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from collections import defaultdict
import argparse
def getChromosomeColor(refName):
if refName == "chr1":
return "sea green"
elif refName == "chr2":
return "tomato"
elif refName == "chr3":
return "dark orange"
elif refName == "chr4":
return "dark orchid"
elif refName == "chr5":
return "firebrick"
elif refName == "chr6":
return "deep pink"
elif refName == "chr7":
return "#800000"
elif refName == "chr8":
return "web green"
elif refName == "chr9":
return "green yellow"
elif refName == "chr10":
return "gold"
elif refName == "chr11":
return "midnight blue"
elif refName == "chr12":
return "light coral"
elif refName == "chr13":
return "light green"
elif refName == "chr14":
return "red"
elif refName == "chr15":
return "aquamarine"
elif refName == "chr16":
return "dodger blue"
elif refName == "chr17":
return "orange red"
elif refName == "chr18":
return "yellow"
elif refName == "chr19":
return "teal"
elif refName == "chr20":
return "aqua"
elif refName == "chr21":
return "hot pink"
elif refName == "chr22":
return "light salmon"
elif refName == "chrX":
return "yellow green"
elif refName == "chrY":
return "olive drab"
else:
print("Warning using gray for unknown chromosome: " + refName)
return "gray"
def main(path):
primaryAlignments = defaultdict(lambda: defaultdict(int))
with open(path, 'r') as file:
for l,line in enumerate(file):
tokens = line.strip().split('\t')
queryName = tokens[0]
refName = tokens[5]
length = int(tokens[10])
if not refName.startswith("chr") or len(refName) > 5:
continue
# Store all alignment lengths in a dictionary
primaryAlignments[queryName][refName] += length
with open("GfaLabels.csv", 'w') as file:
file.write("name,color,refName\n")
for queryName,alignments in primaryAlignments.items():
maxLength = 0
bestRef = None
# Find the reference contig with the most aligned length
for refName,length in alignments.items():
print(queryName, refName, length)
if length > maxLength:
maxLength = length
bestRef = refName
file.write(queryName)
file.write(',')
file.write(getChromosomeColor(bestRef))
file.write(',')
file.write(bestRef)
file.write('\n')
if __name__ == "__main__":
parser = argparse.ArgumentParser(prog='generateBandageLabelsFromAlignment',
formatter_class=argparse.RawDescriptionHelpFormatter,
epilog="Program description:\n\tuse a PAF alignment tsv to generate a "
"karyotype-style coloring and labeling for Bandage")
parser.add_argument(
"--input","-i",
required=True,
type=str,
help="Path to any PAF formatted TSV that was generated from minimap2/winnowmap for the shasta contigs."
"Only chromosomes with names chr1-22 or chrX/Y will be colored"
)
args = parser.parse_args()
main(
path=args.input
)
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