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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,60 +1,61 @@ | ||
| import csv | ||
| import pysam | ||
| import pandas as pd | ||
| import numpy as np | ||
| import os | ||
| import logging | ||
| import gfapy | ||
| import matplotlib.pyplot as plt | ||
| logging.getLogger("matplotlib.font_manager").disabled = True | ||
| import matplotlib as mt | ||
| import gfapy | ||
| import os | ||
|
|
||
| import pysam | ||
| import pandas as pd | ||
| import numpy as np | ||
| from strainy.params import * | ||
| logging.getLogger("matplotlib.font_manager").disabled = True | ||
|
|
||
|
|
||
| def write_bam(edge, I, AF, cl_file=None,file=None): | ||
| infile = pysam.AlignmentFile(StRainyArgs().bam, "rb") | ||
| if file==None: | ||
| outfile = pysam.AlignmentFile("%s/bam/coloredBAM_unitig_%s.bam" % (StRainyArgs().output_intermediate, edge), "wb", template=infile) | ||
| else: | ||
| outfile = pysam.AlignmentFile(file,"wb", template=infile) | ||
| if cl_file==None: | ||
| cl = pd.read_csv("%s/clusters/clusters_%s_%s_%s.csv" % (StRainyArgs().output_intermediate, edge, I, AF),keep_default_na=False) | ||
| else: | ||
| cl = pd.read_csv(cl_file,keep_default_na=False) | ||
| iter = infile.fetch(edge,until_eof=True) | ||
| def write_bam(edge, cl, infile,outfile): | ||
| """Creates new bam file based on ifnfile and add YC tag to the alignment based on csv file""" | ||
| iterbam = infile.fetch(edge,until_eof=True) | ||
| cmap = plt.get_cmap("viridis") | ||
| cl.loc[cl["Cluster"] == "NA", "Cluster"] = 0 | ||
| #clusters=sorted(set(cl["Cluster"].astype(int))) | ||
| clusters = set(cl["Cluster"]) | ||
| cmap = cmap(np.linspace(0, 1, len(clusters))) | ||
| colors={} | ||
| i=0 | ||
| colors[0] = "#505050" | ||
|
|
||
| try: | ||
| clusters.remove("0") | ||
| except: KeyError | ||
| except KeyError: | ||
| pass | ||
| for cluster in clusters: | ||
| colors[cluster] = mt.colors.to_hex(cmap[i]) | ||
| i = i+1 | ||
| cl_dict = dict(zip(cl.ReadName, cl.Cluster)) | ||
|
|
||
| for read in iter: | ||
| for read in iterbam: | ||
| try: | ||
| #clN = int(cl_dict[str(read).split()[0]]) | ||
| clN = cl_dict[str(read).split()[0]] | ||
| tag = colors[clN] | ||
| cl_n = cl_dict[str(read).split()[0]] | ||
| tag = colors[cl_n] | ||
| read.set_tag("YC", tag, replace=False) | ||
| outfile.write(read) | ||
| except (KeyError): | ||
| except KeyError: | ||
| continue | ||
| outfile.close() | ||
|
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||
|
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||
| def color(edge,cl_file=None,file=None): | ||
| """Creates colored edge bam based on strainy csv file with clusters IDs by default""" | ||
| try: | ||
| write_bam(edge, I, StRainyArgs().AF,cl_file,file) | ||
| except (FileNotFoundError): | ||
| infile = pysam.AlignmentFile(StRainyArgs().bam, "rb") | ||
| if file is None: | ||
| outfile = pysam.AlignmentFile( | ||
| f"{StRainyArgs().output_intermediate}/bam/coloredBAM_unitig_{edge}.bam", | ||
| "wb", template=infile) | ||
| else: | ||
| outfile = pysam.AlignmentFile(file,"wb", template=infile) | ||
| if cl_file is None: | ||
| cl = pd.read_csv( | ||
| f"{StRainyArgs().output_intermediate}/clusters/clusters_{edge}_{I}_{StRainyArgs().AF}.csv", | ||
| keep_default_na=False) | ||
| else: | ||
| cl = pd.read_csv(cl_file,keep_default_na=False) | ||
| write_bam(edge,cl,infile,outfile) | ||
| except FileNotFoundError: | ||
| pass | ||
|
|