---> output : gff3 file
+    """
+    data = data
+    filename = output
+    with filename as f:
+        f.write("#gff-version 3\n")
+        for value in data:
+            f.write(
+                "{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\n".format(
+                    value[0],
+                    value[1],
+                    value[2],
+                    value[3],
+                    value[4],
+                    value[5],
+                    value[6],
+                    value[7],
+                    value[8],
+                )
+            )
+    f.close()
+
+
+def find_tmd(pair, minimum=10, maximum=30, TMDmin=10, TMDmax=20, isp_mode=False, peri_min=18, peri_max=206):
+    """ 
+        Function that searches for lysine snorkels and then for a spanning hydrophobic region that indicates a potential TMD
+        ---> pair : Input of tuple with description and AA sequence (str)
+        ---> minimum : How close from the initial start codon a TMD can be within
+        ---> maximum : How far from the initial start codon a TMD can be within
+        ---> TMDmin : The minimum size that a transmembrane can be (default = 10)
+        ---> TMDmax : The maximum size tha ta transmembrane can be (default = 20)
+    """
+    # hydrophobicAAs = ['P', 'F', 'I', 'W', 'L', 'V', 'M', 'Y', 'C', 'A', 'T', 'G', 'S']
+    tmd = []
+    s = str(pair[1])  # sequence being analyzed
+    # print(s) # for trouble shooting
+    if maximum > len(s):
+        maximum = len(s)
+    search_region = s[minimum - 1 : maximum + 1]
+    #print(f"this is the search region: {search_region}")
+    # print(search_region) # for trouble shooting
+
+    for tmsize in range(TMDmin, TMDmax+1, 1):
+        #print(f"this is the current tmsize we're trying: {tmsize}")
+        # print('==============='+str(tmsize)+'================') # print for troubleshooting
+        pattern = "[PFIWLVMYCATGS]{"+str(tmsize)+"}"  # searches for these hydrophobic residues tmsize total times
+        #print(pattern)
+        #print(f"sending to regex: {search_region}")
+        if re.search(
+            ("[K]"), search_region[1:8]):  # grabbing one below with search region, so I want to grab one ahead here when I query.
+            store_search = re.search(("[K]"), search_region[1:8])  # storing regex object
+            where_we_are = store_search.start()  # finding where we got the hit
+            if re.search(
+                ("[PFIWLVMYCATGS]"), search_region[where_we_are + 1]
+            ) and re.search(
+                ("[PFIWLVMYCATGS]"), search_region[where_we_are - 1]
+            ):  # hydrophobic neighbor
+                #try:
+                g = re.search(("[PFIWLVMYCATGS]"), search_region[where_we_are + 1]).group()
+                backend = check_back_end_snorkels(search_region, tmsize)
+                if backend == "match":
+                    if isp_mode:
+                        g = re.search((pattern), search_region).group()
+                        end_of_tmd = re.search((g), s).end()+1
+                        amt_peri = len(s) - end_of_tmd
+                        if peri_min <= amt_peri <= peri_max:
+                            pair_desc = pair[0] + ", peri_count~="+str(amt_peri)
+                            new_pair = (pair_desc,pair[1])
+                            tmd.append(new_pair)
+                    else:
+                        tmd.append(pair)
+                else:
+                    continue
+        #else:
+            #print("I'm continuing out of snorkel loop")
+            #print(f"{search_region}")
+            #continue
+        if re.search((pattern), search_region):
+            #print(f"found match: {}")
+            #print("I AM HEREEEEEEEEEEEEEEEEEEEEEEE")
+            #try:
+            if isp_mode:
+                g = re.search((pattern), search_region).group()
+                end_of_tmd = re.search((g), s).end()+1
+                amt_peri = len(s) - end_of_tmd
+                if peri_min <= amt_peri <= peri_max:
+                    pair_desc = pair[0] + ", peri_count~="+str(amt_peri)
+                    new_pair = (pair_desc,pair[1])
+                    tmd.append(new_pair)
+            else:
+                tmd.append(pair)
+        else:
+            continue
+
+        return tmd
+
+
+def find_lipobox(pair, minimum=10, maximum=50, min_after=30, max_after=185, regex=1, osp_mode=False):
+    """
+        Function that takes an input tuple, and will return pairs of sequences to their description that have a lipoobox
+        ---> minimum - min distance from start codon to first AA of lipobox
+        ---> maximum - max distance from start codon to first AA of lipobox
+        ---> regex - option 1 (default) => more strict regular expression ; option 2 => looser selection, imported from LipoRy
+        
+    """
+    if regex == 1:
+        pattern = "[ILMFTV][^REKD][GAS]C"  # regex for Lipobox from findSpanin.pl
+    elif regex == 2:
+        pattern = "[ACGSILMFTV][^REKD][GAS]C"  # regex for Lipobox from LipoRy
+
+    candidates = []
+    s = str(pair[1])
+    # print(s) # trouble shooting
+    search_region = s[minimum-1 : maximum + 5] # properly slice the input... add 4 to catch if it hangs off at max input
+    # print(search_region) # trouble shooting
+    patterns = ["[ILMFTV][^REKD][GAS]C","AW[AGS]C"]
+    for pattern in patterns:
+        #print(pattern)  # trouble shooting
+        if re.search((pattern), search_region):  # lipobox must be WITHIN the range...
+            # searches the sequence with the input RegEx AND omits if
+            g = re.search((pattern), search_region).group() # find the exact group match
+            amt_peri = len(s) - re.search((g), s).end() + 1
+            if min_after <= amt_peri <= max_after: # find the lipobox end region
+                if osp_mode:
+                    pair_desc = pair[0] + ", peri_count~="+str(amt_peri)
+                    new_pair = (pair_desc,pair[1])
+                    candidates.append(new_pair)
+                else:
+                    candidates.append(pair)
+
+                return candidates
+
+
+def tuple_fasta(fasta_file):
+    """
+        #### INPUT: Fasta File
+        #### OUTPUT: zipped (zip) : pairwise relationship of description to sequence
+        #### 
+    """
+    fasta = SeqIO.parse(fasta_file, "fasta")
+    descriptions = []
+    sequences = []
+    for r in fasta:  # iterates and stores each description and sequence
+        description = r.description
+        sequence = str(r.seq)
+        if (
+            sequence[0] != "I"
+        ):  # the translation table currently has I as a potential start codon ==> this will remove all ORFs that start with I
+            descriptions.append(description)
+            sequences.append(sequence)
+        else:
+            continue
+
+    return zip(descriptions, sequences)
+
+
+def lineWrapper(text, charactersize=60):
+
+    if len(text) <= charactersize:
+        return text
+    else:
+        return (
+            text[:charactersize]
+            + "\n"
+            + lineWrapper(text[charactersize:], charactersize)
+        )
+
+
+def getDescriptions(fasta):
+    """
+    Takes an output FASTA file, and parses retrieves the description headers. These headers contain information needed
+    for finding locations of a potential i-spanin and o-spanin proximity to one another.
+    """
+    desc = []
+    with fasta as f:
+        for line in f:
+            if line.startswith(">"):
+                desc.append(line)
+    return desc
+
+
+def splitStrands(text, strand="+"):
+    # positive_strands = []
+    # negative_strands = []
+    if strand == "+":
+        if re.search(("(\[1\])"), text):
+            return text
+    elif strand == "-":
+        if re.search(("(\[-1\])"), text):
+            return text
+    # return positive_strands, negative_strands
+
+
+def parse_a_range(pair, start, end):
+    """
+        Takes an input data tuple from a fasta tuple pair and keeps only those within the input sequence range
+        ---> data : fasta tuple data
+        ---> start : start range to keep
+        ---> end : end range to keep (will need to + 1)
+    """
+    matches = []
+    for each_pair in pair:
+
+        s = re.search(("[\d]+\.\."), each_pair[0]).group(0)  # Start of the sequence
+        s = int(s.split("..")[0])
+        e = re.search(("\.\.[\d]+"), each_pair[0]).group(0)
+        e = int(e.split("..")[1])
+        if start - 1 <= s and e <= end + 1:
+            matches.append(each_pair)
+        else:
+            continue
+    # else:
+    # continue
+    # if matches != []:
+    return matches
+    # else:
+    # print('no candidates within selected range')
+
+
+def grabLocs(text):
+    """
+    Grabs the locations of the spanin based on NT location (seen from ORF). Grabs the ORF name, as per named from the ORF class/module
+    from cpt.py
+    """
+    start = re.search(("[\d]+\.\."), text).group(0)  # Start of the sequence ; looks for [numbers]..
+    end = re.search(("\.\.[\d]+"), text).group(0)  # End of the sequence ; Looks for ..[numbers]
+    orf = re.search(("(ORF)[\d]+"), text).group(0)  # Looks for ORF and the numbers that are after it
+    if re.search(("(\[1\])"), text): # stores strand
+        strand = "+"
+    elif re.search(("(\[-1\])"), text): # stores strand
+        strand = "-"
+    start = int(start.split("..")[0])
+    end = int(end.split("..")[1])
+    vals = [start, end, orf, strand]
+
+    return vals
+
+
+def spaninProximity(isp, osp, max_dist=30):
+    """
+    _NOTE THIS FUNCTION COULD BE MODIFIED TO RETURN SEQUENCES_
+    Compares the locations of i-spanins and o-spanins. max_dist is the distance in NT measurement from i-spanin END site
+    to o-spanin START. The user will be inputting AA distance, so a conversion will be necessary (<user_input> * 3)
+    I modified this on 07.30.2020 to bypass the pick + or - strand. To 
+    INPUT: list of OSP and ISP candidates
+    OUTPUT: Return (improved) candidates for overlapping, embedded, and separate list
+    """
+
+    embedded = {}
+    overlap = {}
+    separate = {}
+    for iseq in isp:
+        embedded[iseq[2]] = []
+        overlap[iseq[2]] = []
+        separate[iseq[2]] = []
+        for oseq in osp:
+            if iseq[3] == "+":
+                if oseq[3] == "+":
+                    if iseq[0] < oseq[0] < iseq[1] and oseq[1] < iseq[1]:
+                        ### EMBEDDED ###
+                        combo = [
+                            iseq[0],
+                            iseq[1],
+                            oseq[2],
+                            oseq[0],
+                            oseq[1],
+                            iseq[3],
+                        ]  # ordering a return for dic
+                        embedded[iseq[2]] += [combo]
+                    elif iseq[0] < oseq[0] <= iseq[1] and oseq[1] > iseq[1]:
+                        ### OVERLAP / SEPARATE ###
+                        if (iseq[1] - oseq[0]) < 6:
+                            combo = [iseq[0], iseq[1], oseq[2], oseq[0], oseq[1],iseq[3]]
+                            separate[iseq[2]] += [combo]
+                        else:
+                            combo = [iseq[0], iseq[1], oseq[2], oseq[0], oseq[1],iseq[3]]
+                            overlap[iseq[2]] += [combo]
+                    elif iseq[1] <= oseq[0] <= iseq[1] + max_dist:
+                        combo = [iseq[0], iseq[1], oseq[2], oseq[0], oseq[1],iseq[3]]
+                        separate[iseq[2]] += [combo]
+                    else:
+                        continue
+            if iseq[3] == "-":
+                if oseq[3] == "-":
+                    if iseq[0] <= oseq[1] <= iseq[1] and oseq[0] > iseq[0]:
+                        ### EMBEDDED ###
+                        combo = [
+                            iseq[0],
+                            iseq[1],
+                            oseq[2],
+                            oseq[0],
+                            oseq[1],
+                            iseq[3],
+                        ]  # ordering a return for dict
+                        embedded[iseq[2]] += [combo]
+                    elif iseq[0] <= oseq[1] <= iseq[1] and oseq[0] < iseq[0]:
+                        if (oseq[1] - iseq[0]) < 6:
+                            combo = [iseq[0], iseq[1], oseq[2], oseq[0], oseq[1],iseq[3]]
+                            separate[iseq[2]] += [combo]
+                        else:
+                            combo = [iseq[0], iseq[1], oseq[2], oseq[0], oseq[1],iseq[3]]
+                            overlap[iseq[2]] += [combo]
+                    elif iseq[0] - 10 < oseq[1] < iseq[0]:
+                        combo = [iseq[0], iseq[1], oseq[2], oseq[0], oseq[1],iseq[3]]
+                        separate[iseq[2]] += [combo]
+                    else:
+                        continue
+
+    embedded = {k: embedded[k] for k in embedded if embedded[k]}
+    overlap = {k: overlap[k] for k in overlap if overlap[k]}
+    separate = {k: separate[k] for k in separate if separate[k]}
+
+    return embedded, overlap, separate
+
+
+def check_for_usp():
+    " pass "
+
+############################################### TEST RANGE #########################################################################
+####################################################################################################################################
+if __name__ == "__main__":
+
+    #### TMD TEST
+    test_desc = ["one", "two", "three", "four", "five"]
+    test_seq = [
+        "XXXXXXXXXXXXXXXFMCFMCFMCFMCFMCXXXXXXXXXXXXXXXXXXXXXXXXXX",
+        "XXXXXXXXAAKKKKKKKKKKKKKKKXXXXXXXXXXXXX",
+        "XXXXXXX",
+        "XXXXXXXXXXXKXXXXXXXXXX",
+        "XXXXXXXXXXAKXXXXXXXXXXAKXXXXXXXX",
+    ]
+    # for l in
+    # combo = zip(test_desc,test_seq)
+    pairs = zip(test_desc, test_seq)
+    tmd = []
+    for each_pair in pairs:
+        # print(each_pair)
+        try:
+            tmd += find_tmd(pair=each_pair)
+        except (IndexError, TypeError):
+            continue
+        # try:s = each_pair[1]
+        # tmd += find_tmd(seq=s, tmsize=15)
+    # print('\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n')
+    # print(tmd)
+    # print('\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n')
+
+    #### tuple-fasta TEST
+    # fasta_file = 'out_isp.fa'
+    # ret = tuple_fasta(fasta_file)
+    # print('=============')
+    # for i in ret:
+    # print(i[1])
+
+    #### LipoBox TEST
+    test_desc = ["one", "two", "three", "four", "five", "six", "seven"]
+    test_seq = [
+        "XXXXXXXXXTGGCXXXXXXXXXXXXXXXX",
+        "XXXXXXXXAAKKKKKKKKKKKKKKKXXXXXXXXXXXXX",
+        "XXXXXXX",
+        "AGGCXXXXXXXXXXXXXXXXXXXXTT",
+        "XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTGGC",
+        "XXXXXXXXXXXXXXXXXXXXXXXXXXTGGC",
+        "MSTLRELRLRRALKEQSMRYLLSIKKTLPRWKGALIGLFLICVATISGCASESKLPEPPMVSVDSSLMVEPNLTTEMLNVFSQ*",
+    ]
+    pairs = zip(test_desc, test_seq)
+    lipo = []
+    for each_pair in pairs:
+        #print(each_pair)
+        # try:
+        try:
+            lipo += find_lipobox(pair=each_pair, regex=2)  # , minimum=8)
+        except TypeError:  # catches if something doesnt have the min/max requirements (something is too small)
+            continue
+        # except:
+        # continue
+    # print('\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n')
+    #############################3
+    # g = prep_a_gff3(fa='putative_isp.fa', spanin_type='isp')
+    # print(g)
+    # write_gff3(data=g)