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Try to filter to only nhmmer valid
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This is for RNAcentral/rnacentral-sequence-search#103. We should only
have parsable sequences in the sequence search dataset. This should
select only the sequences that nhmmer can work with.
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blakesweeney committed Feb 7, 2020
1 parent 87a3918 commit f6ecef2
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion sequence-search-export.nf
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ process create_fasta {
script:
def ordered = "${name}-ordered.fasta"
"""
json2fasta.py ${json} ${ordered}
json2fasta.py ${json} - | rnac ftp-export sequences valid-nhmmer - ${ordered}
md5sum ${ordered} > ${name}.hash
seqkit shuffle --two-pass ${ordered} > ${name}.fasta
esl-seqstat ${name}.fasta > ${name}.seqstat
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