#scraps.md
Printed
❯ display_spinning_icon() {
> what="""
> display_spinning_icon()
> -----------------------
> Display \"spinning icon\" while a background process runs
>
> :param 1: PID of the last program the shell ran in the background (int)
> :param 2: message to be displayed next to the spinning icon (chr)
>
> #TODO Checks...
> """
> spin="/|\\–"
> i=0
> while kill -0 "${1}" 2> /dev/null; do
> i=$(( (i + 1) % 4 ))
> printf "\r${spin:$i:1} %s" "${2}"
> sleep .15
> done
> }
❯ list_tally_flags() {
> what="""
> list_tally_flags()
> ------------------
> List and tally flags in a bam infile; function acts on a bam infile to
> perform piped commands (samtools view, cut, sort, uniq -c, sort -nr) that
> list and tally flags; function writes the results to a txt outfile, the
> name of which is derived from the txt infile
>
> :param 1: name of bam infile, including path (chr)
>
> #TODO Checks...
> """
> start="$(date +%s)"
>
> samtools view "${1}" \
> | cut -f 2 \
> | sort \
> | uniq -c \
> | sort -nr \
> > "${1/.bam/.flags.txt}" &
> display_spinning_icon $! \
> "Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on $(basename "${1}")... "
>
> end="$(date +%s)"
> echo ""
> calculate_run_time "${start}" "${end}" \
> "List and tally flags in $(basename "${1}")."
> }
❯ p_data="${HOME}/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams"
❯ unset bams
❯ typeset -a bams=(
> "${p_data}/Brn1_Q_rep1_ChIP.bam"
> "${p_data}/Brn1_Q_rep1_input.bam"
> "${p_data}/Brn1_Q_rep2_ChIP.bam"
> "${p_data}/Brn1_Q_rep2_input.bam"
> "${p_data}/Brn1_Q_rep3_ChIP.bam"
> "${p_data}/Brn1_Q_rep3_input.bam"
> "${p_data}/Brn1_Q_all_input.bam"
> "${p_data}/Brn1_Q_all_ChIP.bam"
> "${p_data}/Brn1_log_rep1_ChIP.bam"
> "${p_data}/Brn1_log_rep1_input.bam"
> "${p_data}/Brn1_log_rep2_ChIP.bam"
> "${p_data}/Brn1_log_rep2_input.bam"
> "${p_data}/Brn1_log_rep3_ChIP.bam"
> "${p_data}/Brn1_log_rep3_input.bam"
> "${p_data}/Brn1_log_all_ChIP.bam"
> "${p_data}/Brn1_log_all_input.bam"
> )
❯ for i in "${bams[@]}"; do echo "${i}"; done
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_rep1_ChIP.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_rep1_input.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_rep2_ChIP.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_rep2_input.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_rep3_ChIP.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_rep3_input.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_all_input.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_all_ChIP.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_rep1_ChIP.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_rep1_input.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_rep2_ChIP.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_rep2_input.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_rep3_ChIP.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_rep3_input.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_all_ChIP.bam
/home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_all_input.bam
❯ for i in "${bams[@]}"; do ., "${i}"; done
-rw-rw---- 1 kalavatt 1.2G May 29 12:54 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_rep1_ChIP.bam
-rw-rw---- 1 kalavatt 1.8G May 29 12:55 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_rep1_input.bam
-rw-rw---- 1 kalavatt 1.1G May 29 12:55 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_rep2_ChIP.bam
-rw-rw---- 1 kalavatt 2.1G May 29 12:56 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_rep2_input.bam
-rw-rw---- 1 kalavatt 1.6G May 29 12:57 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_rep3_ChIP.bam
-rw-rw---- 1 kalavatt 1.8G May 29 12:57 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_rep3_input.bam
-rw-rw---- 1 kalavatt 5.7G May 29 12:59 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_all_input.bam
-rw-rw---- 1 kalavatt 3.8G May 29 13:01 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_all_ChIP.bam
-rw-rw---- 1 kalavatt 1.1G May 29 13:01 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_rep1_ChIP.bam
-rw-rw---- 1 kalavatt 2.5G May 29 13:02 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_rep1_input.bam
-rw-rw---- 1 kalavatt 5.1G May 29 13:04 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_rep2_ChIP.bam
-rw-rw---- 1 kalavatt 2.0G May 29 13:04 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_rep2_input.bam
-rw-rw---- 1 kalavatt 1.4G May 29 13:05 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_rep3_ChIP.bam
-rw-rw---- 1 kalavatt 1.5G May 29 13:06 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_rep3_input.bam
-rw-rw---- 1 kalavatt 7.6G May 29 13:08 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_all_ChIP.bam
-rw-rw---- 1 kalavatt 5.8G May 29 13:11 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_all_input.bam
❯ for i in "${bams[@]}"; do
> # i="${bams[0]}" # echo "${i}"
> echo "#### $(basename ${i}) ####"
> list_tally_flags "${i}"
> echo ""
>done
#### Brn1_Q_rep1_ChIP.bam ####
[1] 9115
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_Q_rep1_ChIP.bam...
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_Q_rep1_ChIP.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_Q_rep1_ChIP.bam.
Run time: 0h:0m:6s
#### Brn1_Q_rep1_input.bam ####
[1] 9204
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_Q_rep1_input.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_Q_rep1_input.bam.
Run time: 0h:0m:10s
#### Brn1_Q_rep2_ChIP.bam ####
[1] 9299
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_Q_rep2_ChIP.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_Q_rep2_ChIP.bam.
Run time: 0h:0m:5s
#### Brn1_Q_rep2_input.bam ####
[1] 9363
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_Q_rep2_input.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_Q_rep2_input.bam.
Run time: 0h:0m:11s
#### Brn1_Q_rep3_ChIP.bam ####
[1] 9479
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_Q_rep3_ChIP.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_Q_rep3_ChIP.bam.
Run time: 0h:0m:8s
#### Brn1_Q_rep3_input.bam ####
[1] 9564
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_Q_rep3_input.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_Q_rep3_input.bam.
Run time: 0h:0m:10s
#### Brn1_Q_all_input.bam ####
[1] 9663
\ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_Q_all_input.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_Q_all_input.bam.
Run time: 0h:0m:31s
#### Brn1_Q_all_ChIP.bam ####
[1] 10031
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_Q_all_ChIP.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_Q_all_ChIP.bam.
Run time: 0h:0m:19s
#### Brn1_log_rep1_ChIP.bam ####
[1] 10209
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_log_rep1_ChIP.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_log_rep1_ChIP.bam.
Run time: 0h:0m:6s
#### Brn1_log_rep1_input.bam ####
[1] 10271
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_log_rep1_input.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_log_rep1_input.bam.
Run time: 0h:0m:13s
#### Brn1_log_rep2_ChIP.bam ####
[1] 10400
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_log_rep2_ChIP.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_log_rep2_ChIP.bam.
Run time: 0h:0m:26s
#### Brn1_log_rep2_input.bam ####
[1] 10642
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_log_rep2_input.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_log_rep2_input.bam.
Run time: 0h:0m:11s
#### Brn1_log_rep3_ChIP.bam ####
[1] 10794
\ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_log_rep3_ChIP.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_log_rep3_ChIP.bam.
Run time: 0h:0m:7s
#### Brn1_log_rep3_input.bam ####
[1] 10868
– Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_log_rep3_input.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_log_rep3_input.bam.
Run time: 0h:0m:8s
#### Brn1_log_all_ChIP.bam ####
[1] 10947
/ Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_log_all_ChIP.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_log_all_ChIP.bam.
Run time: 0h:0m:41s
#### Brn1_log_all_input.bam ####
[1] 11316
| Running piped commands (samtools view, cut, sort, uniq -c, sort -nr) on Brn1_log_all_input.bam... [1]+ Done
samtools view "${1}" | cut -d' ' -f 2 | sort | uniq -c | sort -nr > "${1/.bam/.flags.txt}"
List and tally flags in Brn1_log_all_input.bam.
Run time: 0h:0m:31s
❯ for i in "${bams[@]}"; do
> if [[ -f "${i/.bam/.flags.txt}" ]]; then
> echo "#### $(basename ${i}) ####"
> cat "${i/.bam/.flags.txt}"
> echo ""
> fi
>done
#### Brn1_Q_rep1_ChIP.bam ####
2874061 0
2862832 16
1890825 4
#### Brn1_Q_rep1_input.bam ####
5483653 0
5478220 16
370063 4
#### Brn1_Q_rep2_ChIP.bam ####
2846780 0
2843810 16
1190484 4
#### Brn1_Q_rep2_input.bam ####
6351723 0
6342962 16
365205 4
#### Brn1_Q_rep3_ChIP.bam ####
4442444 16
4437645 0
780519 4
#### Brn1_Q_rep3_input.bam ####
5400769 0
5392613 16
367131 4
#### Brn1_Q_all_input.bam ####
17235945 0
17214003 16
1102391 4
#### Brn1_Q_all_ChIP.bam ####
10156605 0
10150983 16
3861812 4
#### Brn1_log_rep1_ChIP.bam ####
3040301 16
3017984 0
585178 4
#### Brn1_log_rep1_input.bam ####
7355182 0
7350937 16
550871 4
#### Brn1_log_rep2_ChIP.bam ####
14450767 0
14447432 16
3176492 4
#### Brn1_log_rep2_input.bam ####
5876887 0
5862547 16
405161 4
#### Brn1_log_rep3_ChIP.bam ####
4177590 16
4176208 0
429674 4
#### Brn1_log_rep3_input.bam ####
4309499 16
4305931 0
306893 4
#### Brn1_log_all_ChIP.bam ####
21661810 16
21648500 0
4191316 4
#### Brn1_log_all_input.bam ####
17538461 0
17522551 16
1262896 4
❯ samtools view "${p_data}/Brn1_log_all_ChIP.bam" | head
SRR7175373.380283 0 I 1 25 31M1I18M * 0 0 CCACACCACACCCACACACCCACACACCACACCCACACACCACACCACAC GGGGGIIIIIIIIIIIIIIIIIIIIIIIGIIIIIIIIIGGGGIGGGGGGI AS:i:90 XS:i:62 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:49 YT:Z:UU
SRR7175373.767277 0 I 1 14 1S31M1I17M * 0 0 CCCACACCACACCCACACACCCACACACCACACCCACACACCACACCACA AGGAAGGGGGG<GA.<GGGAAGGIGGGG....<GGGGGA.A.<AGGGGAA AS:i:88 XS:i:82 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:48 YT:Z:UU
SRR7175373.2091997 0 I 1 37 1S49M * 0 0 CCCACACCACACCCACACACCCACACACCACACCACACACCACACCACAC ...GA<AGAGGA<AAGGAGGGGA<AAAGGAGGIIGGAG<AGGIGAGGIGG AS:i:98 XS:i:67 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:49 YT:Z:UU
SRR7175373.2270050 0 I 1 11 9S41M * 0 0 ACACCACACCCACACCACACCCACACACCCACACACCACACCACACACCA GGGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIG AS:i:82 XS:i:78 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:41 YT:Z:UU
SRR7175373.7025590 0 I 1 14 8S42M * 0 0 CACCACACCCACACCACACCCACACACCCACACACCACACCACACACCAC GAGGAGG<<AG.<.<<<<G<<<GGGGGGGGGGGGGGGGAGGAGAAAAAG# AS:i:84 XS:i:78 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:42 YT:Z:UU
SRR7175373.8104795 0 I 1 21 4S46M * 0 0 ACACCCACACCACACCCACACACCCACACACCACACCACACACCACACCA GGGGGIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:92 XS:i:68 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:46 YT:Z:UU
SRR7175373.8877369 0 I 1 1 4S31M1I14M * 0 0 ACACCCACACCACACCCACACACCCACACACCACACCCACACACCACACC AGA.AGGGGIAGAGGGGGGGGGGG.<.<GAGAGG.<.G<AAGGGG##### AS:i:82 XS:i:82 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:45 YT:Z:UU
SRR7175373.9602499 0 I 1 14 5S45M * 0 0 CACACCCACACCACACCCACACACCCACACACCACACCACACACCACACC GGAGAGGGIIIIGIIIIIIIIIIIIIIIIIIIIIIIIGIIIIIIIIIIII AS:i:90 XS:i:82 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:45 YT:Z:UU
SRR7175373.9864638 0 I 1 14 7S43M * 0 0 ACCACACCCACACCACACCCACACACCCACACACCACACCACACACCACA GGAAGIGIIIIIGGGIIIIIGIGGIIGGIIIGGGGIIIGIIGGGGIGIGG AS:i:86 XS:i:80 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:43 YT:Z:UU
SRR7175373.11488836 0 I 1 11 2S31M1I16M * 0 0 ACCCACACCACACCCACACACCCACACACCACACCCACACACCACACCAC AAAAGAAAGGGGAGGGGIIII.AAAAGGGGGGIG.GGGI<GG<.<AAAGA AS:i:86 XS:i:82 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:47 YT:Z:UU
❯ # Initialize functions for doing floating point arithmetic -------------------
❯ calc_6f() { awk "BEGIN{ printf \"%.6f\n\", $* }"; }
❯ calc_2f() { awk "BEGIN{ printf \"%.2f\n\", $* }"; }
❯ ml SAMtools/1.16.1-GCC-11.2.0 Bowtie2/2.4.4-GCC-11.2.0
❯ # Get situated, initialize array of sample datasets --------------------------
❯ ml SAMtools/1.16.1-GCC-11.2.0 Bowtie2/2.4.4-GCC-11.2.0
❯ cd "${HOME}/tsukiyamalab/Kris/2023_rDNA/results" ||
> echo "cd'ing failed; check on this..."
❯ p_data="${HOME}/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams"
❯ unset bams
❯ typeset -a bams=(
> "${p_data}/Brn1_Q_rep1_ChIP.bam"
> "${p_data}/Brn1_Q_rep1_input.bam"
> "${p_data}/Brn1_Q_rep2_ChIP.bam"
> "${p_data}/Brn1_Q_rep2_input.bam"
> "${p_data}/Brn1_Q_rep3_ChIP.bam"
> "${p_data}/Brn1_Q_rep3_input.bam"
> "${p_data}/Brn1_Q_all_input.bam"
> "${p_data}/Brn1_Q_all_ChIP.bam"
> "${p_data}/Brn1_log_rep1_ChIP.bam"
> "${p_data}/Brn1_log_rep1_input.bam"
> "${p_data}/Brn1_log_rep2_ChIP.bam"
> "${p_data}/Brn1_log_rep2_input.bam"
> "${p_data}/Brn1_log_rep3_ChIP.bam"
> "${p_data}/Brn1_log_rep3_input.bam"
> "${p_data}/Brn1_log_all_ChIP.bam"
> "${p_data}/Brn1_log_all_input.bam"
>)
❯ for i in "${bams[@]}"; do ., "${i}"; done
-rw-rw---- 1 kalavatt 1.2G May 29 12:54 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_rep1_ChIP.bam
-rw-rw---- 1 kalavatt 1.8G May 29 12:55 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_rep1_input.bam
-rw-rw---- 1 kalavatt 1.1G May 29 12:55 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_rep2_ChIP.bam
-rw-rw---- 1 kalavatt 2.1G May 29 12:56 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_rep2_input.bam
-rw-rw---- 1 kalavatt 1.6G May 29 12:57 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_rep3_ChIP.bam
-rw-rw---- 1 kalavatt 1.8G May 29 12:57 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_rep3_input.bam
-rw-rw---- 1 kalavatt 5.7G May 29 12:59 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_all_input.bam
-rw-rw---- 1 kalavatt 3.8G May 29 13:01 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_Q_all_ChIP.bam
-rw-rw---- 1 kalavatt 1.1G May 29 13:01 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_rep1_ChIP.bam
-rw-rw---- 1 kalavatt 2.5G May 29 13:02 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_rep1_input.bam
-rw-rw---- 1 kalavatt 5.1G May 29 13:04 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_rep2_ChIP.bam
-rw-rw---- 1 kalavatt 2.0G May 29 13:04 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_rep2_input.bam
-rw-rw---- 1 kalavatt 1.4G May 29 13:05 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_rep3_ChIP.bam
-rw-rw---- 1 kalavatt 1.5G May 29 13:06 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_rep3_input.bam
-rw-rw---- 1 kalavatt 7.6G May 29 13:08 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_all_ChIP.bam
-rw-rw---- 1 kalavatt 5.8G May 29 13:11 /home/kalavatt/tsukiyamalab/Kris/2023_rDNA/results/2023-0406_tutorial_ChIP-seq_analysis/bams/Brn1_log_all_input.bam
❯ unset tallies
❯ typeset -A tallies
❯ for i in "${bams[@]}"; do
> # i="${bams[0]}" # echo "${i}"
> echo "#### $(basename ${i}) ####"
>
> sample="$(basename "${i}" .bam)" # echo "${sample}"
> total="${sample}_total" # echo "${total}"
> mapped="${sample}_mapped" # echo "${mapped}"
> unmapped="${sample}_unmapped" # echo "${unmapped}"
> SC="${sample}_SC" # echo "${SC}"
> SP="${sample}_SP" # echo "${SP}"
> SP2SC="${sample}_SP_to_SC" # echo "${SP2SC}"
> SC2SP="${sample}_SC_to_SP" # echo "${SC2SP}"
>
> tallies["${total}"]="$(samtools view -c "${i}")" # echo "${tallies["${total}"]}"
> tallies["${mapped}"]="$(samtools view -F 4 -c "${i}")" # echo "${tallies["${mapped}"]}"
> tallies["${unmapped}"]="$(samtools view -f 4 -c "${i}")" # echo "${tallies["${unmapped}"]}"
> tallies["${SC}"]="$(samtools view -F 4 -c "${i}" I II III IV V VI VII VIII IX X XI XII XIII XIV XV XVI Mito)" # echo "${tallies["${SC}"]}"
> tallies["${SP}"]="$(samtools view -F 4 -c "${i}" SP_II_TG SP_I SP_II SP_III SP_MTR SP_Mito)" # echo "${tallies["${SP}"]}"
> tallies["${SP2SC}"]="$(calc_6f "${tallies["${SP}"]}"/"${tallies["${SC}"]}")" # echo "${tallies["${SP2SC}"]}"
> tallies["${SC2SP}"]="$(calc_2f "${tallies["${SC}"]}"/"${tallies["${SP}"]}")" # echo "${tallies["${SC2SP}"]}"
>
> echo "${sample} ${tallies["${total}"]} ${tallies["${mapped}"]} ${tallies["${unmapped}"]} ${tallies["${SC}"]} ${tallies["${SP}"]} ${tallies["${SP2SC}"]} ${tallies["${SC2SP}"]}" \
> >> "2023-0406_tutorial_ChIP-seq_analysis/bams/tmp.txt"
>
> echo "${sample} ${tallies["${total}"]} ${tallies["${mapped}"]} ${tallies["${unmapped}"]} ${tallies["${SC}"]} ${tallies["${SP}"]} ${tallies["${SP2SC}"]} ${tallies["${SC2SP}"]}"
> echo ""
>done
#### Brn1_Q_rep1_ChIP.bam ####
Brn1_Q_rep1_ChIP 7627718 5736893 1890825 5487671 249222 0.045415 22.02
#### Brn1_Q_rep1_input.bam ####
Brn1_Q_rep1_input 11331936 10961873 370063 10749022 212851 0.019802 50.50
#### Brn1_Q_rep2_ChIP.bam ####
Brn1_Q_rep2_ChIP 6881074 5690590 1190484 5462233 228357 0.041807 23.92
#### Brn1_Q_rep2_input.bam ####
Brn1_Q_rep2_input 13059890 12694685 365205 12405031 289654 0.023350 42.83
#### Brn1_Q_rep3_ChIP.bam ####
Brn1_Q_rep3_ChIP 9660608 8880089 780519 8797438 82651 0.009395 106.44
#### Brn1_Q_rep3_input.bam ####
Brn1_Q_rep3_input 11160513 10793382 367131 10749642 43740 0.004069 245.76
#### Brn1_Q_all_input.bam ####
Brn1_Q_all_input 35552339 34449948 1102391 33903904 546044 0.016106 62.09
#### Brn1_Q_all_ChIP.bam ####
Brn1_Q_all_ChIP 24169400 20307588 3861812 19748404 559184 0.028315 35.32
#### Brn1_log_rep1_ChIP.bam ####
Brn1_log_rep1_ChIP 6643463 6058285 585178 5906242 152043 0.025743 38.85
#### Brn1_log_rep1_input.bam ####
Brn1_log_rep1_input 15256990 14706119 550871 14390918 315201 0.021903 45.66
#### Brn1_log_rep2_ChIP.bam ####
Brn1_log_rep2_ChIP 32074691 28898199 3176492 28145866 752333 0.026730 37.41
#### Brn1_log_rep2_input.bam ####
Brn1_log_rep2_input 12144595 11739434 405161 11478196 261238 0.022759 43.94
#### Brn1_log_rep3_ChIP.bam ####
Brn1_log_rep3_ChIP 8783472 8353798 429674 8263429 90369 0.010936 91.44
#### Brn1_log_rep3_input.bam ####
Brn1_log_rep3_input 8922323 8615430 306893 8573141 42289 0.004933 202.73
#### Brn1_log_all_ChIP.bam ####
Brn1_log_all_ChIP 47501626 43310310 4191316 42314977 995333 0.023522 42.51
#### Brn1_log_all_input.bam ####
Brn1_log_all_input 36323908 35061012 1262896 34442035 618977 0.017972 55.64
❯ cat "2023-0406_tutorial_ChIP-seq_analysis/bams/tmp.txt" | sed 's/\ /\t/g' > "2023-0406_tutorial_ChIP-seq_analysis/bams/tallies.tsv"
❯ cat "2023-0406_tutorial_ChIP-seq_analysis/bams/tallies.tsv"
sample total mapped unmapped SC SP SP-to-SC SC-to-SP
Brn1_Q_rep1_ChIP 7627718 5736893 1890825 5487671 249222 0.045415 22.02
Brn1_Q_rep1_input 11331936 10961873 370063 10749022 212851 0.019802 50.50
Brn1_Q_rep2_ChIP 6881074 5690590 1190484 5462233 228357 0.041807 23.92
Brn1_Q_rep2_input 13059890 12694685 365205 12405031 289654 0.023350 42.83
Brn1_Q_rep3_ChIP 9660608 8880089 780519 8797438 82651 0.009395 106.44
Brn1_Q_rep3_input 11160513 10793382 367131 10749642 43740 0.004069 245.76
Brn1_Q_all_input 35552339 34449948 1102391 33903904 546044 0.016106 62.09
Brn1_Q_all_ChIP 24169400 20307588 3861812 19748404 559184 0.028315 35.32
Brn1_log_rep1_ChIP 6643463 6058285 585178 5906242 152043 0.025743 38.85
Brn1_log_rep1_input 15256990 14706119 550871 14390918 315201 0.021903 45.66
Brn1_log_rep2_ChIP 32074691 28898199 3176492 28145866 752333 0.026730 37.41
Brn1_log_rep2_input 12144595 11739434 405161 11478196 261238 0.022759 43.94
Brn1_log_rep3_ChIP 8783472 8353798 429674 8263429 90369 0.010936 91.44
Brn1_log_rep3_input 8922323 8615430 306893 8573141 42289 0.004933 202.73
Brn1_log_all_ChIP 47501626 43310310 4191316 42314977 995333 0.023522 42.51
Brn1_log_all_input 36323908 35061012 1262896 34442035 618977 0.017972 55.64
❯ if [[ -f "2023-0406_tutorial_ChIP-seq_analysis/bams/tallies.tsv" ]]; then
> rm "2023-0406_tutorial_ChIP-seq_analysis/bams/tmp.txt"
>fiPrinted:
Environment "R_env" is not installed.
Creating environment R_env
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/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (1.3.1) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['bioconductor-annotationdbi', 'bioconductor-chipqc', 'bioconductor-chipseeker', 'bioconductor-clusterprofiler', 'bioconductor-deseq2', 'bioconductor-diffbind', 'bioconductor-edger', 'bioconductor-enhancedvolcano', 'bioconductor-genomicfeatures', 'bioconductor-genomicranges', 'bioconductor-ihw', 'bioconductor-iranges', 'bioconductor-pcatools', 'bioconductor-sva', 'deeptools', 'phantompeakqualtools', 'r-argparse', 'r-dendextend', 'r-devtools', 'r-ggalt', 'r-ggpubr', 'r-ggrepel', 'r-pheatmap', 'r-readxl', 'r-rjson', 'r-tidyverse', 'r-upsetr', 'r-venneuler', 'r-writexl', 'r-xml2', 'rename']
bioconda/linux-64 Using cache
bioconda/noarch Using cache
conda-forge/linux-64 Using cache
conda-forge/noarch Using cache
pkgs/r/noarch No change
pkgs/r/linux-64 No change
pkgs/main/noarch No change
pkgs/main/linux-64 No change
Transaction
Prefix: /home/kalavatt/miniconda3/envs/R_env
Updating specs:
- bioconductor-annotationdbi
- bioconductor-chipqc
- bioconductor-chipseeker
- bioconductor-clusterprofiler
- bioconductor-deseq2
- bioconductor-diffbind
- bioconductor-edger
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- bioconductor-genomicfeatures
- bioconductor-genomicranges
- bioconductor-ihw
- bioconductor-iranges
- bioconductor-pcatools
- bioconductor-sva
- deeptools
- phantompeakqualtools
- r-argparse
- r-dendextend
- r-devtools
- r-ggalt
- r-ggpubr
- r-ggrepel
- r-pheatmap
- r-readxl
- r-rjson
- r-tidyverse
- r-upsetr
- r-venneuler
- r-writexl
- r-xml2
- rename
Package Version Build Channel Size
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
Install:
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
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+ r-matrixstats 1.2.0 r43h57805ef_0 conda-forge/linux-64 466kB
+ r-memoise 2.0.1 r43hc72bb7e_2 conda-forge/noarch Cached
+ r-mgcv 1.9_1 r43h316c678_0 conda-forge/linux-64 3MB
+ r-mime 0.12 r43h57805ef_2 conda-forge/linux-64 Cached
+ r-miniui 0.1.1.1 r43hc72bb7e_1004 conda-forge/noarch 54kB
+ r-minqa 1.2.6 r43hcf54a89_0 conda-forge/linux-64 143kB
+ r-mixsqp 0.3_54 r43h08d816e_0 conda-forge/linux-64 202kB
+ r-modelmetrics 1.2.2.2 r43ha503ecb_3 conda-forge/linux-64 159kB
+ r-modelr 0.1.11 r43hc72bb7e_1 conda-forge/noarch Cached
+ r-munsell 0.5.0 r43hc72bb7e_1006 conda-forge/noarch Cached
+ r-mvtnorm 1.2_4 r43hd9ac46e_0 conda-forge/linux-64 740kB
+ r-nlme 3.1_164 r43h61816a4_0 conda-forge/linux-64 Cached
+ r-nloptr 2.0.3 r43hcf54a89_2 conda-forge/linux-64 412kB
+ r-nnet 7.3_19 r43h57805ef_1 conda-forge/linux-64 131kB
+ r-nozzle.r1 1.1_1.1 r43ha770c72_2 conda-forge/noarch 370kB
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+ r-openssl 2.1.1 r43hb353fa6_0 conda-forge/linux-64 Cached
+ r-parallelly 1.37.1 r43h57805ef_0 conda-forge/linux-64 370kB
+ r-patchwork 1.2.0 r43hc72bb7e_0 conda-forge/noarch 3MB
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+ r-pkgbuild 1.4.2 r43hc72bb7e_0 conda-forge/noarch 205kB
+ r-pkgconfig 2.0.3 r43hc72bb7e_3 conda-forge/noarch Cached
+ r-pkgdown 2.0.7 r43hc72bb7e_1 conda-forge/noarch 722kB
+ r-pkgload 1.3.4 r43hc72bb7e_0 conda-forge/noarch 196kB
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+ r-prettyunits 1.2.0 r43hc72bb7e_0 conda-forge/noarch Cached
+ r-proc 1.18.5 r43ha503ecb_0 conda-forge/linux-64 839kB
+ r-processx 3.8.3 r43h57805ef_0 conda-forge/linux-64 323kB
+ r-prodlim 2023.08.28 r43ha503ecb_0 conda-forge/linux-64 433kB
+ r-profvis 0.3.8 r43h57805ef_3 conda-forge/linux-64 206kB
+ r-progress 1.2.3 r43hc72bb7e_0 conda-forge/noarch Cached
+ r-progressr 0.14.0 r43hc72bb7e_0 conda-forge/noarch 350kB
+ r-proj4 1.0_14 r43h595fb24_0 conda-forge/linux-64 40kB
+ r-promises 1.2.1 r43ha503ecb_0 conda-forge/linux-64 Cached
+ r-proxy 0.4_27 r43h57805ef_2 conda-forge/linux-64 185kB
+ r-ps 1.7.6 r43h57805ef_0 conda-forge/linux-64 313kB
+ r-purrr 1.0.2 r43h57805ef_0 conda-forge/linux-64 Cached
+ r-quantreg 5.97 r43hd9ac46e_0 conda-forge/linux-64 2MB
+ r-r.methodss3 1.8.2 r43hc72bb7e_2 conda-forge/noarch 97kB
+ r-r.oo 1.26.0 r43hc72bb7e_0 conda-forge/noarch 975kB
+ r-r.utils 2.12.3 r43hc72bb7e_0 conda-forge/noarch 1MB
+ r-r6 2.5.1 r43hc72bb7e_2 conda-forge/noarch Cached
+ r-ragg 1.2.5 r43hd759249_3 conda-forge/linux-64 438kB
+ r-rappdirs 0.3.3 r43h57805ef_2 conda-forge/linux-64 Cached
+ r-rcmdcheck 1.4.0 r43h785f33e_2 conda-forge/noarch 177kB
+ r-rcolorbrewer 1.1_3 r43h785f33e_2 conda-forge/noarch Cached
+ r-rcpp 1.0.12 r43h7df8631_0 conda-forge/linux-64 2MB
+ r-rcpparmadillo 0.12.8.1.0 r43h08d816e_0 conda-forge/linux-64 917kB
+ r-rcppeigen 0.3.4.0.0 r43h08d816e_0 conda-forge/linux-64 1MB
+ r-rcppnumerical 0.6_0 r43ha503ecb_0 conda-forge/linux-64 225kB
+ r-rcurl 1.98_1.14 r43hf9611b0_0 conda-forge/linux-64 826kB
+ r-readr 2.1.5 r43ha503ecb_0 conda-forge/linux-64 788kB
+ r-readxl 1.4.3 r43ha5c9fba_0 conda-forge/linux-64 Cached
+ r-recipes 1.0.10 r43hc72bb7e_0 conda-forge/noarch 2MB
+ r-rematch 2.0.0 r43hc72bb7e_0 conda-forge/noarch Cached
+ r-rematch2 2.1.2 r43hc72bb7e_3 conda-forge/noarch Cached
+ r-remotes 2.4.2.1 r43hc72bb7e_0 conda-forge/noarch 402kB
+ r-reprex 2.1.0 r43hc72bb7e_0 conda-forge/noarch 499kB
+ r-reshape2 1.4.4 r43ha503ecb_3 conda-forge/linux-64 122kB
+ r-restfulr 0.0.15 r43h56115f1_3 bioconda/linux-64 441kB
+ r-rio 1.0.1 r43hc72bb7e_0 conda-forge/noarch 551kB
+ r-rjava 1.0_11 r43h57805ef_0 conda-forge/linux-64 782kB
+ r-rjson 0.2.21 r43ha503ecb_3 conda-forge/linux-64 155kB
+ r-rlang 1.1.3 r43ha503ecb_0 conda-forge/linux-64 2MB
+ r-rmarkdown 2.26 r43hc72bb7e_0 conda-forge/noarch 2MB
+ r-roxygen2 7.3.1 r43ha503ecb_0 conda-forge/linux-64 685kB
+ r-rpart 4.1.23 r43h57805ef_0 conda-forge/linux-64 700kB
+ r-rprojroot 2.0.4 r43hc72bb7e_0 conda-forge/noarch 109kB
+ r-rsqlite 2.3.4 r43ha503ecb_0 conda-forge/linux-64 1MB
+ r-rstatix 0.7.2 r43hc72bb7e_1 conda-forge/noarch 616kB
+ r-rstudioapi 0.15.0 r43hc72bb7e_0 conda-forge/noarch Cached
+ r-rsvd 1.0.5 r43hc72bb7e_2 conda-forge/noarch 4MB
+ r-rttf2pt1 1.3.12 r43h57805ef_1 conda-forge/linux-64 109kB
+ r-rversions 2.1.2 r43hc72bb7e_2 conda-forge/noarch 73kB
+ r-rvest 1.0.4 r43hc72bb7e_0 conda-forge/noarch 298kB
+ r-sass 0.4.8 r43ha503ecb_0 conda-forge/linux-64 Cached
+ r-scales 1.3.0 r43hc72bb7e_0 conda-forge/noarch Cached
+ r-scatterpie 0.2.1 r43hc72bb7e_1 conda-forge/noarch 141kB
+ r-selectr 0.4_2 r43hc72bb7e_3 conda-forge/noarch Cached
+ r-sessioninfo 1.2.2 r43hc72bb7e_2 conda-forge/noarch 198kB
+ r-shadowtext 0.1.3 r43hc72bb7e_0 conda-forge/noarch 221kB
+ r-shape 1.4.6.1 r43ha770c72_0 conda-forge/noarch 761kB
+ r-shiny 1.8.0 r43h785f33e_0 conda-forge/noarch 4MB
+ r-sitmo 2.0.2 r43ha503ecb_2 conda-forge/linux-64 142kB
+ r-slam 0.1_50 r43h1df0287_3 conda-forge/linux-64 197kB
+ r-snow 0.4_4 r43hc72bb7e_2 conda-forge/noarch 115kB
+ r-snowfall 1.84_6.3 r43hc72bb7e_0 conda-forge/noarch 261kB
+ r-sourcetools 0.1.7_1 r43ha503ecb_1 conda-forge/linux-64 54kB
+ r-sp 2.1_3 r43h57805ef_0 conda-forge/linux-64 2MB
+ r-sparsem 1.81 r43h61816a4_2 conda-forge/linux-64 937kB
+ r-spp 1.16.0 r43h21a89ab_9 bioconda/linux-64 359kB
+ r-squarem 2021.1 r43hc72bb7e_2 conda-forge/noarch 195kB
+ r-statmod 1.5.0 r43hd8f1df9_1 conda-forge/linux-64 313kB
+ r-stringi 1.8.3 r43h9facbd6_0 conda-forge/linux-64 898kB
+ r-stringr 1.5.1 r43h785f33e_0 conda-forge/noarch Cached
+ r-survival 3.5_8 r43h57805ef_0 conda-forge/linux-64 6MB
+ r-sys 3.4.2 r43h57805ef_1 conda-forge/linux-64 Cached
+ r-systemfonts 1.0.5 r43haf97adc_0 conda-forge/linux-64 Cached
+ r-testthat 3.2.1 r43ha503ecb_0 conda-forge/linux-64 2MB
+ r-textshaping 0.3.7 r43hd87b9d6_0 conda-forge/linux-64 Cached
+ r-tibble 3.2.1 r43h57805ef_2 conda-forge/linux-64 Cached
+ r-tidygraph 1.3.0 r43ha503ecb_0 conda-forge/linux-64 557kB
+ r-tidyr 1.3.1 r43ha503ecb_0 conda-forge/linux-64 1MB
+ r-tidyselect 1.2.0 r43hc72bb7e_1 conda-forge/linux-64 Cached
+ r-tidytree 0.4.6 r43hc72bb7e_0 conda-forge/noarch 348kB
+ r-tidyverse 2.0.0 r43h785f33e_1 conda-forge/noarch Cached
+ r-timechange 0.3.0 r43ha503ecb_0 conda-forge/linux-64 191kB
+ r-timedate 4032.109 r43hc72bb7e_0 conda-forge/noarch 1MB
+ r-tinytex 0.49 r43hc72bb7e_1 conda-forge/noarch 147kB
+ r-truncnorm 1.0_9 r43h57805ef_1 conda-forge/linux-64 41kB
+ r-tweenr 2.0.3 r43ha503ecb_0 conda-forge/linux-64 442kB
+ r-tzdb 0.4.0 r43ha503ecb_1 conda-forge/linux-64 Cached
+ r-upsetr 1.4.0 r43hc72bb7e_4 conda-forge/noarch 3MB
+ r-urlchecker 1.0.1 r43hc72bb7e_2 conda-forge/noarch 52kB
+ r-usethis 2.2.3 r43hc72bb7e_0 conda-forge/noarch 858kB
+ r-utf8 1.2.4 r43h57805ef_0 conda-forge/linux-64 Cached
+ r-uuid 1.2_0 r43h57805ef_0 conda-forge/linux-64 55kB
+ r-vctrs 0.6.5 r43ha503ecb_0 conda-forge/linux-64 Cached
+ r-venneuler 1.1_4 r43hc72bb7e_0 conda-forge/noarch 62kB
+ r-viridis 0.6.5 r43hc72bb7e_0 conda-forge/noarch 3MB
+ r-viridislite 0.4.2 r43hc72bb7e_1 conda-forge/noarch Cached
+ r-vroom 1.6.5 r43ha503ecb_0 conda-forge/linux-64 Cached
+ r-waldo 0.5.2 r43hc72bb7e_0 conda-forge/noarch 112kB
+ r-whisker 0.4.1 r43hc72bb7e_1 conda-forge/noarch 82kB
+ r-withr 3.0.0 r43hc72bb7e_0 conda-forge/noarch 249kB
+ r-writexl 1.5.0 r43h57805ef_0 conda-forge/linux-64 140kB
+ r-xfun 0.42 r43ha503ecb_0 conda-forge/linux-64 467kB
+ r-xml 3.99_0.16.1 r43hc6530ce_0 conda-forge/linux-64 2MB
+ r-xml2 1.3.6 r43hbfba7a4_1 conda-forge/linux-64 346kB
+ r-xopen 1.0.0 r43hc72bb7e_1005 conda-forge/noarch 30kB
+ r-xtable 1.8_4 r43hc72bb7e_5 conda-forge/noarch 697kB
+ r-yaml 2.3.8 r43h57805ef_0 conda-forge/linux-64 118kB
+ r-yulab.utils 0.1.4 r43hc72bb7e_0 conda-forge/noarch 87kB
+ r-zip 2.3.1 r43h57805ef_0 conda-forge/linux-64 134kB
+ re2 2023.09.01 h7f4b329_2 conda-forge/linux-64 27kB
+ readline 8.2 h8228510_1 conda-forge/linux-64 Cached
+ rename 1.601 hdfd78af_1 bioconda/noarch Cached
+ s2n 1.4.5 h06160fa_0 conda-forge/linux-64 338kB
+ samtools 1.19.2 h50ea8bc_1 bioconda/linux-64 463kB
+ scipy 1.12.0 py310hb13e2d6_2 conda-forge/linux-64 16MB
+ sed 4.8 he412f7d_0 conda-forge/linux-64 Cached
+ setuptools 69.1.1 pyhd8ed1ab_0 conda-forge/noarch 470kB
+ six 1.16.0 pyh6c4a22f_0 conda-forge/noarch Cached
+ snappy 1.1.10 h9fff704_0 conda-forge/linux-64 Cached
+ sqlite 3.45.1 h2c6b66d_0 conda-forge/linux-64 848kB
+ sysroot_linux-64 2.12 he073ed8_17 conda-forge/noarch 15MB
+ tenacity 8.2.3 pyhd8ed1ab_0 conda-forge/noarch 23kB
+ tk 8.6.13 noxft_h4845f30_101 conda-forge/linux-64 Cached
+ tktable 2.10 h0c5db8f_5 conda-forge/linux-64 Cached
+ toml 0.10.2 pyhd8ed1ab_0 conda-forge/noarch Cached
+ tomlkit 0.12.4 pyha770c72_0 conda-forge/noarch 37kB
+ tzdata 2024a h0c530f3_0 conda-forge/noarch Cached
+ unicodedata2 15.1.0 py310h2372a71_0 conda-forge/linux-64 Cached
+ wheel 0.42.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ xmltodict 0.13.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ xorg-fixesproto 5.0 h7f98852_1002 conda-forge/linux-64 Cached
+ xorg-inputproto 2.3.2 h7f98852_1002 conda-forge/linux-64 Cached
+ xorg-kbproto 1.0.7 h7f98852_1002 conda-forge/linux-64 Cached
+ xorg-libice 1.1.1 hd590300_0 conda-forge/linux-64 Cached
+ xorg-libsm 1.2.4 h7391055_0 conda-forge/linux-64 Cached
+ xorg-libx11 1.8.7 h8ee46fc_0 conda-forge/linux-64 Cached
+ xorg-libxau 1.0.11 hd590300_0 conda-forge/linux-64 Cached
+ xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge/linux-64 Cached
+ xorg-libxext 1.3.4 h0b41bf4_2 conda-forge/linux-64 Cached
+ xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge/linux-64 Cached
+ xorg-libxi 1.7.10 h7f98852_0 conda-forge/linux-64 Cached
+ xorg-libxrender 0.9.11 hd590300_0 conda-forge/linux-64 Cached
+ xorg-libxt 1.3.0 hd590300_1 conda-forge/linux-64 Cached
+ xorg-libxtst 1.2.3 h7f98852_1002 conda-forge/linux-64 Cached
+ xorg-recordproto 1.14.2 h7f98852_1002 conda-forge/linux-64 Cached
+ xorg-renderproto 0.11.1 h7f98852_1002 conda-forge/linux-64 Cached
+ xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge/linux-64 Cached
+ xorg-xproto 7.0.31 h7f98852_1007 conda-forge/linux-64 Cached
+ xz 5.2.6 h166bdaf_0 conda-forge/linux-64 Cached
+ yaml 0.2.5 h7f98852_2 conda-forge/linux-64 Cached
+ yq 3.2.3 pyhd8ed1ab_0 conda-forge/noarch 23kB
+ zipp 3.17.0 pyhd8ed1ab_0 conda-forge/noarch Cached
+ zlib 1.2.13 hd590300_5 conda-forge/linux-64 Cached
+ zstd 1.5.5 hfc55251_0 conda-forge/linux-64 Cached
Summary:
Install: 572 packages
Total download: 491MB
──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
c-ares 163.6kB @ 848.9kB/s 0.2s
aws-c-common 225.6kB @ 895.3kB/s 0.3s
libre2-11 232.6kB @ 913.5kB/s 0.1s
s2n 337.9kB @ 1.1MB/s 0.1s
aws-c-cal 55.1kB @ 172.6kB/s 0.1s
libabseil 1.3MB @ 3.4MB/s 0.4s
aws-c-io 157.2kB @ 414.7kB/s 0.1s
aws-c-http 195.0kB @ 448.4kB/s 0.1s
libboost-headers 13.7MB @ 27.2MB/s 0.5s
aws-crt-cpp 333.8kB @ 598.8kB/s 0.1s
gawk 1.2MB @ 2.1MB/s 0.3s
libgrpc 7.0MB @ 11.6MB/s 0.3s
proj 3.0MB @ 4.8MB/s 0.2s
libarrow-acero 577.2kB @ 816.0kB/s 0.2s
libarrow-dataset 580.9kB @ 818.4kB/s 0.2s
r-rpart 700.1kB @ 869.9kB/s 0.1s
pandoc 21.0MB @ 25.6MB/s 0.8s
htslib 3.0MB @ 3.7MB/s 0.2s
r-gower 225.0kB @ 252.2kB/s 0.2s
r-foreign 266.9kB @ 298.6kB/s 0.1s
r-mvtnorm 740.2kB @ 825.4kB/s 0.1s
r-bdsmatrix 316.7kB @ 330.1kB/s 0.2s
r-gtools 367.1kB @ 378.3kB/s 0.1s
r-filelock 33.0kB @ 31.3kB/s 0.2s
r-xml 1.8MB @ 1.7MB/s 0.2s
r-commonmark 138.2kB @ 130.9kB/s 0.1s
r-ps 312.8kB @ 295.6kB/s 0.1s
r-proj4 40.2kB @ 34.8kB/s 0.1s
r-uuid 55.2kB @ 47.7kB/s 0.1s
r-kernsmooth 100.3kB @ 81.0kB/s 0.2s
r-ash 46.9kB @ 37.7kB/s 0.2s
sysroot_linux-64 15.1MB @ 11.3MB/s 0.7s
r-rlang 1.5MB @ 1.1MB/s 0.2s
r-rcpp 2.0MB @ 1.5MB/s 0.2s
r-class 106.8kB @ 79.6kB/s 0.1s
r-minqa 143.0kB @ 91.1kB/s 0.4s
r-rcpparmadillo 916.6kB @ 558.7kB/s 0.4s
r-plyr 823.8kB @ 490.7kB/s 0.4s
r-maptools 1.8MB @ 1.0MB/s 0.5s
r-proc 839.5kB @ 464.8kB/s 0.2s
r-interp 1.5MB @ 819.8kB/s 0.2s
r-rcppnumerical 225.3kB @ 122.8kB/s 0.2s
r-matrix 3.9MB @ 2.0MB/s 0.7s
r-r.methodss3 96.9kB @ 49.6kB/s 0.2s
r-timedate 1.3MB @ 622.9kB/s 0.2s
r-invgamma 35.1kB @ 17.4kB/s 0.2s
r-squarem 194.8kB @ 96.8kB/s 0.3s
r-ini 33.0kB @ 15.6kB/s 0.2s
r-whisker 81.5kB @ 37.5kB/s 0.2s
r-codetools 108.4kB @ 49.7kB/s 0.2s
r-hwriter 123.2kB @ 56.5kB/s 0.2s
r-rprojroot 109.3kB @ 48.0kB/s 0.1s
r-remotes 401.9kB @ 176.2kB/s 0.2s
r-extrafontdb 21.6kB @ 9.5kB/s 0.2s
r-polynom 396.2kB @ 163.3kB/s 0.3s
r-urlchecker 51.6kB @ 21.3kB/s 0.2s
r-rversions 72.7kB @ 29.9kB/s 0.2s
r-credentials 225.8kB @ 92.8kB/s 0.3s
r-sessioninfo 198.0kB @ 77.0kB/s 0.2s
r-desc 333.6kB @ 128.3kB/s 0.2s
r-latticeextra 2.2MB @ 833.0kB/s 0.2s
r-corrplot 3.8MB @ 1.4MB/s 0.7s
r-futile.logger 105.3kB @ 38.5kB/s 0.2s
r-r.utils 1.4MB @ 510.7kB/s 0.2s
deeptoolsintervals 77.9kB @ 27.6kB/s 0.1s
r-extrafont 68.4kB @ 24.2kB/s 0.5s
bioconductor-limma 2.9MB @ 1.0MB/s 0.3s
plotly 6.1MB @ 2.1MB/s 0.4s
bioconductor-biocparallel 1.7MB @ 573.0kB/s 0.3s
r-timechange 191.2kB @ 63.4kB/s 0.1s
r-dqrng 164.2kB @ 53.8kB/s 0.2s
r-prodlim 432.6kB @ 138.4kB/s 0.1s
r-httpuv 797.7kB @ 254.8kB/s 0.1s
r-ipred 392.1kB @ 121.9kB/s 0.1s
libboost-python 118.6kB @ 35.9kB/s 0.2s
numpy 7.0MB @ 2.1MB/s 0.4s
r-lme4 4.2MB @ 1.2MB/s 0.2s
r-restfulr 441.0kB @ 126.0kB/s 0.2s
bioconductor-biocgenerics 655.4kB @ 186.9kB/s 0.8s
r-httr2 539.0kB @ 150.8kB/s 0.1s
r-pkgbuild 204.5kB @ 55.5kB/s 0.1s
r-gh 107.9kB @ 29.3kB/s 0.1s
bioconductor-beachmat 1.4MB @ 355.9kB/s 0.5s
r-pkgload 196.1kB @ 50.8kB/s 0.2s
r-usethis 858.0kB @ 221.7kB/s 0.2s
bioconductor-data-packages 416.2kB @ 103.1kB/s 0.2s
bioconductor-delayedarray 2.4MB @ 581.4kB/s 0.7s
bioconductor-delayedmatrixstats 802.2kB @ 196.5kB/s 0.3s
scipy 16.5MB @ 4.0MB/s 1.1s
r-profvis 205.6kB @ 49.5kB/s 0.2s
bioconductor-scaledmatrix 658.5kB @ 154.8kB/s 0.5s
r-pkgdown 722.4kB @ 168.7kB/s 0.1s
r-rvest 298.2kB @ 67.0kB/s 0.3s
r-waldo 112.0kB @ 25.2kB/s 0.2s
bioconductor-genomicranges 2.3MB @ 510.7kB/s 0.5s
r-patchwork 3.3MB @ 716.9kB/s 0.3s
r-viridis 3.0MB @ 652.9kB/s 0.2s
r-aplot 75.7kB @ 15.8kB/s 0.3s
r-plotly 2.9MB @ 583.9kB/s 0.5s
bioconductor-summarizedexperiment 1.9MB @ 383.0kB/s 0.5s
bioconductor-qvalue 2.8MB @ 566.8kB/s 0.4s
r-ggrepel 271.5kB @ 53.3kB/s 0.2s
bioconductor-biostrings 14.3MB @ 2.7MB/s 1.1s
r-conquer 536.7kB @ 103.0kB/s 0.1s
r-caret 3.6MB @ 682.3kB/s 0.2s
bioconductor-go.db 8.9kB @ 1.7kB/s 0.4s
bioconductor-ggtree 904.8kB @ 168.9kB/s 0.6s
r-scatterpie 141.5kB @ 26.0kB/s 0.2s
bioconductor-genomicalignments 2.4MB @ 446.6kB/s 0.3s
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Downloading and Extracting Packages
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
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$ mamba deactivate
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-conda-linux-gnu (64-bit)
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> if (!requireNamespace("colorout", quietly = TRUE)) {
+ devtools::install_github("jalvesaq/colorout")
+ }
Downloading GitHub repo jalvesaq/colorout@HEAD
── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/tmp/RtmpczZKwR/remotes125c74cbd5e2/jalvesaq-colorout-c6113a2/DESCRIPTION’ (550ms)
─ preparing ‘colorout’:
✔ checking DESCRIPTION meta-information
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘colorout_1.3-0.2.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'
* installing *source* package ‘colorout’ ...
** using staged installation
** libs
using C compiler: ‘x86_64-conda-linux-gnu-cc (conda-forge gcc 13.2.0-5) 13.2.0’
x86_64-conda-linux-gnu-cc -I"/home/kalavatt/miniconda3/envs/R_env/lib/R/include" -DNDEBUG -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/kalavatt/miniconda3/envs/R_env/include -I/home/kalavatt/miniconda3/envs/R_env/include -Wl,-rpath-link,/home/kalavatt/miniconda3/envs/R_env/lib -fpic -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/kalavatt/miniconda3/envs/R_env/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base-split_1695319594214/work=/usr/local/src/conda/r-base-4.3.1 -fdebug-prefix-map=/home/kalavatt/miniconda3/envs/R_env=/usr/local/src/conda-prefix -c colorout.c -o colorout.o
x86_64-conda-linux-gnu-cc -shared -L/home/kalavatt/miniconda3/envs/R_env/lib/R/lib -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/kalavatt/miniconda3/envs/R_env/lib -Wl,-rpath-link,/home/kalavatt/miniconda3/envs/R_env/lib -L/home/kalavatt/miniconda3/envs/R_env/lib -o colorout.so colorout.o -L/home/kalavatt/miniconda3/envs/R_env/lib/R/lib -lR
installing to /home/kalavatt/miniconda3/envs/R_env/lib/R/library/00LOCK-colorout/00new/colorout/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (colorout)