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johnsolk/fasta_to_table.py

Last active October 12, 2017 17:27
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fasta_to_table.py
# From within a py3 virtualenv
# or
# sudo pip install screed
# source ~/bin/py3/bin/activate
import screed
with open("table.txt",'w') as fq:
for r in screed.open('trinity.nema.full.fasta'):
fq.write(r.name+"\n")
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head nema_transcript_gene_id.txt
Output:

comp12_c0_seq1  comp12
comp16_c0_seq1  comp16
comp53_c0_seq1  comp53
comp53_c1_seq1  comp53
comp64_c0_seq1  comp64
comp67_c0_seq1  comp67
comp86_c0_seq1  comp86
comp90_c0_seq1  comp90
comp100_c0_seq1         comp100
comp104_c0_seq1         comp104

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