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
extract_seq_len.py
#!/usr/bin/python
from Bio import SeqIO
import sys
# open FASTA and list of sequences
try:
secu = sys.argv[1]
lis = sys.argv[2]
except:
secu = raw_input("Sequence FASTA file: ")
lis = raw_input("List name file: ")
secu = SeqIO.parse(open(secu), "fasta")
lista = [line.strip() for line in open(lis)]
# create lists
names = []
seque = []
# create a dictionary with name and sequence
print "\nCreating database...\n"
for a in secu:
names.append(a.id)
seque.append(a.seq)
dictio = dict(zip(names, seque))
# print output
output = open(lis + ".len", "w")
i = 0
j = 0
for b in lista:
try:
output.write("%s\t%s\n" % (b,len(str(dictio[b]))))
print "Getting sequence %s" % b
i += 1
except:
print "Not found " + b
j += 1
pass
print "\nFOUND " + str(i) + " sequences"
print "\nNOT FOUND " + str(j) + " sequences"