Notebook

In [1]:

%%bash
echo "TODAY'S DATE:"
date
echo "------------"
echo ""
#Display operating system info
lsb_release -a
echo ""
echo "------------"
echo "HOSTNAME: "; hostname 
echo ""
echo "------------"
echo "Computer Specs:"
echo ""
lscpu
echo ""
echo "------------"
echo ""
echo "Memory Specs"
echo ""
free -mh

TODAY'S DATE:
Tue Nov  5 07:39:45 PST 2019
------------

Distributor ID:	Ubuntu
Description:	Ubuntu 16.04.6 LTS
Release:	16.04
Codename:	xenial

------------
HOSTNAME: 
swoose

------------
Computer Specs:

Architecture:          x86_64
CPU op-mode(s):        32-bit, 64-bit
Byte Order:            Little Endian
CPU(s):                24
On-line CPU(s) list:   0-23
Thread(s) per core:    2
Core(s) per socket:    6
Socket(s):             2
NUMA node(s):          1
Vendor ID:             GenuineIntel
CPU family:            6
Model:                 44
Model name:            Intel(R) Xeon(R) CPU           X5670  @ 2.93GHz
Stepping:              2
CPU MHz:               2925.971
BogoMIPS:              5851.97
Virtualization:        VT-x
L1d cache:             32K
L1i cache:             32K
L2 cache:              256K
L3 cache:              12288K
NUMA node0 CPU(s):     0-23
Flags:                 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb ssbd ibrs ibpb stibp kaiser tpr_shadow vnmi flexpriority ept vpid dtherm ida arat flush_l1d

------------

Memory Specs

              total        used        free      shared  buff/cache   available
Mem:            70G         29G        388M        575M         40G         39G
Swap:          4.7G        548M        4.1G

No LSB modules are available.

Set variables¶

%env variables are good for passing to bash cells

In [2]:

# Set workding directory
%env wd=/home/sam/analyses/20191105_swoose_pgen_v074_renaming
wd="/home/sam/analyses/20191105_swoose_pgen_v074_renaming"

%env rsync_owl=owl:/volume1/web/halfshell/genomic-databank/
%env wget_command=--directory-prefix=${wd} --quiety --no-directories --no-check-certificate  https://owl.fish.washington.edu/halfshell/genomic-databank/

%env new_prefix=Panopea-generosa-v1.0
%env fa_prefix=Pgenerosa_v074
%env gff_prefix=Panopea-generosa-vv0.74

env: wd=/home/sam/analyses/20191105_swoose_pgen_v074_renaming
env: rsync_owl=owl:/volume1/web/halfshell/genomic-databank/
env: files_list=Panopea-generosa-vv0.74.a4.CDS.gff3 Panopea-generosa-vv0.74.a4.exon.gff3 Panopea-generosa-vv0.74.a4.gene.gff3 Panopea-generosa-vv0.74.a4.mRNA.gff3 Panopea-generosa-vv0.74.a4.repeat_region.gff3 Panopea-generosa-vv0.74.a4.rRNA.gff3 Panopea-generosa-vv0.74.a4.tRNA.gff3 Pgenerosa_v074.fa Pgenerosa_v074.fa.fai Pgenerosa_v074.CpG.gff Panopea-generosa-vv0.74.a4.intergenic.bed  Panopea-generosa-vv0.74.a4.introns.bed Panopea-generosa-vv0.74.a4.repeats.DNA.gff3 Panopea-generosa-vv0.74.a4.repeats.LTR.gff3 Panopea-generosa-vv0.74.a4.repeats.SINE.gff3 Panopea-generosa-vv0.74.a4.repeats.Unknown.gff3 Panopea-generosa-vv0.74.a4.repeats.LINE.gff3 Panopea-generosa-vv0.74.a4.repeats.RC.gff3 Panopea-generosa-vv0.74.a4.repeats.Simple_repeat.gff3
env: wget_command=--directory-prefix=$/home/sam/analyses/20191105_swoose_pgen_v074_renaming --quiety --no-directories --no-check-certificate  https://owl.fish.washington.edu/halfshell/genomic-databank/
env: new_prefix=Panopea-generosa-v1.0
env: fa_prefix=Pgenerosa_v074
env: gff_prefix=Panopea-generosa-vv0.74

