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add new way to call extract reads #3

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add new way to call extract reads #3

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469ad5b
add new way to call extract reads
yangyxt Nov 19, 2020
b654d9f
add execution block
yangyxt Nov 19, 2020
a3142a6
move mkdir to main func
yangyxt Nov 19, 2020
baf4ac9
add logging
yangyxt Nov 29, 2020
f06b09b
open file with "r" mode, otherwise will raise NotADirectory error
yangyxt Nov 30, 2020
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open file with "r" mode, otherwise will raise NotADirectory error
@yangyxt
yangyxt committed Nov 30, 2020
commit f06b09b71ffd45c741fab662b0dc218910295dd2
2 changes: 1 addition & 1 deletion 2-generate_gaps/extract_gaps.py
View file
Original file line number Diff line number Diff line change
@@ -271,7 +271,7 @@ def interval_merge(intervals):
# splitting up the reference genome into the gaps
########################################################

fasta_fn = open(sys.argv[2])
fasta_fn = open(sys.argv[2], "r")
output_fn = open(sys.argv[4], "w")

gap_offset = 0
2 changes: 1 addition & 1 deletion run_pipeline.sh
View file
Original file line number Diff line number Diff line change
@@ -15,7 +15,7 @@ THREAD=${10}


function generate_chain(){
bash "${SRCFOLDER}/1-generate_chain/chain_install.sh" "${OUTPUT}/"
bash "${SRCFOLDER}/1-generate_chain/chain_install.sh" "${OUTPUT}"
bash "${SRCFOLDER}/1-generate_chain/sample_run.sh" \
"${OLDREF}" \
"${NEWREF}" \