https://github.com/fjruizruano/ngs-protocols
Tip revision: 39a091d1fa569a7fc717ac73c4b3de07f0a1204d authored by fjruizruano on 03 August 2023, 11:48:27 UTC
adding gfa2fas.py and extract_gfa.py
adding gfa2fas.py and extract_gfa.py
Tip revision: 39a091d
alignment_copy_paste.py
#!/usr/bin/python
from Bio import AlignIO
import sys
print "Usage: align_copy_paste.py AlignFileFasta Point"
try:
file = sys.argv[1]
except:
raw_input = ("Introduce Alignment in FASTA format: ")
try:
point = sys.argv[2]
except:
raw_input = ("Introduce last nucleotide of the alignmente left side: ")
label = file[0:3]
#open output file
out = open(file+".cut.fas","w")
#load alignment
align = AlignIO.read(open(file),"fasta")
point = int(point)
left = align[0:,:point]
right = align[0:,point:]
new_ali = right+left
i = 1
for el in new_ali:
i_str = str(i)
while len(i_str) < 4:
i_str = "0" + i_str
out.write(">%s%s\n%s\n" % (label,i_str,str(el.seq)))
i += 1
out.close()