Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

merge in main to branch #37

Closed
wants to merge 6 commits into from
Closed

merge in main to branch #37

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
a8231b6
fixed missing arg in find_ambiguities func
ammaraziz Apr 2, 2024
348a3c0
revert files to original state
ammaraziz Apr 4, 2024
55aa31b
Merge pull request #36 from ammaraziz/readme
aineniamh Apr 12, 2024
258303a
Merge branch 'master' into master
aineniamh Apr 12, 2024
863e518
Merge pull request #33 from ammaraziz/master
aineniamh Apr 12, 2024
2b61123
reverting the find am script change
aineniamh Apr 12, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
22 changes: 7 additions & 15 deletions snipit/command.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,6 @@
import sys
import os
import argparse
import textwrap
import pkg_resources
import collections

Expand All @@ -28,7 +27,6 @@ def main(sysargs = sys.argv[1:]):

i_group = parser.add_argument_group('Input options')
i_group.add_argument('alignment',help="Input alignment fasta file")
i_group.add_argument("-t","--sequence-type", choices=['nt','aa'], action="store",help="Input sequence type: aa or nt", default="nt", dest="sequence_type")
i_group.add_argument("-r","--reference", action="store",help="Indicates which sequence in the alignment is\nthe reference (by sequence ID).\nDefault: first sequence in alignment", dest="reference")
i_group.add_argument("-l","--labels", action="store",help="Optional csv file of labels to show in output snipit plot. Default: sequence names", dest="labels")
i_group.add_argument("--l-header", action="store",help="Comma separated string of column headers in label csv. First field indicates sequence name column, second the label column. Default: 'name,label'", dest="label_headers",default="name,label")
Expand All @@ -49,10 +47,7 @@ def main(sysargs = sys.argv[1:]):
f_group.add_argument("--width",action="store",type=float,help="Overwrite the default figure width",default=0)
f_group.add_argument("--size-option",action="store",help="Specify options for sizing. Options: expand, scale",dest="size_option",default="scale")
f_group.add_argument("--solid-background",action="store_true",help="Force the plot to have a solid background, rather than a transparent one.",dest="solid_background")
f_group.add_argument("-c","--colour-palette",dest="colour_palette",action="store",
help="Specify colour palette. Options: [classic, classic_extended, primary, purine-pyrimidine, greyscale, wes, verity, ugene]. Use ugene for protein alignments.",default="classic",
choices=["classic","classic_extended","primary","purine-pyrimidine","greyscale","wes","verity","ugene"],
metavar='')
f_group.add_argument("-c","--colour-palette",dest="colour_palette",action="store",help="Specify colour palette. Options: primary, classic, purine-pyrimidine, greyscale, wes, verity",default="classic")
f_group.add_argument("--flip-vertical",action='store_true',help="Flip the orientation of the plot so sequences are below the reference rather than above it.",dest="flip_vertical")
f_group.add_argument("--sort-by-mutation-number", action='store_true',
help="Render the graph with sequences sorted by the number of SNPs relative to the reference (fewest to most). Default: False", dest="sort_by_mutation_number")
Expand All @@ -67,11 +62,8 @@ def main(sysargs = sys.argv[1:]):
s_group.add_argument("--show-indels",action='store_true',help="Include insertion and deletion mutations in snipit plot.",dest="show_indels")
s_group.add_argument('--include-positions', dest='included_positions', type=sfunks.bp_range, nargs='+', default=None, help="One or more range (closed, inclusive; one-indexed) or specific position only included in the output. Ex. '100-150' or Ex. '100 101' Considered before '--exclude-positions'.")
s_group.add_argument('--exclude-positions', dest='excluded_positions', type=sfunks.bp_range, nargs='+', default=None, help="One or more range (closed, inclusive; one-indexed) or specific position to exclude in the output. Ex. '100-150' or Ex. '100 101' Considered after '--include-positions'.")
s_group.add_argument("--ambig-mode", dest="ambig_mode",choices=['all', 'snps', 'exclude'], default='snpsambi',
help=textwrap.dedent('''Controls how ambiguous bases are handled -
[all] include all ambig such as N,Y,B in all positions;
[snps] only include ambig if a snp is present at the same position;
[exclude] remove all ambig, same as depreciated --exclude-ambig-pos'''))
s_group.add_argument("--exclude-ambig-pos",dest="exclude_ambig_pos",action='store_true',help="Exclude positions with ambig base in any sequences. Considered after '--include-positions'")

misc_group = parser.add_argument_group('Misc options')
misc_group.add_argument("-v","--version", action='version', version=f"snipit {__version__}")

Expand Down Expand Up @@ -105,9 +97,9 @@ def main(sysargs = sys.argv[1:]):

reference,alignment = sfunks.get_ref_and_alignment(args.alignment,ref_input,label_map)

snp_dict,record_snps,num_snps = sfunks.find_snps(reference,alignment,args.show_indels,args.sequence_type,args.ambig_mode)
snp_dict,record_snps,num_snps = sfunks.find_snps(reference,alignment,args.show_indels)

record_ambs = sfunks.find_ambiguities(alignment, snp_dict, args.sequence_type)
record_ambs = sfunks.find_ambiguities(alignment, snp_dict)

colours = sfunks.get_colours(args.colour_palette)

Expand All @@ -131,14 +123,14 @@ def main(sysargs = sys.argv[1:]):
args.flip_vertical,
args.included_positions,
args.excluded_positions,
args.ambig_mode,
args.exclude_ambig_pos,
args.sort_by_mutation_number,
args.high_to_low,
args.sort_by_id,
args.sort_by_mutations,
args.recombi_mode,
args.recombi_references)
print(sfunks.green(f"Snipping Complete: {output}"))


if __name__ == '__main__':
main()
53 changes: 11 additions & 42 deletions snipit/scripts/snp_functions.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,6 @@
import math
from itertools import groupby, count
from collections import OrderedDict
from enum import Enum

# imports from other modules
from Bio import SeqIO
Expand All @@ -31,11 +30,6 @@
CYAN = '\u001b[36m'
DIM = '\033[2m'

NT_BASES = ["A","T","G","C"]
NT_AMBIG = ["W","S","M","K","R","Y","B","D","H","V","N"]
AA_BASES = ["A","R","N","D","C","Q","E","G","H","I","L","K","M","F","P","S","T","W","Y","V"]
AA_AMBIG = ["X","B","Z","J"]


def bp_range(s):
"""
Expand Down Expand Up @@ -223,24 +217,8 @@ def merge_indels(indel_list,prefix):

return indel_list

def find_snps(reference_seq,input_seqs,show_indels,sequence_type,ambig_mode):

# set the appropriate genetic code to use for snp calling
if sequence_type == 'nt':
if ambig_mode == 'snps':
gcode = NT_BASES
elif ambig_mode == 'all':
gcode = NT_BASES + NT_AMBIG
else: # exclude
gcode = NT_BASES
if sequence_type == 'aa':
if ambig_mode == 'snps':
gcode = AA_BASES
elif ambig_mode == 'all':
gcode = AA_BASES + AA_AMBIG
else: #exclude
gcode = AA_BASES

def find_snps(reference_seq,input_seqs,show_indels):
non_amb = ["A","T","G","C"]
snp_dict = {}

record_snps = {}
Expand All @@ -252,7 +230,7 @@ def find_snps(reference_seq,input_seqs,show_indels,sequence_type,ambig_mode):
for i in range(len(query_seq)):
bases = [query_seq[i],reference_seq[i]]
if bases[0] != bases[1]:
if bases[0] in gcode and bases[1] in gcode:
if bases[0] in non_amb and bases[1] in non_amb:

snp = f"{i+1}:{bases[1]}{bases[0]}" # position-reference-query

Expand Down Expand Up @@ -283,12 +261,11 @@ def find_snps(reference_seq,input_seqs,show_indels,sequence_type,ambig_mode):

return snp_dict,record_snps,len(var_counter)

def find_ambiguities(alignment, snp_dict):
def find_ambiguities(alignment,snp_dict):




if type == "nt":
amb = NT_AMBIG
if type == "aa":
amb = AA_AMBIG

snp_sites = collections.defaultdict(list)
for seq in snp_dict:
Expand All @@ -308,7 +285,7 @@ def find_ambiguities(alignment, snp_dict):
for i in snp_sites:
bases = [query_seq[i],snp_sites[i]] #if query not same as ref allele
if bases[0] != bases[1]:
if bases[0] not in amb:
if bases[0] not in ["A","T","G","C"]:

snp = f"{i+1}:{bases[1]}{bases[0]}" # position-outgroup-query
snps.append(snp)
Expand Down Expand Up @@ -371,10 +348,10 @@ def make_graph(num_seqs,
height,
size_option,
solid_background,
ambig_mode,
flip_vertical=False,
included_positions=None,
excluded_positions=None,
exclude_ambig_pos=False,
sort_by_mutation_number=False,
high_to_low=True,
sort_by_id=False,
Expand Down Expand Up @@ -475,7 +452,7 @@ def make_graph(num_seqs,
x_position = int(pos)

# if positions with any ambiguities should be ignored, note the position
if ambig_mode == 'exclude':
if exclude_ambig_pos:
excluded_positions.add(x_position)
else:
ref = var[0]
Expand Down Expand Up @@ -658,21 +635,13 @@ def make_graph(num_seqs,
def get_colours(colour_palette):

palettes = {"classic": {"A":"steelblue","C":"indianred","T":"darkseagreen","G":"skyblue"},
"classic_extended": {"A":"steelblue","C":"indianred","T":"darkseagreen",
"G":"skyblue","W":"#FFCC00","S":"#66FF00","M":"#6600FF",
"K":"#66FFCC","R":"#FF00FF","Y":"#FFFF99","B":"#CCFF99",
"D":"#FFFF00","H":"##33FF00","V":"#FF6699","N":"#333333"},
"wes": {"A":"#CC8B3C","C":"#456355","T":"#541F12","G":"#B62A3D"},
"primary": {"A":"green","C":"goldenrod","T":"steelblue","G":"indianred"},
"purine-pyrimidine":{"A":"indianred","C":"teal","T":"teal","G":"indianred"},
"greyscale":{"A":"#CCCCCC","C":"#999999","T":"#666666","G":"#333333"},
"blues":{"A":"#3DB19D","C":"#76C5BF","T":"#423761","G":"steelblue"},
"verity":{"A":"#EC799A","C":"#df6eb7","T":"#FF0080","G":"#9F0251"},
"recombi":{"lineage_1":"steelblue","lineage_2":"#EA5463","Both":"darkseagreen","Private":"goldenrod"},
"ugene":{"A":"#00ccff","R":"#d5c700","N":"#33ff00","D":"#ffff00","C":"#6600ff","Q":"#3399ff",
"E":"#c0bdbb","G":"#ff5082","H":"#fff233","I":"#00abed","L":"#008fc6","K":"#ffee00",
"M":"#1dc0ff","F":"#3df490","P":"#d5426c","S":"#ff83a7","T":"#ffd0dd","W":"#33cc78",
"Y":"#65ffab","V":"#ff6699","X":"#999999","B":"#999999","Z":"#999999","J":"#999999"}
"recombi":{"lineage_1":"steelblue","lineage_2":"#EA5463","Both":"darkseagreen","Private":"goldenrod"}
}
if colour_palette not in palettes:
sys.stderr.write(red(f"Error: please select one of {palettes} for --colour-palette option\n"))
Expand Down
Loading