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plotting util and transcript changes
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,97 +1,2 @@ | ||
| import numpy as np | ||
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| class SNPInfo(object): | ||
| """ Docstring | ||
| """ | ||
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| def __init__(self, position): | ||
| self.position = position | ||
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| def __call__(self, position): | ||
| pass | ||
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| class Exon(object): | ||
| """ A region | ||
| """ | ||
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| def __init__(self, region, start, end): | ||
| self.region = region | ||
| try: | ||
| self.start = int(start) | ||
| self.end = int(end) | ||
| except ValueError: | ||
| print("Start and End positions need to be integers") | ||
|
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| class Transcript(object): | ||
| """ A collection of exons | ||
| """ | ||
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| def __init__(self, exons=[]): | ||
| self.exons = exons | ||
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| class Gene(object): | ||
| """ A collection of transcripts | ||
| """ | ||
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| def __init__(self, transcripts=[]): | ||
| self.transcripts = [] | ||
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| def _unique_junctions(self): | ||
| pass | ||
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| def hmm(self): | ||
| pass | ||
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| def break_exons(exon1, exon2): | ||
| """ Returns a list of new exons | ||
| Breaks a interval into 2 intervals if it overlaps, upstream exon always | ||
| comes first. | ||
| """ | ||
| if exon1.region == exon2.region: | ||
| if exon2.start > exon1.start and exon2.end < exon1.end: | ||
| # Case where exon1 is wholly enclosed in exon2 | ||
| return([Exon(exon1.region, exon1.start, exon2.start), | ||
| Exon(exon1.region, exon2.start, exon2.end), | ||
| Exon(exon1.region, exon2.end, exon1.end)]) | ||
| elif exon2.end < exon1.end: | ||
| return([Exon(exon1.region, exon1.start, exon2.start), | ||
| Exon(exon1.region, exon2.start, exon1.end), | ||
| Exon(exon1.region, exon1.end, exon2.end)]) | ||
| else: | ||
| # Do nothing if there is no overlap | ||
| return(exon1, exon2) | ||
| else: | ||
| pass | ||
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| def unique_sets(set_list): | ||
| """ Returns a list of sets | ||
| Calculates the unique regions defined such that only the same elements | ||
| are bound to it. | ||
| """ | ||
|
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| # Since most exons are shared, remove the most common elements first | ||
| common_set = reduce( lambda x, y: x & y, list_of_sets) | ||
| rs = [i - common_set for i in list_of_sets] | ||
| out_sets = [] | ||
| all_unique = True | ||
| n = len(set_list) | ||
| for i in set_list: | ||
| intersection = [t & i for t in set_list] | ||
| # uniqufy the intersections | ||
| u_s = set(intersection) | ||
| for t in u_s: | ||
| pass | ||
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| set_list = [i] | ||
| while len(rs) > 0: | ||
| intersection = [t & i for i in set_list] | ||
| out_sets.append(i) | ||
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| return(out_sets) | ||
| from .transcript_utils import * | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,160 @@ | ||
|
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||
|
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| class SNPInfo(object): | ||
| """ Docstring | ||
| """ | ||
|
|
||
| def __init__(self, position): | ||
| self.position = position | ||
|
|
||
| def __call__(self, position): | ||
| pass | ||
|
|
||
|
|
||
| class Exon(object): | ||
| """ A region | ||
| """ | ||
|
|
||
| def __init__(self, region, start, end): | ||
| self.region = region | ||
| try: | ||
| self.start = int(start) | ||
| self.end = int(end) | ||
| except ValueError: | ||
| print("Start and End positions need to be integers") | ||
|
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||
|
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| class Transcript(object): | ||
| """ A collection of exons | ||
| """ | ||
|
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| def __init__(self, exons=[]): | ||
| self.exons = exons | ||
|
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|
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| class Gene(object): | ||
| """ A collection of transcripts | ||
| """ | ||
|
|
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| def __init__(self, transcripts=[]): | ||
| self.transcripts = [] | ||
|
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| def _unique_junctions(self): | ||
| pass | ||
|
|
||
| def hmm(self): | ||
| pass | ||
|
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||
|
|
||
| def break_exons(exon1, exon2): | ||
| """ Returns a list of new exons | ||
| Breaks a interval into 2 intervals if it overlaps, upstream exon always | ||
| comes first. | ||
| """ | ||
| if exon1.region == exon2.region: | ||
| if exon2.start > exon1.start and exon2.end < exon1.end: | ||
| # Case where exon1 is wholly enclosed in exon2 | ||
| return([Exon(exon1.region, exon1.start, exon2.start), | ||
| Exon(exon1.region, exon2.start, exon2.end), | ||
| Exon(exon1.region, exon2.end, exon1.end)]) | ||
| elif exon2.end < exon1.end: | ||
| return([Exon(exon1.region, exon1.start, exon2.start), | ||
| Exon(exon1.region, exon2.start, exon1.end), | ||
| Exon(exon1.region, exon1.end, exon2.end)]) | ||
| else: | ||
| # Do nothing if there is no overlap | ||
| return(exon1, exon2) | ||
| else: | ||
| pass | ||
|
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||
|
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||
| def unique_sets(set_list): | ||
| """ Returns a list of sets | ||
| Calculates the unique regions defined such that only the same elements | ||
| are bound to it. | ||
| """ | ||
|
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||
| # Since most exons are shared, remove the most common elements first | ||
| common_set = reduce( lambda x, y: x & y, list_of_sets) | ||
| rs = [i - common_set for i in list_of_sets] | ||
| out_sets = [] | ||
| all_unique = True | ||
| n = len(set_list) | ||
| for i in set_list: | ||
| intersection = [t & i for t in set_list] | ||
| # uniqufy the intersections | ||
| u_s = set(intersection) | ||
| for t in u_s: | ||
| pass | ||
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| set_list = [i] | ||
| while len(rs) > 0: | ||
| intersection = [t & i for i in set_list] | ||
| out_sets.append(i) | ||
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| return(out_sets) | ||
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| def compare_two_transcripts(trans1, trans2, transcript_dict): | ||
| """ | ||
| Returns the splice differences between two transcripts. | ||
| Note this ignores TSS and just looks for splice junctions | ||
| Parameters | ||
| ---------- | ||
| :TODO refactor this | ||
| :TODO still not finished | ||
| """ | ||
|
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| t1 = transcript_dict[trans1] | ||
| t2 = transcript_dict[trans2] | ||
|
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| starts1 = [i[0] for i in t1] | ||
| starts2 = [i[0] for i in t2] | ||
| # Assume sorted | ||
| reverse = False | ||
| if min(starts1) >= min(starts2): | ||
| s1 = t2 | ||
| s2 = t1 | ||
| reverse = True | ||
| else: | ||
| s1 = t1 | ||
| s2 = t2 | ||
| # Assume sorted order, ordering in reverse by construction | ||
| if reverse: | ||
| torder = (trans2, trans1) | ||
| else: | ||
| torder = (trans1, trans2) | ||
| oc = 0 | ||
| #start_matches = False | ||
| exclusive_juncs = [] | ||
| matching_exons = [] | ||
| skipped_exons = [] | ||
| for i in s1: | ||
| if (i[0] < s2[0][0]) and (i[1] <= s2[0][0]): | ||
| pass | ||
| elif (i[0] < s2[oc][0]) and (i[1] > s2[oc][0]): | ||
| # 5' difference | ||
| print('5 primt diff') | ||
| sdiff = i[0] - s2[oc][0] | ||
| ediff = i[1] - s2[oc][1] | ||
| print(s2[oc]) | ||
| exclusive_juncs.append((i[0], s2[oc][0], | ||
| sdiff, ediff, (i[2], s2[oc][2]))) | ||
| oc += 1 | ||
| elif (i[0] > s2[oc][0]) and (i[0] < s2[oc][1]): | ||
| print('3 prime diff') | ||
| print(i[0] - s2[oc][0]) | ||
| print(i) | ||
| print(s2[oc]) | ||
| #:TODO FIX this | ||
| oc += 1 | ||
| elif (i[0] == s2[oc][0]) and (i[1] == s2[oc][1]): | ||
| matching_exons.append((i[2], s2[oc][2])) | ||
| oc += 1 | ||
| pass | ||
| return(exclusive_juncs, torder) |