Create necessary directories¶

In [3]:

%%bash
mkdir --parents ${wd}

In [4]:

cd {wd}

/home/sam/analyses/20191105_swoose_pgen_v074_renaming

Download Pgen_v074 files¶

In [16]:

%%bash
# Create array of files from list
files_array=(Panopea-generosa-vv0.74.a4.CDS.gff3 Panopea-generosa-vv0.74.a4.exon.gff3 Panopea-generosa-vv0.74.a4.gene.gff3 Panopea-generosa-vv0.74.a4.mRNA.gff3 Panopea-generosa-vv0.74.a4.repeat_region.gff3 Panopea-generosa-vv0.74.a4.rRNA.gff3 Panopea-generosa-vv0.74.a4.tRNA.gff3 Pgenerosa_v074.fa Pgenerosa_v074.fa.fai Pgenerosa_v074.CpG.gff Panopea-generosa-vv0.74.a4.intergenic.bed Panopea-generosa-vv0.74.a4.introns.bed Panopea-generosa-vv0.74.a4.repeats.DNA.gff3 Panopea-generosa-vv0.74.a4.repeats.LTR.gff3 Panopea-generosa-vv0.74.a4.repeats.SINE.gff3 Panopea-generosa-vv0.74.a4.repeats.Unknown.gff3 Panopea-generosa-vv0.74.a4.repeats.LINE.gff3 Panopea-generosa-vv0.74.a4.repeats.RC.gff3 Panopea-generosa-vv0.74.a4.repeats.Simple_repeat.gff3)


for file in "${files_array[@]}"
do
  rsync \
  --archive \
  --progress \
  --verbose \
  "${rsync_owl}${file}" \
  .
done

ls -lh

receiving incremental file list
Panopea-generosa-vv0.74.a4.CDS.gff3
     62,862,005 100%   27.44MB/s    0:00:02 (xfr#1, to-chk=0/1)

sent 30 bytes  received 62,869,800 bytes  9,672,281.54 bytes/sec
total size is 62,862,005  speedup is 1.00
receiving incremental file list
Panopea-generosa-vv0.74.a4.exon.gff3
     64,663,603 100%   26.86MB/s    0:00:02 (xfr#1, to-chk=0/1)

sent 30 bytes  received 64,671,619 bytes  9,949,484.46 bytes/sec
total size is 64,663,603  speedup is 1.00
receiving incremental file list
Panopea-generosa-vv0.74.a4.gene.gff3
     10,997,681 100%   25.90MB/s    0:00:00 (xfr#1, to-chk=0/1)

sent 30 bytes  received 10,999,145 bytes  3,142,621.43 bytes/sec
total size is 10,997,681  speedup is 1.00
receiving incremental file list
Panopea-generosa-vv0.74.a4.mRNA.gff3
     10,666,540 100%   22.46MB/s    0:00:00 (xfr#1, to-chk=0/1)

sent 30 bytes  received 10,667,964 bytes  7,111,996.00 bytes/sec
total size is 10,666,540  speedup is 1.00
receiving incremental file list
Panopea-generosa-vv0.74.a4.repeat_region.gff3
    390,130,212 100%   27.11MB/s    0:00:13 (xfr#1, to-chk=0/1)

sent 30 bytes  received 390,177,965 bytes  21,090,702.43 bytes/sec
total size is 390,130,212  speedup is 1.00
receiving incremental file list
Panopea-generosa-vv0.74.a4.rRNA.gff3
          1,447 100%    1.38MB/s    0:00:00 (xfr#1, to-chk=0/1)

sent 30 bytes  received 1,570 bytes  640.00 bytes/sec
total size is 1,447  speedup is 0.90
receiving incremental file list
Panopea-generosa-vv0.74.a4.tRNA.gff3
      2,836,671 100%   29.41MB/s    0:00:00 (xfr#1, to-chk=0/1)

sent 30 bytes  received 2,837,138 bytes  1,134,867.20 bytes/sec
total size is 2,836,671  speedup is 1.00
receiving incremental file list
Pgenerosa_v074.fa
    958,059,901 100%   22.77MB/s    0:00:40 (xfr#1, to-chk=0/1)

sent 30 bytes  received 958,176,954 bytes  23,088,602.02 bytes/sec
total size is 958,059,901  speedup is 1.00
receiving incremental file list
Pgenerosa_v074.fa.fai
          1,230 100%    1.17MB/s    0:00:00 (xfr#1, to-chk=0/1)

sent 30 bytes  received 1,338 bytes  547.20 bytes/sec
total size is 1,230  speedup is 0.90
receiving incremental file list
Pgenerosa_v074.CpG.gff
  2,623,644,046 100%   27.02MB/s    0:01:32 (xfr#1, to-chk=0/1)

sent 30 bytes  received 2,623,964,425 bytes  28,063,790.96 bytes/sec
total size is 2,623,644,046  speedup is 1.00
receiving incremental file list
Panopea-generosa-vv0.74.a4.intergenic.bed
      2,113,935 100%   28.80MB/s    0:00:00 (xfr#1, to-chk=0/1)

sent 30 bytes  received 2,114,319 bytes  1,409,566.00 bytes/sec
total size is 2,113,935  speedup is 1.00
receiving incremental file list
Panopea-generosa-vv0.74.a4.introns.bed
      9,488,151 100%   30.26MB/s    0:00:00 (xfr#1, to-chk=0/1)

sent 30 bytes  received 9,489,433 bytes  6,326,308.67 bytes/sec
total size is 9,488,151  speedup is 1.00
receiving incremental file list
Panopea-generosa-vv0.74.a4.repeats.DNA.gff3
      5,560,657 100%   29.96MB/s    0:00:00 (xfr#1, to-chk=0/1)

sent 30 bytes  received 5,561,463 bytes  3,707,662.00 bytes/sec
total size is 5,560,657  speedup is 1.00
receiving incremental file list
Panopea-generosa-vv0.74.a4.repeats.LTR.gff3
        752,111 100%   32.60MB/s    0:00:00 (xfr#1, to-chk=0/1)

sent 30 bytes  received 752,329 bytes  501,572.67 bytes/sec
total size is 752,111  speedup is 1.00
receiving incremental file list
Panopea-generosa-vv0.74.a4.repeats.SINE.gff3
     10,492,279 100%   29.78MB/s    0:00:00 (xfr#1, to-chk=0/1)

sent 30 bytes  received 10,493,691 bytes  6,995,814.00 bytes/sec
total size is 10,492,279  speedup is 1.00
receiving incremental file list
Panopea-generosa-vv0.74.a4.repeats.Unknown.gff3
    350,419,849 100%   29.33MB/s    0:00:11 (xfr#1, to-chk=0/1)

sent 30 bytes  received 350,462,756 bytes  28,037,022.88 bytes/sec
total size is 350,419,849  speedup is 1.00
receiving incremental file list
Panopea-generosa-vv0.74.a4.repeats.LINE.gff3
     18,049,492 100%   13.58MB/s    0:00:01 (xfr#1, to-chk=0/1)

sent 30 bytes  received 18,051,824 bytes  3,282,155.27 bytes/sec
total size is 18,049,492  speedup is 1.00
receiving incremental file list
Panopea-generosa-vv0.74.a4.repeats.RC.gff3
        143,208 100%   45.52MB/s    0:00:00 (xfr#1, to-chk=0/1)

sent 30 bytes  received 143,353 bytes  95,588.67 bytes/sec
total size is 143,208  speedup is 1.00
receiving incremental file list
Panopea-generosa-vv0.74.a4.repeats.Simple_repeat.gff3
      4,716,710 100%    8.63MB/s    0:00:00 (xfr#1, to-chk=0/1)

sent 30 bytes  received 4,717,422 bytes  3,144,968.00 bytes/sec
total size is 4,716,710  speedup is 1.00
total 4.3G
-rwxr--r-- 1 sam users  60M Oct 14 10:13 Panopea-generosa-vv0.74.a4.CDS.gff3
-rwxr--r-- 1 sam users  62M Oct 14 10:13 Panopea-generosa-vv0.74.a4.exon.gff3
-rwxr--r-- 1 sam users  11M Oct 14 10:13 Panopea-generosa-vv0.74.a4.gene.gff3
-rw-rw-r-- 1 sam users 2.1M Oct 30 08:41 Panopea-generosa-vv0.74.a4.intergenic.bed
-rw-rw-r-- 1 sam users 9.1M Oct 30 08:41 Panopea-generosa-vv0.74.a4.introns.bed
-rwxr--r-- 1 sam users  11M Oct 14 10:13 Panopea-generosa-vv0.74.a4.mRNA.gff3
-rwxr--r-- 1 sam users 373M Oct 14 10:13 Panopea-generosa-vv0.74.a4.repeat_region.gff3
-rw-rw-r-- 1 sam users 5.4M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.DNA.gff3
-rw-rw-r-- 1 sam users  18M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.LINE.gff3
-rw-rw-r-- 1 sam users 735K Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.LTR.gff3
-rw-rw-r-- 1 sam users 140K Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.RC.gff3
-rw-rw-r-- 1 sam users 4.5M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.Simple_repeat.gff3
-rw-rw-r-- 1 sam users  11M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.SINE.gff3
-rw-rw-r-- 1 sam users 335M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.Unknown.gff3
-rwxr--r-- 1 sam users 1.5K Oct 14 10:13 Panopea-generosa-vv0.74.a4.rRNA.gff3
-rwxr--r-- 1 sam users 2.8M Oct 14 10:13 Panopea-generosa-vv0.74.a4.tRNA.gff3
-rw-rw-r-- 1 sam users 2.5G Aug 21 11:45 Pgenerosa_v074.CpG.gff
-rw-rw-rw- 1 sam users 914M Jun 26 08:49 Pgenerosa_v074.fa
-rw-rw-rw- 1 sam users 1.3K Jun 26 08:54 Pgenerosa_v074.fa.fai

If need to download via wget, uncomment lines in the cell below¶

In [7]:

# %%bash
# time \
# wget "${wget_gffs}"
# wget "${wget_fasta}"
# ls -lh ${wd}

Change scaffold names and file names¶

In [18]:

%%bash

files_array=(Panopea-generosa-vv0.74.a4.CDS.gff3 Panopea-generosa-vv0.74.a4.exon.gff3 Panopea-generosa-vv0.74.a4.gene.gff3 Panopea-generosa-vv0.74.a4.mRNA.gff3 Panopea-generosa-vv0.74.a4.repeat_region.gff3 Panopea-generosa-vv0.74.a4.rRNA.gff3 Panopea-generosa-vv0.74.a4.tRNA.gff3 Pgenerosa_v074.fa Pgenerosa_v074.fa.fai Pgenerosa_v074.CpG.gff Panopea-generosa-vv0.74.a4.intergenic.bed Panopea-generosa-vv0.74.a4.introns.bed Panopea-generosa-vv0.74.a4.repeats.DNA.gff3 Panopea-generosa-vv0.74.a4.repeats.LTR.gff3 Panopea-generosa-vv0.74.a4.repeats.SINE.gff3 Panopea-generosa-vv0.74.a4.repeats.Unknown.gff3 Panopea-generosa-vv0.74.a4.repeats.LINE.gff3 Panopea-generosa-vv0.74.a4.repeats.RC.gff3 Panopea-generosa-vv0.74.a4.repeats.Simple_repeat.gff3)

# Array of old scaffold names
# Uses first column of FastA index file to get scaffold names
mapfile -t orig_scaffold_names < <(awk '{print $1}' Pgenerosa_v074.fa.fai)

# Array of new scaffold names
mapfile -t new_scaffold_names < <(for number in {01..18}; do echo "Scaffold_${number}"; done)


for file in "${files_array[@]}"
do
  # Set new filename, depending if FastA or GFF
  name_check="${file%%.*}"
  if [ "${name_check}" = "${fa_prefix}" ]
  then
    new_name=${file/$fa_prefix/$new_prefix}
  else
    new_name=${file/$gff_prefix/$new_prefix}
  fi
  # sed substitution
  # creates sed script to find original scaffold names and replace them with new scafold names
  # and passes to sed via stdin
  for index in "${!orig_scaffold_names[@]}"
  do
    printf "s/%s/%s/\n" "${orig_scaffold_names[index]}" "${new_scaffold_names[index]}"
  done | sed --file - "${file}" \
  >> "${new_name}"
done

ls -ltrh

total 7.9G
-rw-rw-rw- 1 sam users 914M Jun 26 08:49 Pgenerosa_v074.fa
-rw-rw-rw- 1 sam users 1.3K Jun 26 08:54 Pgenerosa_v074.fa.fai
-rw-rw-r-- 1 sam users 2.5G Aug 21 11:45 Pgenerosa_v074.CpG.gff
-rwxr--r-- 1 sam users  60M Oct 14 10:13 Panopea-generosa-vv0.74.a4.CDS.gff3
-rwxr--r-- 1 sam users  62M Oct 14 10:13 Panopea-generosa-vv0.74.a4.exon.gff3
-rwxr--r-- 1 sam users  11M Oct 14 10:13 Panopea-generosa-vv0.74.a4.gene.gff3
-rwxr--r-- 1 sam users  11M Oct 14 10:13 Panopea-generosa-vv0.74.a4.mRNA.gff3
-rwxr--r-- 1 sam users 373M Oct 14 10:13 Panopea-generosa-vv0.74.a4.repeat_region.gff3
-rwxr--r-- 1 sam users 1.5K Oct 14 10:13 Panopea-generosa-vv0.74.a4.rRNA.gff3
-rwxr--r-- 1 sam users 2.8M Oct 14 10:13 Panopea-generosa-vv0.74.a4.tRNA.gff3
-rw-rw-r-- 1 sam users  11M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.SINE.gff3
-rw-rw-r-- 1 sam users 4.5M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.Simple_repeat.gff3
-rw-rw-r-- 1 sam users 140K Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.RC.gff3
-rw-rw-r-- 1 sam users 735K Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.LTR.gff3
-rw-rw-r-- 1 sam users  18M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.LINE.gff3
-rw-rw-r-- 1 sam users 5.4M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.DNA.gff3
-rw-rw-r-- 1 sam users 335M Oct 29 08:52 Panopea-generosa-vv0.74.a4.repeats.Unknown.gff3
-rw-rw-r-- 1 sam users 2.1M Oct 30 08:41 Panopea-generosa-vv0.74.a4.intergenic.bed
-rw-rw-r-- 1 sam users 9.1M Oct 30 08:41 Panopea-generosa-vv0.74.a4.introns.bed
-rw-rw-r-- 1 sam users  53M Nov  5 08:55 Panopea-generosa-v1.0.a4.CDS.gff3
-rw-rw-r-- 1 sam users  55M Nov  5 08:55 Panopea-generosa-v1.0.a4.exon.gff3
-rw-rw-r-- 1 sam users 9.5M Nov  5 08:55 Panopea-generosa-v1.0.a4.gene.gff3
-rw-rw-r-- 1 sam users 9.1M Nov  5 08:55 Panopea-generosa-v1.0.a4.mRNA.gff3
-rw-rw-r-- 1 sam users 326M Nov  5 08:55 Panopea-generosa-v1.0.a4.repeat_region.gff3
-rw-rw-r-- 1 sam users 1.2K Nov  5 08:55 Panopea-generosa-v1.0.a4.rRNA.gff3
-rw-rw-r-- 1 sam users 2.3M Nov  5 08:55 Panopea-generosa-v1.0.a4.tRNA.gff3
-rw-rw-r-- 1 sam users 914M Nov  5 08:56 Panopea-generosa-v1.0.fa
-rw-rw-r-- 1 sam users  658 Nov  5 08:56 Panopea-generosa-v1.0.fa.fai
-rw-rw-r-- 1 sam users 2.0G Nov  5 08:59 Panopea-generosa-v1.0.CpG.gff
-rw-rw-r-- 1 sam users 996K Nov  5 08:59 Panopea-generosa-v1.0.a4.intergenic.bed
-rw-rw-r-- 1 sam users 4.4M Nov  5 08:59 Panopea-generosa-v1.0.a4.introns.bed
-rw-rw-r-- 1 sam users 4.7M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.DNA.gff3
-rw-rw-r-- 1 sam users 645K Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.LTR.gff3
-rw-rw-r-- 1 sam users 8.9M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.SINE.gff3
-rw-rw-r-- 1 sam users 293M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.Unknown.gff3
-rw-rw-r-- 1 sam users  16M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.LINE.gff3
-rw-rw-r-- 1 sam users 123K Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.RC.gff3
-rw-rw-r-- 1 sam users 4.0M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.Simple_repeat.gff3

In [19]:

%%bash
head Panopea-generosa-v1.0.a4.CDS.gff3

echo ""
echo "--------------------"
awk '{print $1}' Panopea-generosa-v1.0.a4.CDS.gff3 | sort | uniq

##gff-version 3
##Generated using GenSAS, Monday 7th of October 2019 04:54:37 AM
##Project Name : Pgenerosa_v074
Scaffold_01	GenSAS_5d9637f372b5d-publish	CDS	2	125	.	+	0	ID=PGEN_.00g000010.m01.CDS01;Name=PGEN_.00g000010.m01.CDS01;Parent=PGEN_.00g000010.m01;original_ID=cds.21510-PGEN_.00g234140.m01;Alias=cds.21510-PGEN_.00g234140.m01
Scaffold_01	GenSAS_5d9637f372b5d-publish	CDS	1995	2095	.	+	1	ID=PGEN_.00g000010.m01.CDS02;Name=PGEN_.00g000010.m01.CDS02;Parent=PGEN_.00g000010.m01;original_ID=cds.21510-PGEN_.00g234140.m01;Alias=cds.21510-PGEN_.00g234140.m01
Scaffold_01	GenSAS_5d9637f372b5d-publish	CDS	3325	3495	.	+	0	ID=PGEN_.00g000010.m01.CDS03;Name=PGEN_.00g000010.m01.CDS03;Parent=PGEN_.00g000010.m01;original_ID=cds.21510-PGEN_.00g234140.m01;Alias=cds.21510-PGEN_.00g234140.m01
Scaffold_01	GenSAS_5d9637f372b5d-publish	CDS	4651	4719	.	+	0	ID=PGEN_.00g000010.m01.CDS04;Name=PGEN_.00g000010.m01.CDS04;Parent=PGEN_.00g000010.m01;original_ID=cds.21510-PGEN_.00g234140.m01;Alias=cds.21510-PGEN_.00g234140.m01
Scaffold_01	GenSAS_5d9637f372b5d-publish	CDS	19808	19943	.	-	2	ID=PGEN_.00g000020.m01.CDS01;Name=PGEN_.00g000020.m01.CDS01;Parent=PGEN_.00g000020.m01;original_ID=cds.21510-PGEN_.00g234150.m01;Alias=cds.21510-PGEN_.00g234150.m01
Scaffold_01	GenSAS_5d9637f372b5d-publish	CDS	21133	21362	.	-	0	ID=PGEN_.00g000020.m01.CDS02;Name=PGEN_.00g000020.m01.CDS02;Parent=PGEN_.00g000020.m01;original_ID=cds.21510-PGEN_.00g234150.m01;Alias=cds.21510-PGEN_.00g234150.m01
Scaffold_01	GenSAS_5d9637f372b5d-publish	CDS	22487	22613	.	-	2	ID=PGEN_.00g000020.m01.CDS03;Name=PGEN_.00g000020.m01.CDS03;Parent=PGEN_.00g000020.m01;original_ID=cds.21510-PGEN_.00g234150.m01;Alias=cds.21510-PGEN_.00g234150.m01

--------------------
##Generated
##gff-version
##Project
Scaffold_01
Scaffold_02
Scaffold_03
Scaffold_04
Scaffold_05
Scaffold_06
Scaffold_07
Scaffold_08
Scaffold_09
Scaffold_10
Scaffold_11
Scaffold_12
Scaffold_13
Scaffold_14
Scaffold_15
Scaffold_16
Scaffold_17
Scaffold_18

In [20]:

%%bash
files_array=(Panopea-generosa-vv0.74.a4.CDS.gff3 Panopea-generosa-vv0.74.a4.exon.gff3 Panopea-generosa-vv0.74.a4.gene.gff3 Panopea-generosa-vv0.74.a4.mRNA.gff3 Panopea-generosa-vv0.74.a4.repeat_region.gff3 Panopea-generosa-vv0.74.a4.rRNA.gff3 Panopea-generosa-vv0.74.a4.tRNA.gff3 Pgenerosa_v074.fa Pgenerosa_v074.fa.fai Pgenerosa_v074.CpG.gff Panopea-generosa-vv0.74.a4.intergenic.bed Panopea-generosa-vv0.74.a4.introns.bed Panopea-generosa-vv0.74.a4.repeats.DNA.gff3 Panopea-generosa-vv0.74.a4.repeats.LTR.gff3 Panopea-generosa-vv0.74.a4.repeats.SINE.gff3 Panopea-generosa-vv0.74.a4.repeats.Unknown.gff3 Panopea-generosa-vv0.74.a4.repeats.LINE.gff3 Panopea-generosa-vv0.74.a4.repeats.RC.gff3 Panopea-generosa-vv0.74.a4.repeats.Simple_repeat.gff3)

for file in "${files_array[@]}"
do
  rm "${file}"
done

ls -ltrh

total 3.7G
-rw-rw-r-- 1 sam users  53M Nov  5 08:55 Panopea-generosa-v1.0.a4.CDS.gff3
-rw-rw-r-- 1 sam users  55M Nov  5 08:55 Panopea-generosa-v1.0.a4.exon.gff3
-rw-rw-r-- 1 sam users 9.5M Nov  5 08:55 Panopea-generosa-v1.0.a4.gene.gff3
-rw-rw-r-- 1 sam users 9.1M Nov  5 08:55 Panopea-generosa-v1.0.a4.mRNA.gff3
-rw-rw-r-- 1 sam users 326M Nov  5 08:55 Panopea-generosa-v1.0.a4.repeat_region.gff3
-rw-rw-r-- 1 sam users 1.2K Nov  5 08:55 Panopea-generosa-v1.0.a4.rRNA.gff3
-rw-rw-r-- 1 sam users 2.3M Nov  5 08:55 Panopea-generosa-v1.0.a4.tRNA.gff3
-rw-rw-r-- 1 sam users 914M Nov  5 08:56 Panopea-generosa-v1.0.fa
-rw-rw-r-- 1 sam users  658 Nov  5 08:56 Panopea-generosa-v1.0.fa.fai
-rw-rw-r-- 1 sam users 2.0G Nov  5 08:59 Panopea-generosa-v1.0.CpG.gff
-rw-rw-r-- 1 sam users 996K Nov  5 08:59 Panopea-generosa-v1.0.a4.intergenic.bed
-rw-rw-r-- 1 sam users 4.4M Nov  5 08:59 Panopea-generosa-v1.0.a4.introns.bed
-rw-rw-r-- 1 sam users 4.7M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.DNA.gff3
-rw-rw-r-- 1 sam users 645K Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.LTR.gff3
-rw-rw-r-- 1 sam users 8.9M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.SINE.gff3
-rw-rw-r-- 1 sam users 293M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.Unknown.gff3
-rw-rw-r-- 1 sam users  16M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.LINE.gff3
-rw-rw-r-- 1 sam users 123K Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.RC.gff3
-rw-rw-r-- 1 sam users 4.0M Nov  5 08:59 Panopea-generosa-v1.0.a4.repeats.Simple_repeat.gff3

In [ ]: