Using the intersectBed function to classify our target loci with respect to oyster genomic regions

In [5]: 
cd /Users/Shared/Apps/bedtools-2.17.0 

/Users/Shared/Apps/bedtools-2.17.0
In [7]: 
cd bin

/Users/Shared/Apps/bedtools-2.17.0/bin
In [8]: 
!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Lineage_specific_loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_exon.txt -u
In [9]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_exon.txt

      45     180    1685 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_exon.txt
In [10]: 
!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Lineage_specific_loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_gene.txt -u
In [11]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_gene.txt

     197     788    7398 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_gene.txt
In [12]: 
!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Lineage_specific_loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_intron.txt -u
In [13]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_intron.txt

     152     608    5713 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_intron.txt
In [59]: 
!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Lineage_specific_loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_TE.txt -u
In [60]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_TE.txt

      80     320    2988 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_TE.txt
In [16]: 
!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Lineage_specific_loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_promoter.txt -u
In [17]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_promoter.txt

      24      96     910 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_promoter.txt
In [19]: 
!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Lineage_specific_loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_COMP_gene_prom_TE.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_COMP.txt -u
In [20]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_COMP.txt

     214     856    7808 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_COMP.txt
Lineage specific counts 45 exon 197 gene 152 intron 80 TE 24 promoter 214 complement (other)
In [21]: 
!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Developmentally_Different_Loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_exon.txt -u
In [22]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_exon.txt

      30     120    1061 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_exon.txt
In [23]: 
!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Developmentally_Different_Loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_gene.txt -u
In [24]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_gene.txt

     167     668    5976 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_gene.txt
In [25]: 
!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Developmentally_Different_Loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_intron.txt -u
In [26]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_intron.txt

     137     548    4915 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_intron.txt
In [27]: 
!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Developmentally_Different_Loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_TE.txt -u
In [28]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_TE.txt

      57     228    1983 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_TE.txt
In [29]: 
!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Developmentally_Different_Loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_1k5p_gene_promoter.txt -u
In [30]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_promoter.txt

      18      72     634 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_1k5p_gene_promoter.txt
In [32]: 
!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Developmentally_Different_Loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_COMP_gene_prom_TE.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_COMP.txt -u
In [33]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_COMP.txt

     176     704    6052 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_COMP.txt
Developmentally different counts 30 exon 167 gene 137 intron 57 TE 18 promoter 176 complement (other)
In [34]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_exon.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_exon.txt -u
In [35]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_exon.txt

 1129658 11296580 110957829 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_exon.txt
In [36]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_gene.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_gene.txt -u
In [37]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_gene.txt

 3938356 39383560 387141916 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_gene.txt
In [38]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_intron.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_intron.txt -u
In [39]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_intron.txt

 2815997 28159970 276901690 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_intron.txt
In [72]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_TE.txt -u
In [73]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_TE.txt

  589509 5895090 57596188 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_TE.txt
In [42]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_1k5p_gene_promoter.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_promoter.txt -u
In [43]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_promoter.txt

  593081 5930810 58106466 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_promoter.txt
In [46]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_COMP_gene_prom_TE.bed > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_COMP.txt -u
In [47]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_COMP.txt

 5121236 51212360 499097421 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_COMP.txt
In [57]: 
!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Lineage_specific_loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_TE_names.txt -wb
In [58]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_TE_names.txt

     112    1456   10347 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/lineage_TE_names.txt
In [69]: 
!intersectBed -a /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Developmentally_Different_Loci.bed -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_TE_names.txt -wb
In [70]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_TE_names.txt

      88    1144    7777 /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/develop_TE_names.txt
In [75]: 
!intersectBed -a /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_CG.gff -b /Volumes/web-1/trilobite/Crassostrea_gigas_v9_tracks/Cgigas_v9_TE.gff > /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_TE_names.txt -wb
In [74]: 
!wc /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_TE_names.txt 

wc: /Volumes/web-1/Mollusk/bs_larvae_exp/ID_Target_Loci_Check/Genomic_Features/CG_TE_names.txt: open: No such file or directory
In []: