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:
Wed Oct 30 08:34:26 PDT 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        7.0G        688M         34G         39G
Swap:          4.7G         15M        4.6G

No LSB modules are available.

Set variables¶

%env variables are good for passing to bash cells

In [18]:

# Set workding directory
%env wd=/home/sam/analyses/20191030_pgen_v074.a4_intron_intergenic_features
wd="/home/sam/analyses/20191030_pgen_v074.a4_intron_intergenic_features"


%env rsync_owl=owl:/volume1/web/halfshell/genomic-databank/
%env genome_fasta=Pgenerosa_v074.fa
%env chrome_sizes=Pgenerosa_v074.sizes.txt
%env gffs=Panopea-generosa-vv0.74.a4.[eg]*.gff
%env exon_gff=Panopea-generosa-vv0.74.a4.exon.gff3
%env exon_gff_sorted=Panopea-generosa-vv0.74.a4.exon.sorted.gff3
%env gene_gff=Panopea-generosa-vv0.74.a4.gene.gff3
%env gene_gff_sorted=Panopea-generosa-vv0.74.a4.gene.sorted.gff3
%env wget_gff=--directory-prefix=${wd} --recursive --quiet --no-directories --no-check-certificate --no-parent --accept 'Panopea-generosa-vv0.74.a4.[eg]*.gff' https://owl.fish.washington.edu/halfshell/genomic-databank/
%env wget_fasta=--no-check-certificate https://owl.fish.washington.edu/halfshell/genomic-databank/"${genome_fasta}"
%env exon_comp_bed=Panopea-generosa-vv0.74.a4.exon.sorted.comp.bed
%env intron_bed=Panopea-generosa-vv0.74.a4.introns.bed
%env intergenic_bed=Panopea-generosa-vv0.74.a4.intergenic.bed

# Programs
%env bedtools_dir=/home/sam/programs/bedtools-2.28.0/bin
%env samtools=/home/sam/programs/samtools-1.9/samtools

env: wd=/home/sam/analyses/20191030_pgen_v074.a4_intron_intergenic_features
env: rsync_owl=owl:/volume1/web/halfshell/genomic-databank/
env: genome_fasta=Pgenerosa_v074.fa
env: chrome_sizes=Pgenerosa_v074.sizes.txt
env: gffs=Panopea-generosa-vv0.74.a4.[eg]*.gff
env: exon_gff=Panopea-generosa-vv0.74.a4.exon.gff3
env: exon_gff_sorted=Panopea-generosa-vv0.74.a4.exon.sorted.gff3
env: gene_gff=Panopea-generosa-vv0.74.a4.gene.gff3
env: gene_gff_sorted=Panopea-generosa-vv0.74.a4.gene.sorted.gff3
env: wget_gff=--directory-prefix=$/home/sam/analyses/20191030_pgen_v074.a4_intron_intergenic_features --recursive --quiet --no-directories --no-check-certificate --no-parent --accept 'Panopea-generosa-vv0.74.a4.[eg]*.gff' https://owl.fish.washington.edu/halfshell/genomic-databank/
env: wget_fasta=--no-check-certificate https://owl.fish.washington.edu/halfshell/genomic-databank/"${genome_fasta}"
env: exon_comp_bed=Panopea-generosa-vv0.74.a4.exon.sorted.comp.bed
env: intron_bed=Panopea-generosa-vv0.74.a4.introns.bed
env: intergenic_bed=Panopea-generosa-vv0.74.a4.intergenic.bed
env: bedtools_dir=/home/sam/programs/bedtools-2.28.0/bin
env: samtools=/home/sam/programs/samtools-1.9/samtools

Create necessary directories¶

In [11]:

%%bash
mkdir --parents ${wd}

In [12]:

cd {wd}

/home/sam/analyses/20191030_pgen_v074.a4_intron_intergenic_features

Download Panopea generosa GFFs for v074.a4.¶

Info on GFFs is here: [https://github.com/RobertsLab/resources/wiki/Genomic-Resources#genome-feature-tracks-3)

In [14]:

%%bash

input_files_array=("${genome_fasta}" "${exon_gff}" "${gene_gff}")

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

ls -lh

receiving incremental file list
Pgenerosa_v074.fa

sent 30 bytes  received 958,176,954 bytes  27,773,245.91 bytes/sec
total size is 958,059,901  speedup is 1.00
receiving incremental file list
Panopea-generosa-vv0.74.a4.exon.gff3

sent 30 bytes  received 64,671,619 bytes  14,371,477.56 bytes/sec
total size is 64,663,603  speedup is 1.00
receiving incremental file list
Panopea-generosa-vv0.74.a4.gene.gff3

sent 30 bytes  received 10,999,145 bytes  4,399,670.00 bytes/sec
total size is 10,997,681  speedup is 1.00


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

total 986M
-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-rw- 1 sam users 914M Jun 26 08:49 Pgenerosa_v074.fa

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

In [15]:

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

In [16]:

%%bash
echo ${exon_gff}
head ${exon_gff}
echo ""
echo "----------------------"
echo ""
echo ${gene_gff}
head ${gene_gff}

Panopea-generosa-vv0.74.a4.exon.gff3
##gff-version 3
##Generated using GenSAS, Monday 7th of October 2019 04:54:37 AM
##Project Name : Pgenerosa_v074
PGA_scaffold1__77_contigs__length_89643857	GenSAS_5d9637f372b5d-publish	exon	2	125	.	+	.	ID=PGEN_.00g000010.m01.exon01;Name=PGEN_.00g000010.m01.exon01;Parent=PGEN_.00g000010.m01;original_ID=21510-PGEN_.00g234140.m01.exon1;Alias=21510-PGEN_.00g234140.m01.exon1
PGA_scaffold1__77_contigs__length_89643857	GenSAS_5d9637f372b5d-publish	exon	1995	2095	.	+	.	ID=PGEN_.00g000010.m01.exon02;Name=PGEN_.00g000010.m01.exon02;Parent=PGEN_.00g000010.m01;original_ID=21510-PGEN_.00g234140.m01.exon2;Alias=21510-PGEN_.00g234140.m01.exon2
PGA_scaffold1__77_contigs__length_89643857	GenSAS_5d9637f372b5d-publish	exon	3325	3495	.	+	.	ID=PGEN_.00g000010.m01.exon03;Name=PGEN_.00g000010.m01.exon03;Parent=PGEN_.00g000010.m01;original_ID=21510-PGEN_.00g234140.m01.exon3;Alias=21510-PGEN_.00g234140.m01.exon3
PGA_scaffold1__77_contigs__length_89643857	GenSAS_5d9637f372b5d-publish	exon	4651	4719	.	+	.	ID=PGEN_.00g000010.m01.exon04;Name=PGEN_.00g000010.m01.exon04;Parent=PGEN_.00g000010.m01;original_ID=21510-PGEN_.00g234140.m01.exon4;Alias=21510-PGEN_.00g234140.m01.exon4
PGA_scaffold1__77_contigs__length_89643857	GenSAS_5d9637f372b5d-publish	exon	19808	19943	.	-	.	ID=PGEN_.00g000020.m01.exon01;Name=PGEN_.00g000020.m01.exon01;Parent=PGEN_.00g000020.m01;original_ID=21510-PGEN_.00g234150.m01.exon10;Alias=21510-PGEN_.00g234150.m01.exon10
PGA_scaffold1__77_contigs__length_89643857	GenSAS_5d9637f372b5d-publish	exon	21133	21362	.	-	.	ID=PGEN_.00g000020.m01.exon02;Name=PGEN_.00g000020.m01.exon02;Parent=PGEN_.00g000020.m01;original_ID=21510-PGEN_.00g234150.m01.exon9;Alias=21510-PGEN_.00g234150.m01.exon9
PGA_scaffold1__77_contigs__length_89643857	GenSAS_5d9637f372b5d-publish	exon	22487	22613	.	-	.	ID=PGEN_.00g000020.m01.exon03;Name=PGEN_.00g000020.m01.exon03;Parent=PGEN_.00g000020.m01;original_ID=21510-PGEN_.00g234150.m01.exon8;Alias=21510-PGEN_.00g234150.m01.exon8

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

Panopea-generosa-vv0.74.a4.gene.gff3
##gff-version 3
##Generated using GenSAS, Monday 7th of October 2019 04:54:37 AM
##Project Name : Pgenerosa_v074
PGA_scaffold1__77_contigs__length_89643857	GenSAS_5d9637f372b5d-publish	gene	2	4719	.	+	.	ID=PGEN_.00g000010;Name=PGEN_.00g000010;original_ID=21510-PGEN_.00g234140;Alias=21510-PGEN_.00g234140;original_name=21510-PGEN_.00g234140;Notes=sp|Q86IC9|CAMT1_DICDI [BLAST protein vs protein (blastp) 2.7.1],PF01596.12 [Pfam 1.6]
PGA_scaffold1__77_contigs__length_89643857	GenSAS_5d9637f372b5d-publish	gene	19808	36739	.	-	.	ID=PGEN_.00g000020;Name=PGEN_.00g000020;original_ID=21510-PGEN_.00g234150;Alias=21510-PGEN_.00g234150;original_name=21510-PGEN_.00g234150;Notes=sp|P04177|TY3H_RAT [BLAST protein vs protein (blastp) 2.7.1],sp|P04177|TY3H_RAT [DIAMOND Functional 0.9.22],IPR036951 [InterProScan 5.29-68.0],PF00351.16 [Pfam 1.6]
PGA_scaffold1__77_contigs__length_89643857	GenSAS_5d9637f372b5d-publish	gene	49248	52578	.	-	.	ID=PGEN_.00g000030;Name=PGEN_.00g000030;original_ID=21510-PGEN_.00g234160;Alias=21510-PGEN_.00g234160;original_name=21510-PGEN_.00g234160;Notes=PF08054.6 [Pfam 1.6]
PGA_scaffold1__77_contigs__length_89643857	GenSAS_5d9637f372b5d-publish	gene	55792	67546	.	+	.	ID=PGEN_.00g000040;Name=PGEN_.00g000040;original_ID=21510-PGEN_.00g234170;Alias=21510-PGEN_.00g234170;original_name=21510-PGEN_.00g234170
PGA_scaffold1__77_contigs__length_89643857	GenSAS_5d9637f372b5d-publish	gene	67586	69113	.	-	.	ID=PGEN_.00g000050;Name=PGEN_.00g000050;original_ID=21510-PGEN_.00g234180;Alias=21510-PGEN_.00g234180;original_name=21510-PGEN_.00g234180;Notes=sp|Q8L840|RQL4A_ARATH [BLAST protein vs protein (blastp) 2.7.1],sp|Q8L840|RQL4A_ARATH [DIAMOND Functional 0.9.22],PF00270.24 [Pfam 1.6]
PGA_scaffold1__77_contigs__length_89643857	GenSAS_5d9637f372b5d-publish	gene	70713	81099	.	+	.	ID=PGEN_.00g000060;Name=PGEN_.00g000060;original_ID=21510-PGEN_.00g234190;Alias=21510-PGEN_.00g234190;original_name=21510-PGEN_.00g234190;Notes=sp|Q61043|NIN_MOUSE [DIAMOND Functional 0.9.22],PF04443.7 [Pfam 1.6]
PGA_scaffold1__77_contigs__length_89643857	GenSAS_5d9637f372b5d-publish	gene	183686	186073	.	+	.	ID=PGEN_.00g000070;Name=PGEN_.00g000070;original_ID=21510-PGEN_.00g234200;Alias=21510-PGEN_.00g234200;original_name=21510-PGEN_.00g234200;Notes=PF15364.1 [Pfam 1.6]

Sort files¶

Create FastA index file¶

In [19]:

%%bash
${samtools} faidx \
${genome_fasta}

cat ${genome_fasta}.fai

PGA_scaffold1__77_contigs__length_89643857	89643857	44	60	61
PGA_scaffold2__36_contigs__length_69596280	69596280	91138010	60	61
PGA_scaffold3__111_contigs__length_57743597	57743597	161894273	60	61
PGA_scaffold4__129_contigs__length_65288255	65288255	220600309	60	61
PGA_scaffold5__109_contigs__length_67248332	67248332	286976747	60	61
PGA_scaffold6__104_contigs__length_61759565	61759565	355345930	60	61
PGA_scaffold7__69_contigs__length_43120122	43120122	418134866	60	61
PGA_scaffold8__63_contigs__length_61151155	61151155	461973701	60	61
PGA_scaffold9__45_contigs__length_38581958	38581958	524144086	60	61
PGA_scaffold10__49_contigs__length_53961475	53961475	563369122	60	61
PGA_scaffold11__79_contigs__length_51449921	51449921	618230000	60	61
PGA_scaffold12__71_contigs__length_50438331	50438331	670537465	60	61
PGA_scaffold13__52_contigs__length_44396874	44396874	721816480	60	61
PGA_scaffold14__91_contigs__length_45393038	45393038	766953347	60	61
PGA_scaffold15__101_contigs__length_47938513	47938513	813102982	60	61
PGA_scaffold16__33_contigs__length_31980953	31980953	861840516	60	61
PGA_scaffold17__51_contigs__length_34923512	34923512	894354530	60	61
PGA_scaffold18__69_contigs__length_27737463	27737463	929860146	60	61

Create chromosome sizes file¶

In [20]:

%%bash
# Change LC_COLLATE to use C for proper sorting of file
export LC_COLLATE=C

cut -f1,2 ${genome_fasta}.fai | sort > ${chrome_sizes}

cat ${chrome_sizes}

PGA_scaffold10__49_contigs__length_53961475	53961475
PGA_scaffold11__79_contigs__length_51449921	51449921
PGA_scaffold12__71_contigs__length_50438331	50438331
PGA_scaffold13__52_contigs__length_44396874	44396874
PGA_scaffold14__91_contigs__length_45393038	45393038
PGA_scaffold15__101_contigs__length_47938513	47938513
PGA_scaffold16__33_contigs__length_31980953	31980953
PGA_scaffold17__51_contigs__length_34923512	34923512
PGA_scaffold18__69_contigs__length_27737463	27737463
PGA_scaffold1__77_contigs__length_89643857	89643857
PGA_scaffold2__36_contigs__length_69596280	69596280
PGA_scaffold3__111_contigs__length_57743597	57743597
PGA_scaffold4__129_contigs__length_65288255	65288255
PGA_scaffold5__109_contigs__length_67248332	67248332
PGA_scaffold6__104_contigs__length_61759565	61759565
PGA_scaffold7__69_contigs__length_43120122	43120122
PGA_scaffold8__63_contigs__length_61151155	61151155
PGA_scaffold9__45_contigs__length_38581958	38581958

Sort GFFs¶

In [21]:

%%bash
gff_array=("${exon_gff}" "${gene_gff}")
sorted_gff_array=("${exon_gff_sorted}" "${gene_gff_sorted}")

for index in "${!gff_array[@]}"
do
  { awk 'NR<4 {print}' "${gff_array[index]}"
   awk 'NR>3 {print}' "${gff_array[index]}" | "${bedtools_dir}"/bedtools sort -i -
  } >> "${sorted_gff_array[index]}"
  
  # Check out sorted GFFs
  echo "Previewing ${sorted_gff_array[index]}:"
  echo ""
  head "${sorted_gff_array[index]}"
  echo ""
  echo "Confirming sort order of ${sorted_gff_array[index]}:"
  echo ""
  cut -f1 "${sorted_gff_array[index]}" | uniq
  echo ""
done

Previewing Panopea-generosa-vv0.74.a4.exon.sorted.gff3:

##gff-version 3
##Generated using GenSAS, Monday 7th of October 2019 04:54:37 AM
##Project Name : Pgenerosa_v074
PGA_scaffold10__49_contigs__length_53961475	GenSAS_5d9637f372b5d-publish	exon	2	1145	.	+	.	ID=PGEN_.00g204300.m01.exon01;Name=PGEN_.00g204300.m01.exon01;Parent=PGEN_.00g204300.m01;original_ID=21510-PGEN_.00g311420.m01.exon1;Alias=21510-PGEN_.00g311420.m01.exon1
PGA_scaffold10__49_contigs__length_53961475	GenSAS_5d9637f372b5d-publish	exon	19540	19683	.	-	.	ID=PGEN_.00g204310.m01.exon01;Name=PGEN_.00g204310.m01.exon01;Parent=PGEN_.00g204310.m01;original_ID=21510-PGEN_.00g311430.m01.exon9;Alias=21510-PGEN_.00g311430.m01.exon9
PGA_scaffold10__49_contigs__length_53961475	GenSAS_5d9637f372b5d-publish	exon	20883	21134	.	-	.	ID=PGEN_.00g204310.m01.exon02;Name=PGEN_.00g204310.m01.exon02;Parent=PGEN_.00g204310.m01;original_ID=21510-PGEN_.00g311430.m01.exon8;Alias=21510-PGEN_.00g311430.m01.exon8
PGA_scaffold10__49_contigs__length_53961475	GenSAS_5d9637f372b5d-publish	exon	21900	21978	.	-	.	ID=PGEN_.00g204310.m01.exon03;Name=PGEN_.00g204310.m01.exon03;Parent=PGEN_.00g204310.m01;original_ID=21510-PGEN_.00g311430.m01.exon7;Alias=21510-PGEN_.00g311430.m01.exon7
PGA_scaffold10__49_contigs__length_53961475	GenSAS_5d9637f372b5d-publish	exon	23163	23251	.	-	.	ID=PGEN_.00g204310.m01.exon04;Name=PGEN_.00g204310.m01.exon04;Parent=PGEN_.00g204310.m01;original_ID=21510-PGEN_.00g311430.m01.exon6;Alias=21510-PGEN_.00g311430.m01.exon6
PGA_scaffold10__49_contigs__length_53961475	GenSAS_5d9637f372b5d-publish	exon	24166	24255	.	-	.	ID=PGEN_.00g204310.m01.exon05;Name=PGEN_.00g204310.m01.exon05;Parent=PGEN_.00g204310.m01;original_ID=21510-PGEN_.00g311430.m01.exon5;Alias=21510-PGEN_.00g311430.m01.exon5
PGA_scaffold10__49_contigs__length_53961475	GenSAS_5d9637f372b5d-publish	exon	26335	26460	.	-	.	ID=PGEN_.00g204310.m01.exon06;Name=PGEN_.00g204310.m01.exon06;Parent=PGEN_.00g204310.m01;original_ID=21510-PGEN_.00g311430.m01.exon4;Alias=21510-PGEN_.00g311430.m01.exon4

Confirming sort order of Panopea-generosa-vv0.74.a4.exon.sorted.gff3:

##gff-version 3
##Generated using GenSAS, Monday 7th of October 2019 04:54:37 AM
##Project Name : Pgenerosa_v074
PGA_scaffold10__49_contigs__length_53961475
PGA_scaffold11__79_contigs__length_51449921
PGA_scaffold12__71_contigs__length_50438331
PGA_scaffold13__52_contigs__length_44396874
PGA_scaffold14__91_contigs__length_45393038
PGA_scaffold15__101_contigs__length_47938513
PGA_scaffold16__33_contigs__length_31980953
PGA_scaffold17__51_contigs__length_34923512
PGA_scaffold18__69_contigs__length_27737463
PGA_scaffold1__77_contigs__length_89643857
PGA_scaffold2__36_contigs__length_69596280
PGA_scaffold3__111_contigs__length_57743597
PGA_scaffold4__129_contigs__length_65288255
PGA_scaffold5__109_contigs__length_67248332
PGA_scaffold6__104_contigs__length_61759565
PGA_scaffold7__69_contigs__length_43120122
PGA_scaffold8__63_contigs__length_61151155
PGA_scaffold9__45_contigs__length_38581958

Previewing Panopea-generosa-vv0.74.a4.gene.sorted.gff3:

##gff-version 3
##Generated using GenSAS, Monday 7th of October 2019 04:54:37 AM
##Project Name : Pgenerosa_v074
PGA_scaffold10__49_contigs__length_53961475	GenSAS_5d9637f372b5d-publish	gene	2	1145	.	+	.	ID=PGEN_.00g204300;Name=PGEN_.00g204300;original_ID=21510-PGEN_.00g311420;Alias=21510-PGEN_.00g311420;original_name=21510-PGEN_.00g311420
PGA_scaffold10__49_contigs__length_53961475	GenSAS_5d9637f372b5d-publish	gene	19540	36845	.	-	.	ID=PGEN_.00g204310;Name=PGEN_.00g204310;original_ID=21510-PGEN_.00g311430;Alias=21510-PGEN_.00g311430;original_name=21510-PGEN_.00g311430;Notes=sp|F1MNN4|FBXW7_BOVIN [BLAST protein vs protein (blastp) 2.7.1],sp|A1DHW6|SCONB_NEOFI [DIAMOND Functional 0.9.22],IPR001680 [InterProScan 5.29-68.0],PF04041.8 [Pfam 1.6]
PGA_scaffold10__49_contigs__length_53961475	GenSAS_5d9637f372b5d-publish	gene	36984	37535	.	-	.	ID=PGEN_.00g204320;Name=PGEN_.00g204320;original_ID=21510-PGEN_.00g311440;Alias=21510-PGEN_.00g311440;original_name=21510-PGEN_.00g311440;Notes=IPR036322 [InterProScan 5.29-68.0],PF11163.3 [Pfam 1.6]
PGA_scaffold10__49_contigs__length_53961475	GenSAS_5d9637f372b5d-publish	gene	41157	41960	.	-	.	ID=PGEN_.00g204330;Name=PGEN_.00g204330;original_ID=21510-PGEN_.00g311450;Alias=21510-PGEN_.00g311450;original_name=21510-PGEN_.00g311450
PGA_scaffold10__49_contigs__length_53961475	GenSAS_5d9637f372b5d-publish	gene	61914	82099	.	+	.	ID=PGEN_.00g204340;Name=PGEN_.00g204340;original_ID=21510-PGEN_.00g311460;Alias=21510-PGEN_.00g311460;original_name=21510-PGEN_.00g311460;Notes=sp|Q3KRG3|TSR2_DANRE [BLAST protein vs protein (blastp) 2.7.1],sp|Q3KRG3|TSR2_DANRE [DIAMOND Functional 0.9.22],IPR019398 [InterProScan 5.29-68.0],PF10273.4 [Pfam 1.6]
PGA_scaffold10__49_contigs__length_53961475	GenSAS_5d9637f372b5d-publish	gene	90961	109412	.	-	.	ID=PGEN_.00g204350;Name=PGEN_.00g204350;original_ID=21510-PGEN_.00g311470;Alias=21510-PGEN_.00g311470;original_name=21510-PGEN_.00g311470;Notes=PF07495.8 [Pfam 1.6]
PGA_scaffold10__49_contigs__length_53961475	GenSAS_5d9637f372b5d-publish	gene	135015	215664	.	-	.	ID=PGEN_.00g204360;Name=PGEN_.00g204360;original_ID=21510-PGEN_.00g311480;Alias=21510-PGEN_.00g311480;original_name=21510-PGEN_.00g311480;Notes=sp|Q7TMY8|HUWE1_MOUSE [BLAST protein vs protein (blastp) 2.7.1],sp|Q7Z6Z7|HUWE1_HUMAN [DIAMOND Functional 0.9.22],PF06012.7 [Pfam 1.6]

Confirming sort order of Panopea-generosa-vv0.74.a4.gene.sorted.gff3:

##gff-version 3
##Generated using GenSAS, Monday 7th of October 2019 04:54:37 AM
##Project Name : Pgenerosa_v074
PGA_scaffold10__49_contigs__length_53961475
PGA_scaffold11__79_contigs__length_51449921
PGA_scaffold12__71_contigs__length_50438331
PGA_scaffold13__52_contigs__length_44396874
PGA_scaffold14__91_contigs__length_45393038
PGA_scaffold15__101_contigs__length_47938513
PGA_scaffold16__33_contigs__length_31980953
PGA_scaffold17__51_contigs__length_34923512
PGA_scaffold18__69_contigs__length_27737463
PGA_scaffold1__77_contigs__length_89643857
PGA_scaffold2__36_contigs__length_69596280
PGA_scaffold3__111_contigs__length_57743597
PGA_scaffold4__129_contigs__length_65288255
PGA_scaffold5__109_contigs__length_67248332
PGA_scaffold6__104_contigs__length_61759565
PGA_scaffold7__69_contigs__length_43120122
PGA_scaffold8__63_contigs__length_61151155
PGA_scaffold9__45_contigs__length_38581958

Create intergenic BED file¶

In [22]:

%%bash

"${bedtools_dir}"/complementBed \
-i "${gene_gff_sorted}" \
-g "${chrome_sizes}" \
> "${intergenic_bed}"

echo "Previewing ${intergenic_bed}:"
echo ""
head "${intergenic_bed}"

Previewing Panopea-generosa-vv0.74.a4.intergenic.bed:

PGA_scaffold10__49_contigs__length_53961475	0	1
PGA_scaffold10__49_contigs__length_53961475	1145	19539
PGA_scaffold10__49_contigs__length_53961475	36845	36983
PGA_scaffold10__49_contigs__length_53961475	37535	41156
PGA_scaffold10__49_contigs__length_53961475	41960	61913
PGA_scaffold10__49_contigs__length_53961475	82099	90960
PGA_scaffold10__49_contigs__length_53961475	109412	135014
PGA_scaffold10__49_contigs__length_53961475	215664	218086
PGA_scaffold10__49_contigs__length_53961475	219013	225102
PGA_scaffold10__49_contigs__length_53961475	230053	232785

Make intron BED file¶

In [23]:

%%bash
"${bedtools_dir}"/complementBed \
-i "${exon_gff_sorted}" \
-g "${chrome_sizes}" \
> "${exon_comp_bed}"

echo "Previewing ${exon_comp_bed}:"
echo ""
head "${exon_comp_bed}"
echo ""
echo "---------------------"

"${bedtools_dir}"/intersectBed \
-a "${gene_gff_sorted}" \
-b "${exon_comp_bed}" \
| awk -v OFS='\t' '{print $1,$4,$5}' \
> "${intron_bed}"

echo ""
echo "Previewing ${intron_bed}:"
echo ""
head "${intron_bed}"

Previewing Panopea-generosa-vv0.74.a4.exon.sorted.comp.bed:

PGA_scaffold10__49_contigs__length_53961475	0	1
PGA_scaffold10__49_contigs__length_53961475	1145	19539
PGA_scaffold10__49_contigs__length_53961475	19683	20882
PGA_scaffold10__49_contigs__length_53961475	21134	21899
PGA_scaffold10__49_contigs__length_53961475	21978	23162
PGA_scaffold10__49_contigs__length_53961475	23251	24165
PGA_scaffold10__49_contigs__length_53961475	24255	26334
PGA_scaffold10__49_contigs__length_53961475	26460	28467
PGA_scaffold10__49_contigs__length_53961475	28623	35328
PGA_scaffold10__49_contigs__length_53961475	35935	36093

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

Previewing Panopea-generosa-vv0.74.a4.introns.bed:

PGA_scaffold10__49_contigs__length_53961475	19684	20882
PGA_scaffold10__49_contigs__length_53961475	21135	21899
PGA_scaffold10__49_contigs__length_53961475	21979	23162
PGA_scaffold10__49_contigs__length_53961475	23252	24165
PGA_scaffold10__49_contigs__length_53961475	24256	26334
PGA_scaffold10__49_contigs__length_53961475	26461	28467
PGA_scaffold10__49_contigs__length_53961475	35936	36093
PGA_scaffold10__49_contigs__length_53961475	28624	35328
PGA_scaffold10__49_contigs__length_53961475	61983	65309
PGA_scaffold10__49_contigs__length_53961475	65860	81002

Cleanup¶

In [25]:

%%bash
rm "${genome_fasta}"* "${exon_comp_bed}" *.gff3 *.txt
ls -ltrh

total 12M
-rw-rw-r-- 1 sam sam 2.1M Oct 30 08:41 Panopea-generosa-vv0.74.a4.intergenic.bed
-rw-rw-r-- 1 sam sam 9.1M Oct 30 08:41 Panopea-generosa-vv0.74.a4.introns.bed

rm: cannot remove 'Pgenerosa_v074.fa*': No such file or directory
rm: cannot remove 'Panopea-generosa-vv0.74.a4.exon.sorted.comp.bed': No such file or directory

In [ ]: